Download Table S2. The cross-validation accuracy of all 544 physicochemical

Table S2. The cross-validation accuracy of all 544 physicochemical properties.
NO.
AAindex ID
Name of feature (References)
Accuracy
1
2
ANDN920101
ARGP820101
3
ARGP820102
4
ARGP820103
5
BEGF750101
6
BEGF750102
7
BEGF750103
8
BHAR880101
9
BIGC670101
10
BIOV880101
11
BIOV880102
12
BROC820101
13
BROC820102
14
BULH740101
15
BULH740102
16
BUNA790101
17
BUNA790102
18
BUNA790103
19
BURA740101
20
BURA740102
21
22
CHAM810101
CHAM820101
23
CHAM820102
alpha-CH chemical shifts (Andersen et al., 1992)
Hydrophobicity index (Argos et al., 1982)
Signal sequence helical potential (Argos et al.,
1982)
Membrane-buried preference parameters (Argos
et al., 1982)
Conformational parameter of inner helix
(Beghin-Dirkx, 1975)
Conformational parameter of beta-structure
(Beghin-Dirkx, 1975)
Conformational parameter of beta-turn
(Beghin-Dirkx, 1975)
Average flexibility indices
(Bhaskaran-Ponnuswamy, 1988)
Residue volume (Bigelow, 1967)
Information value for accessibility; average
fraction 35% (Biou et al., 1988)
Information value for accessibility; average
fraction 23% (Biou et al., 1988)
Retention coefficient in TFA (Browne et al.,
1982)
Retention coefficient in HFBA (Browne et al.,
1982)
Transfer free energy to surface (Bull-Breese,
1974)
Apparent partial specific volume (Bull-Breese,
1974)
alpha-NH chemical shifts (Bundi-Wuthrich,
1979)
alpha-CH chemical shifts (Bundi-Wuthrich,
1979)
Spin-spin coupling constants 3JHalpha-NH
(Bundi-Wuthrich, 1979)
Normalized frequency of alpha-helix (Burgess et
al., 1974)
Normalized frequency of extended structure
(Burgess et al., 1974)
Steric parameter (Charton, 1981)
Polarizability parameter (Charton-Charton, 1982)
Free energy of solution in water, kcal/mole
(Charton-Charton, 1982)
53.55828
55.76798
58.41638
56.9974
53.99155
54.67938
52.42093
52.90836
55.93046
59.6133
60.98354
54.10529
55.21555
53.737
54.09445
52.2422
54.23527
53.08167
52.48592
55.71924
52.48050
54.77145
53.78575
1
24
CHAM830101
25
CHAM830102
26
CHAM830103
27
CHAM830104
28
CHAM830105
29
CHAM830106
30
CHAM830107
31
CHAM830108
32
CHOC750101
33
CHOC760101
34
CHOC760102
35
CHOC760103
36
CHOC760104
37
CHOP780101
38
CHOP780201
39
CHOP780202
40
CHOP780203
41
CHOP780204
42
CHOP780205
43
CHOP780206
44
CHOP780207
The Chou-Fasman parameter of the coil
conformation (Charton-Charton, 1983)
A parameter defined from the residuals obtained
from the best correlation of the Chou-Fasman
parameter of beta-sheet (Charton-Charton, 1983)
The number of atoms in the side chain labelled
1+1 (Charton-Charton, 1983)
The number of atoms in the side chain labelled
2+1 (Charton-Charton, 1983)
The number of atoms in the side chain labelled
3+1 (Charton-Charton, 1983)
The number of bonds in the longest chain
(Charton-Charton, 1983)
A parameter of charge transfer capability
(Charton-Charton, 1983)
A parameter of charge transfer donor capability
(Charton-Charton, 1983)
Average volume of buried residue (Chothia,
1975)
Residue accessible surface area in tripeptide
(Chothia, 1976)
Residue accessible surface area in folded protein
(Chothia, 1976)
Proportion of residues 95% buried (Chothia,
1976)
Proportion of residues 100% buried (Chothia,
1976)
Normalized frequency of beta-turn
(Chou-Fasman, 1978a)
Normalized frequency of alpha-helix
(Chou-Fasman, 1978b)
Normalized frequency of beta-sheet
(Chou-Fasman, 1978b)
Normalized frequency of beta-turn
(Chou-Fasman, 1978b)
Normalized frequency of N-terminal helix
(Chou-Fasman, 1978b)
Normalized frequency of C-terminal helix
(Chou-Fasman, 1978b)
Normalized frequency of N-terminal non helical
region (Chou-Fasman, 1978b)
Normalized frequency of C-terminal non helical
region (Chou-Fasman, 1978b)
53.47704
52.52383
52.81088
54.32734
56.18501
57.84229
51.42439
55.69216
54.47899
56.60745
65.14840
59.68912
58.85507
54.35984
52.43176
54.07821
54.77145
53.60702
63.23657
53.66118
56.37998
2
45
CHOP780208
46
CHOP780209
47
CHOP780210
48
CHOP780211
49
CHOP780212
50
CHOP780213
51
CHOP780214
52
CHOP780215
53
CHOP780216
54
CIDH920101
55
CIDH920102
56
CIDH920103
57
CIDH920104
58
CIDH920105
59
COHE430101
60
CRAJ730101
61
CRAJ730102
62
CRAJ730103
63
64
65
DAWD720101
DAYM780101
DAYM780201
66
DESM900101
67
DESM900102
68
EISD840101
Normalized frequency of N-terminal beta-sheet
(Chou-Fasman, 1978b)
Normalized frequency of C-terminal beta-sheet
(Chou-Fasman, 1978b)
Normalized frequency of N-terminal non beta
region (Chou-Fasman, 1978b)
Normalized frequency of C-terminal non beta
region (Chou-Fasman, 1978b)
Frequency of the 1st residue in turn
(Chou-Fasman, 1978b)
Frequency of the 2nd residue in turn
(Chou-Fasman, 1978b)
Frequency of the 3rd residue in turn
(Chou-Fasman, 1978b)
Frequency of the 4th residue in turn
(Chou-Fasman, 1978b)
Normalized frequency of the 2nd and 3rd
residues in turn (Chou-Fasman, 1978b)
Normalized hydrophobicity scales for
alpha-proteins (Cid et al., 1992)
Normalized hydrophobicity scales for
beta-proteins (Cid et al., 1992)
Normalized hydrophobicity scales for
alpha+beta-proteins (Cid et al., 1992)
Normalized hydrophobicity scales for
alpha/beta-proteins (Cid et al., 1992)
Normalized average hydrophobicity scales (Cid
et al., 1992)
Partial specific volume (Cohn-Edsall, 1943)
Normalized frequency of middle helix (Crawford
et al., 1973)
Normalized frequency of beta-sheet (Crawford et
al., 1973)
Normalized frequency of turn (Crawford et al.,
1973)
Size (Dawson, 1972)
Amino acid composition (Dayhoff et al., 1978a)
Relative mutability (Dayhoff et al., 1978b)
Membrane preference for cytochrome b: MPH89
(Degli Esposti et al., 1990)
Average membrane preference: AMP07 (Degli
Esposti et al., 1990)
Consensus normalized hydrophobicity scale
55.63258
52.82171
54.20819
53.11417
54.38692
57.19779
52.67548
54.50065
55.84380
54.95017
54.95017
54.45191
54.95559
55.41594
54.82019
52.93544
55.18306
53.01127
60.78315
54.27318
55.25888
57.18696
55.87630
59.46166
3
(Eisenberg, 1984)
69
EISD860101
70
EISD860102
71
EISD860103
72
73
74
75
76
FASG760101
FASG760102
FASG760103
FASG760104
FASG760105
77
FAUJ830101
78
FAUJ880101
79
FAUJ880102
80
FAUJ880103
81
FAUJ880104
82
FAUJ880105
83
FAUJ880106
84
FAUJ880107
85
FAUJ880108
86
FAUJ880109
87
FAUJ880110
88
89
90
FAUJ880111
FAUJ880112
FAUJ880113
91
FINA770101
92
FINA910101
93
FINA910102
Solvation free energy (Eisenberg-McLachlan,
1986)
Atom-based hydrophobic moment
(Eisenberg-McLachlan, 1986)
Direction of hydrophobic moment
(Eisenberg-McLachlan, 1986)
Molecular weight (Fasman, 1976)
Melting point (Fasman, 1976)
Optical rotation (Fasman, 1976)
pK-N (Fasman, 1976)
pK-C (Fasman, 1976)
Hydrophobic parameter pi (Fauchere-Pliska,
1983)
Graph shape index (Fauchere et al., 1988)
Smoothed upsilon steric parameter (Fauchere et
al., 1988)
Normalized van der Waals volume (Fauchere et
al., 1988)
STERIMOL length of the side chain (Fauchere et
al., 1988)
STERIMOL minimum width of the side chain
(Fauchere et al., 1988)
STERIMOL maximum width of the side chain
(Fauchere et al., 1988)
N.m.r. chemical shift of alpha-carbon (Fauchere
et al., 1988)
Localized electrical effect (Fauchere et al., 1988)
Number of hydrogen bond donors (Fauchere et
al., 1988)
Number of full nonbonding orbitals (Fauchere et
al., 1988)
Positive charge (Fauchere et al., 1988)
Negative charge (Fauchere et al., 1988)
pK-a(RCOOH) (Fauchere et al., 1988)
Helix-coil equilibrium constant
(Finkelstein-Ptitsyn, 1977)
Helix initiation parameter at posision i-1
(Finkelstein et al., 1991)
Helix initiation parameter at posision i,i+1,i+2
(Finkelstein et al., 1991)
56.59662
60.75607
55.91963
54.09445
53.94281
57.91269
52.49133
53.76950
59.81911
54.04029
51.28899
55.12890
59.86785
53.86698
55.04224
54.76603
54.69562
57.73938
53.48787
62.51083
50.90988
52.92461
54.43566
56.51538
52.92461
4
94
FINA910103
95
FINA910104
96
97
GARJ730101
GEIM800101
98
GEIM800102
99
GEIM800103
100
GEIM800104
101
GEIM800105
102
GEIM800106
103
GEIM800107
104
GEIM800108
105
GEIM800109
106
GEIM800110
107
GEIM800111
108
GOLD730101
109
110
111
112
113
GOLD730102
GRAR740101
GRAR740102
GRAR740103
GUYH850101
114
HOPA770101
115
116
117
118
HOPT810101
HUTJ700101
HUTJ700102
HUTJ700103
119
ISOY800101
120
ISOY800102
121
ISOY800103
Helix termination parameter at posision j-2,j-1,j
(Finkelstein et al., 1991)
Helix termination parameter at posision j+1
(Finkelstein et al., 1991)
Partition coefficient (Garel et al., 1973)
Alpha-helix indices (Geisow-Roberts, 1980)
Alpha-helix indices for alpha-proteins
(Geisow-Roberts, 1980)
Alpha-helix indices for beta-proteins
(Geisow-Roberts, 1980)
Alpha-helix indices for alpha/beta-proteins
(Geisow-Roberts, 1980)
Beta-strand indices (Geisow-Roberts, 1980)
Beta-strand indices for beta-proteins
(Geisow-Roberts, 1980)
Beta-strand indices for alpha/beta-proteins
(Geisow-Roberts, 1980)
Aperiodic indices (Geisow-Roberts, 1980)
Aperiodic indices for alpha-proteins
(Geisow-Roberts, 1980)
Aperiodic indices for beta-proteins
(Geisow-Roberts, 1980)
Aperiodic indices for alpha/beta-proteins
(Geisow-Roberts, 1980)
Hydrophobicity factor (Goldsack-Chalifoux,
1973)
Residue volume (Goldsack-Chalifoux, 1973)
Composition (Grantham, 1974)
Polarity (Grantham, 1974)
Volume (Grantham, 1974)
Partition energy (Guy, 1985)
Hydration number (Hopfinger, 1971), Cited by
Charton-Charton (1982)
Hydrophilicity value (Hopp-Woods, 1981)
Heat capacity (Hutchens, 1970)
Absolute entropy (Hutchens, 1970)
Entropy of formation (Hutchens, 1970)
Normalized relative frequency of alpha-helix
(Isogai et al., 1980)
Normalized relative frequency of extended
structure (Isogai et al., 1980)
Normalized relative frequency of bend (Isogai et
al., 1980)
62.25628
64.18436
55.18847
53.87240
53.13583
51.89558
52.75130
53.65035
53.81824
54.25152
51.52188
53.09792
54.97725
53.10334
56.72660
56.25542
54.07279
55.67591
56.34207
59.84077
57.49025
59.29918
58.27015
60.33362
61.15685
52.58882
56.75910
53.67201
5
122
ISOY800104
123
ISOY800105
124
ISOY800106
125
ISOY800107
126
ISOY800108
127
JANJ780101
128
JANJ780102
129
JANJ780103
130
JANJ790101
131
132
133
JANJ790102
JOND750101
JOND750102
134
JOND920101
135
136
137
JOND920102
JUKT750101
JUNJ780101
138
KANM800101
139
KANM800102
140
KANM800103
141
KANM800104
142
KARP850101
143
KARP850102
144
KARP850103
145
KHAG800101
146
KLEP840101
Normalized relative frequency of bend R (Isogai
et al., 1980)
Normalized relative frequency of bend S (Isogai
et al., 1980)
Normalized relative frequency of helix end
(Isogai et al., 1980)
Normalized relative frequency of double bend
(Isogai et al., 1980)
Normalized relative frequency of coil (Isogai et
al., 1980)
Average accessible surface area (Janin et al.,
1978)
Percentage of buried residues (Janin et al., 1978)
Percentage of exposed residues (Janin et al.,
1978)
Ratio of buried and accessible molar fractions
(Janin, 1979)
Transfer free energy (Janin, 1979)
Hydrophobicity (Jones, 1975)
pK (-COOH) (Jones, 1975)
Relative frequency of occurrence (Jones et al.,
1992)
Relative mutability (Jones et al., 1992)
Amino acid distribution (Jukes et al., 1975)
Sequence frequency (Jungck, 1978)
Average relative probability of helix
(Kanehisa-Tsong, 1980)
Average relative probability of beta-sheet
(Kanehisa-Tsong, 1980)
Average relative probability of inner helix
(Kanehisa-Tsong, 1980)
Average relative probability of inner beta-sheet
(Kanehisa-Tsong, 1980)
Flexibility parameter for no rigid neighbors
(Karplus-Schulz, 1985)
Flexibility parameter for one rigid neighbor
(Karplus-Schulz, 1985)
Flexibility parameter for two rigid neighbors
(Karplus-Schulz, 1985)
The Kerr-constant increments (Khanarian-Moore,
1980)
Net charge (Klein et al., 1984)
57.48484
52.62673
52.58341
52.83795
54.09445
65.40836
61.11352
64.05481
56.32582
64.66833
55.74632
53.88865
54.04571
55.13432
54.22444
55.57301
53.02751
54.21360
52.68631
54.02405
55.12348
56.92699
65.10745
56.48289
64.67179
6
147
KRIW710101
148
KRIW790101
149
KRIW790102
150
151
KRIW790103
KYTJ820101
152
LAWE840101
153
LEVM760101
154
LEVM760102
155
LEVM760103
156
LEVM760104
157
158
159
LEVM760105
LEVM760106
LEVM760107
160
LEVM780101
161
LEVM780102
162
LEVM780103
163
LEVM780104
164
LEVM780105
165
LEVM780106
166
LEWP710101
167
LIFS790101
168
LIFS790102
169
LIFS790103
170
MANP780101
171
MAXF760101
Side chain interaction parameter
(Krigbaum-Rubin, 1971)
Side chain interaction parameter
(Krigbaum-Komoriya, 1979)
Fraction of site occupied by water
(Krigbaum-Komoriya, 1979)
Side chain volume (Krigbaum-Komoriya, 1979)
Hydropathy index (Kyte-Doolittle, 1982)
Transfer free energy, CHP/water (Lawson et al.,
1984)
Hydrophobic parameter (Levitt, 1976)
Distance between C-alpha and centroid of side
chain (Levitt, 1976)
Side chain angle theta(AAR) (Levitt, 1976)
Side chain torsion angle phi(AAAR) (Levitt,
1976)
Radius of gyration of side chain (Levitt, 1976)
van der Waals parameter R0 (Levitt, 1976)
van der Waals parameter epsilon (Levitt, 1976)
Normalized frequency of alpha-helix, with
weights (Levitt, 1978)
Normalized frequency of beta-sheet, with weights
(Levitt, 1978)
Normalized frequency of reverse turn, with
weights (Levitt, 1978)
Normalized frequency of alpha-helix, unweighted
(Levitt, 1978)
Normalized frequency of beta-sheet, unweighted
(Levitt, 1978)
Normalized frequency of reverse turn,
unweighted (Levitt, 1978)
Frequency of occurrence in beta-bends (Lewis et
al., 1971)
Conformational preference for all beta-strands
(Lifson-Sander, 1979)
Conformational preference for parallel
beta-strands (Lifson-Sander, 1979)
Conformational preference for antiparallel
beta-strands (Lifson-Sander, 1979)
Average surrounding hydrophobicity
(Manavalan-Ponnuswamy, 1978)
Normalized frequency of alpha-helix
(Maxfield-Scheraga, 1976)
61.77426
63.11200
64.30741
56.06044
57.07322
53.93739
60.35529
57.37652
53.76408
53.09792
59.81911
53.73159
54.37067
52.12305
53.95906
52.96252
53.23332
54.63063
53.29831
52.89753
53.93198
52.74047
54.62522
54.42483
52.98960
7
172
MAXF760102
173
MAXF760103
174
MAXF760104
175
MAXF760105
176
MAXF760106
177
MCMT640101
178
MEEJ800101
179
MEEJ800102
180
MEEJ810101
181
MEEJ810102
182
MEIH800101
183
MEIH800102
184
MEIH800103
185
MIYS850101
186
NAGK730101
187
NAGK730102
188
NAGK730103
189
NAKH900101
190
NAKH900102
191
NAKH900103
192
NAKH900104
193
NAKH900105
Normalized frequency of extended structure
(Maxfield-Scheraga, 1976)
Normalized frequency of zeta R
(Maxfield-Scheraga, 1976)
Normalized frequency of left-handed alpha-helix
(Maxfield-Scheraga, 1976)
Normalized frequency of zeta L
(Maxfield-Scheraga, 1976)
Normalized frequency of alpha region
(Maxfield-Scheraga, 1976)
Refractivity (McMeekin et al., 1964), Cited by
Jones (1975)
Retention coefficient in HPLC, pH7.4 (Meek,
1980)
Retention coefficient in HPLC, pH2.1 (Meek,
1980)
Retention coefficient in NaClO4 (Meek-Rossetti,
1981)
Retention coefficient in NaH2PO4
(Meek-Rossetti, 1981)
Average reduced distance for C-alpha
(Meirovitch et al., 1980)
Average reduced distance for side chain
(Meirovitch et al., 1980)
Average side chain orientation angle (Meirovitch
et al., 1980)
Effective partition energy (Miyazawa-Jernigan,
1985)
Normalized frequency of alpha-helix (Nagano,
1973)
Normalized frequency of bata-structure (Nagano,
1973)
Normalized frequency of coil (Nagano, 1973)
AA composition of total proteins (Nakashima et
al., 1990)
SD of AA composition of total proteins
(Nakashima et al., 1990)
AA composition of mt-proteins (Nakashima et
al., 1990)
Normalized composition of mt-proteins
(Nakashima et al., 1990)
AA composition of mt-proteins from animal
(Nakashima et al., 1990)
55.39428
51.70602
56.57496
57.12197
52.98960
53.29289
54.41941
55.23180
54.67938
56.72119
58.21599
63.12283
57.97227
60.27946
53.54744
55.35637
52.90295
54.34359
56.69952
54.72812
56.10377
55.64341
8
194
NAKH900106
195
NAKH900107
196
NAKH900108
197
NAKH900109
198
NAKH900110
199
NAKH900111
200
NAKH900112
201
NAKH900113
202
NAKH920101
203
NAKH920102
204
NAKH920103
205
NAKH920104
206
NAKH920105
207
NAKH920106
208
NAKH920107
209
NAKH920108
210
211
NISK800101
NISK860101
212
NOZY710101
213
OOBM770101
214
OOBM770102
215
OOBM770103
216
OOBM770104
Normalized composition from animal
(Nakashima et al., 1990)
AA composition of mt-proteins from fungi and
plant (Nakashima et al., 1990)
Normalized composition from fungi and plant
(Nakashima et al., 1990)
AA composition of membrane proteins
(Nakashima et al., 1990)
Normalized composition of membrane proteins
(Nakashima et al., 1990)
Transmembrane regions of non-mt-proteins
(Nakashima et al., 1990)
Transmembrane regions of mt-proteins
(Nakashima et al., 1990)
Ratio of average and computed composition
(Nakashima et al., 1990)
AA composition of CYT of single-spanning
proteins (Nakashima-Nishikawa, 1992)
AA composition of CYT2 of single-spanning
proteins (Nakashima-Nishikawa, 1992)
AA composition of EXT of single-spanning
proteins (Nakashima-Nishikawa, 1992)
AA composition of EXT2 of single-spanning
proteins (Nakashima-Nishikawa, 1992)
AA composition of MEM of single-spanning
proteins (Nakashima-Nishikawa, 1992)
AA composition of CYT of multi-spanning
proteins (Nakashima-Nishikawa, 1992)
AA composition of EXT of multi-spanning
proteins (Nakashima-Nishikawa, 1992)
AA composition of MEM of multi-spanning
proteins (Nakashima-Nishikawa, 1992)
8 A contact number (Nishikawa-Ooi, 1980)
14 A contact number (Nishikawa-Ooi, 1986)
Transfer energy, organic solvent/water
(Nozaki-Tanford, 1971)
Average non-bonded energy per atom
(Oobatake-Ooi, 1977)
Short and medium range non-bonded energy per
atom (Oobatake-Ooi, 1977)
Long range non-bonded energy per atom
(Oobatake-Ooi, 1977)
Average non-bonded energy per residue
57.01906
54.61438
53.62327
52.79463
59.94367
54.46274
56.04961
54.82561
55.63800
53.96989
55.71382
54.44107
54.70104
56.93241
52.22595
55.59467
56.22834
56.22292
54.19736
63.05243
57.75022
59.35334
53.91031
9
(Oobatake-Ooi, 1977)
217
OOBM770105
218
OOBM850101
219
OOBM850102
220
OOBM850103
221
OOBM850104
222
OOBM850105
223
PALJ810101
224
PALJ810102
225
PALJ810103
226
PALJ810104
227
PALJ810105
228
PALJ810106
229
PALJ810107
230
PALJ810108
231
PALJ810109
232
PALJ810110
233
PALJ810111
234
PALJ810112
235
PALJ810113
236
PALJ810114
237
PALJ810115
Short and medium range non-bonded energy per
residue (Oobatake-Ooi, 1977)
Optimized beta-structure-coil equilibrium
constant (Oobatake et al., 1985)
Optimized propensity to form reverse turn
(Oobatake et al., 1985)
Optimized transfer energy parameter (Oobatake
et al., 1985)
Optimized average non-bonded energy per atom
(Oobatake et al., 1985)
Optimized side chain interaction parameter
(Oobatake et al., 1985)
Normalized frequency of alpha-helix from LG
(Palau et al., 1981)
Normalized frequency of alpha-helix from CF
(Palau et al., 1981)
Normalized frequency of beta-sheet from LG
(Palau et al., 1981)
Normalized frequency of beta-sheet from CF
(Palau et al., 1981)
Normalized frequency of turn from LG (Palau et
al., 1981)
Normalized frequency of turn from CF (Palau et
al., 1981)
Normalized frequency of alpha-helix in all-alpha
class (Palau et al., 1981)
Normalized frequency of alpha-helix in
alpha+beta class (Palau et al., 1981)
Normalized frequency of alpha-helix in
alpha/beta class (Palau et al., 1981)
Normalized frequency of beta-sheet in all-beta
class (Palau et al., 1981)
Normalized frequency of beta-sheet in alpha+beta
class (Palau et al., 1981)
Normalized frequency of beta-sheet in alpha/beta
class (Palau et al., 1981)
Normalized frequency of turn in all-alpha class
(Palau et al., 1981)
Normalized frequency of turn in all-beta class
(Palau et al., 1981)
Normalized frequency of turn in alpha+beta class
(Palau et al., 1981)
52.78921
51.98765
53.19541
57.35485
56.46122
64.61222
53.21166
52.64840
54.38150
53.77491
53.40121
55.17223
52.86503
51.84142
52.91919
53.02751
53.49328
53.74242
54.54398
52.82171
55.16681
10
238
PALJ810116
239
240
PARJ860101
PLIV810101
241
PONP800101
242
PONP800102
243
PONP800103
244
PONP800104
245
PONP800105
246
PONP800106
247
PONP800107
248
PONP800108
249
PRAM820101
250
PRAM820102
251
PRAM820103
252
PRAM900101
253
PRAM900102
254
PRAM900103
255
PRAM900104
256
PTIO830101
257
PTIO830102
258
QIAN880101
259
QIAN880102
260
QIAN880103
Normalized frequency of turn in alpha/beta class
(Palau et al., 1981)
HPLC parameter (Parker et al., 1986)
Partition coefficient (Pliska et al., 1981)
Surrounding hydrophobicity in folded form
(Ponnuswamy et al., 1980)
Average gain in surrounding hydrophobicity
(Ponnuswamy et al., 1980)
Average gain ratio in surrounding hydrophobicity
(Ponnuswamy et al., 1980)
Surrounding hydrophobicity in alpha-helix
(Ponnuswamy et al., 1980)
Surrounding hydrophobicity in beta-sheet
(Ponnuswamy et al., 1980)
Surrounding hydrophobicity in turn
(Ponnuswamy et al., 1980)
Accessibility reduction ratio (Ponnuswamy et al.,
1980)
Average number of surrounding residues
(Ponnuswamy et al., 1980)
Intercept in regression analysis
(Prabhakaran-Ponnuswamy, 1982)
Slope in regression analysis x 1.0E1
(Prabhakaran-Ponnuswamy, 1982)
Correlation coefficient in regression analysis
(Prabhakaran-Ponnuswamy, 1982)
Hydrophobicity (Prabhakaran, 1990)
Relative frequency in alpha-helix (Prabhakaran,
1990)
Relative frequency in beta-sheet (Prabhakaran,
1990)
Relative frequency in reverse-turn (Prabhakaran,
1990)
Helix-coil equilibrium constant
(Ptitsyn-Finkelstein, 1983)
Beta-coil equilibrium constant
(Ptitsyn-Finkelstein, 1983)
Weights for alpha-helix at the window position of
-6 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
-5 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
-4 (Qian-Sejnowski, 1988)
53.39580
54.28943
57.15988
55.96837
58.84424
61.21101
52.05806
54.08904
61.28141
57.31153
57.20862
64.83969
63.22574
57.17071
58.32431
52.12305
53.95906
53.07084
52.05806
54.80936
63.19562
54.28401
51.89558
11
261
QIAN880104
262
QIAN880105
263
QIAN880106
264
QIAN880107
265
QIAN880108
266
QIAN880109
267
QIAN880110
268
QIAN880111
269
QIAN880112
270
QIAN880113
271
QIAN880114
272
QIAN880115
273
QIAN880116
274
QIAN880117
275
QIAN880118
276
QIAN880119
277
QIAN880120
278
QIAN880121
279
QIAN880122
280
QIAN880123
281
QIAN880124
282
QIAN880125
Weights for alpha-helix at the window position of
-3 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
-2 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
-1 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
0 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
1 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
2 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
3 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
4 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
5 (Qian-Sejnowski, 1988)
Weights for alpha-helix at the window position of
6 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
-6 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
-5 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
-4 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
-3 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
-2 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
-1 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
0 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
1 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
2 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
3 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
4 (Qian-Sejnowski, 1988)
Weights for beta-sheet at the window position of
5 (Qian-Sejnowski, 1988)
54.02946
51.29441
51.62478
52.32344
51.77101
53.59077
54.80394
54.06737
55.35095
62.35377
55.37262
54.29484
54.21902
54.92309
52.51300
54.84727
54.26776
54.77686
55.41594
54.00238
56.67786
58.05351
12
283
QIAN880126
284
QIAN880127
285
QIAN880128
286
QIAN880129
287
QIAN880130
288
QIAN880131
289
QIAN880132
290
QIAN880133
291
QIAN880134
292
QIAN880135
293
QIAN880136
294
QIAN880137
295
QIAN880138
296
QIAN880139
297
RACS770101
298
RACS770102
299
RACS770103
300
RACS820101
301
RACS820102
302
RACS820103
303
RACS820104
304
RACS820105
Weights for beta-sheet at the window position of
6 (Qian-Sejnowski, 1988)
Weights for coil at the window position of -6
(Qian-Sejnowski, 1988)
Weights for coil at the window position of -5
(Qian-Sejnowski, 1988)
Weights for coil at the window position of -4
(Qian-Sejnowski, 1988)
Weights for coil at the window position of -3
(Qian-Sejnowski, 1988)
Weights for coil at the window position of -2
(Qian-Sejnowski, 1988)
Weights for coil at the window position of -1
(Qian-Sejnowski, 1988)
Weights for coil at the window position of 0
(Qian-Sejnowski, 1988)
Weights for coil at the window position of 1
(Qian-Sejnowski, 1988)
Weights for coil at the window position of 2
(Qian-Sejnowski, 1988)
Weights for coil at the window position of 3
(Qian-Sejnowski, 1988)
Weights for coil at the window position of 4
(Qian-Sejnowski, 1988)
Weights for coil at the window position of 5
(Qian-Sejnowski, 1988)
Weights for coil at the window position of 6
(Qian-Sejnowski, 1988)
Average reduced distance for C-alpha
(Rackovsky-Scheraga, 1977)
Average reduced distance for side chain
(Rackovsky-Scheraga, 1977)
Side chain orientational preference
(Rackovsky-Scheraga, 1977)
Average relative fractional occurrence in A0(i)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in AR(i)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in AL(i)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in EL(i)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in E0(i)
(Rackovsky-Scheraga, 1982)
55.55676
64.57127
53.44996
57.73938
56.01711
55.45386
54.43566
53.16291
54.66854
53.25498
52.85420
52.49133
54.96101
56.88367
54.41399
62.94952
60.98354
54.61980
51.40273
58.04268
55.67591
58.55178
13
305
RACS820106
306
RACS820107
307
RACS820108
308
RACS820109
309
RACS820110
310
RACS820111
311
RACS820112
312
313
RACS820113
RACS820114
314
RADA880101
315
RADA880102
316
RADA880103
317
RADA880104
318
RADA880105
319
RADA880106
320
RADA880107
321
RADA880108
322
RICJ880101
323
RICJ880102
324
RICJ880103
325
RICJ880104
326
RICJ880105
327
RICJ880106
Average relative fractional occurrence in ER(i)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in A0(i-1)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in AR(i-1)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in AL(i-1)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in EL(i-1)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in E0(i-1)
(Rackovsky-Scheraga, 1982)
Average relative fractional occurrence in ER(i-1)
(Rackovsky-Scheraga, 1982)
Value of theta(i) (Rackovsky-Scheraga, 1982)
Value of theta(i-1) (Rackovsky-Scheraga, 1982)
Transfer free energy from chx to wat
(Radzicka-Wolfenden, 1988)
Transfer free energy from oct to wat
(Radzicka-Wolfenden, 1988)
Transfer free energy from vap to chx
(Radzicka-Wolfenden, 1988)
Transfer free energy from chx to oct
(Radzicka-Wolfenden, 1988)
Transfer free energy from vap to oct
(Radzicka-Wolfenden, 1988)
Accessible surface area (Radzicka-Wolfenden,
1988)
Energy transfer from out to in(95%buried)
(Radzicka-Wolfenden, 1988)
Mean polarity (Radzicka-Wolfenden, 1988)
Relative preference value at N"
(Richardson-Richardson, 1988)
Relative preference value at N'
(Richardson-Richardson, 1988)
Relative preference value at N-cap
(Richardson-Richardson, 1988)
Relative preference value at N1
(Richardson-Richardson, 1988)
Relative preference value at N2
(Richardson-Richardson, 1988)
Relative preference value at N3
(Richardson-Richardson, 1988)
54.88518
53.28748
53.16833
53.63410
50.82322
53.36330
56.02795
51.85225
54.80394
55.99003
54.69021
53.86698
56.2175
56.00628
56.32041
60.98354
61.01062
52.70256
52.70256
53.07626
54.72270
55.56759
51.47314
14
328
RICJ880107
329
RICJ880108
330
RICJ880109
331
RICJ880110
332
RICJ880111
333
RICJ880112
334
RICJ880113
335
RICJ880114
336
RICJ880115
337
RICJ880116
338
RICJ880117
339
ROBB760101
340
ROBB760102
341
ROBB760103
342
ROBB760104
343
ROBB760105
344
ROBB760106
345
ROBB760107
346
ROBB760108
347
ROBB760109
348
ROBB760110
349
ROBB760111
Relative preference value at N4
(Richardson-Richardson, 1988)
Relative preference value at N5
(Richardson-Richardson, 1988)
Relative preference value at Mid
(Richardson-Richardson, 1988)
Relative preference value at C5
(Richardson-Richardson, 1988)
Relative preference value at C4
(Richardson-Richardson, 1988)
Relative preference value at C3
(Richardson-Richardson, 1988)
Relative preference value at C2
(Richardson-Richardson, 1988)
Relative preference value at C1
(Richardson-Richardson, 1988)
Relative preference value at C-cap
(Richardson-Richardson, 1988)
Relative preference value at C'
(Richardson-Richardson, 1988)
Relative preference value at C"
(Richardson-Richardson, 1988)
Information measure for alpha-helix
(Robson-Suzuki, 1976)
Information measure for N-terminal helix
(Robson-Suzuki, 1976)
Information measure for middle helix
(Robson-Suzuki, 1976)
Information measure for C-terminal helix
(Robson-Suzuki, 1976)
Information measure for extended
(Robson-Suzuki, 1976)
Information measure for pleated-sheet
(Robson-Suzuki, 1976)
Information measure for extended without
H-bond (Robson-Suzuki, 1976)
Information measure for turn (Robson-Suzuki,
1976)
Information measure for N-terminal turn
(Robson-Suzuki, 1976)
Information measure for middle turn
(Robson-Suzuki, 1976)
Information measure for C-terminal turn
(Robson-Suzuki, 1976)
54.60897
64.46057
51.88475
55.11265
53.79658
60.95104
58.96880
55.02600
58.44346
55.70299
52.85420
51.89016
56.45581
51.93891
58.50303
55.67049
54.58731
57.23570
52.88670
53.48245
54.31109
53.31997
15
350
ROBB760112
351
ROBB760113
352
ROBB790101
353
354
ROSG850101
ROSG850102
355
ROSM880101
356
ROSM880102
357
ROSM880103
358
SIMZ760101
359
360
361
362
SNEP660101
SNEP660102
SNEP660103
SNEP660104
363
SUEM840101
364
SUEM840102
365
SWER830101
366
TANS770101
367
TANS770102
368
TANS770103
369
TANS770104
370
TANS770105
371
TANS770106
372
TANS770107
373
TANS770108
Information measure for coil (Robson-Suzuki,
1976)
Information measure for loop (Robson-Suzuki,
1976)
Hydration free energy (Robson-Osguthorpe,
1979)
Mean area buried on transfer (Rose et al., 1985)
Mean fractional area loss (Rose et al., 1985)
Side chain hydropathy, uncorrected for solvation
(Roseman, 1988)
Side chain hydropathy, corrected for solvation
(Roseman, 1988)
Loss of Side chain hydropathy by helix formation
(Roseman, 1988)
Transfer free energy (Simon, 1976), Cited by
Charton-Charton (1982)
Principal component I (Sneath, 1966)
Principal component II (Sneath, 1966)
Principal component III (Sneath, 1966)
Principal component IV (Sneath, 1966)
Zimm-Bragg parameter s at 20 C (Sueki et al.,
1984)
Zimm-Bragg parameter sigma x 1.0E4 (Sueki et
al., 1984)
Optimal matching hydrophobicity
(Sweet-Eisenberg, 1983)
Normalized frequency of alpha-helix
(Tanaka-Scheraga, 1977)
Normalized frequency of isolated helix
(Tanaka-Scheraga, 1977)
Normalized frequency of extended structure
(Tanaka-Scheraga, 1977)
Normalized frequency of chain reversal R
(Tanaka-Scheraga, 1977)
Normalized frequency of chain reversal S
(Tanaka-Scheraga, 1977)
Normalized frequency of chain reversal D
(Tanaka-Scheraga, 1977)
Normalized frequency of left-handed helix
(Tanaka-Scheraga, 1977)
Normalized frequency of zeta R
(Tanaka-Scheraga, 1977)
53.16833
53.11958
55.34012
53.16833
63.01993
55.71382
58.28098
55.58384
56.49372
54.86893
51.68436
56.72119
58.94172
52.32344
56.18501
53.93739
53.22249
54.50065
57.11114
54.48440
52.71880
56.34207
56.57496
52.59965
16
374
TANS770109
375
TANS770110
376
VASM830101
377
VASM830102
378
VASM830103
379
VELV850101
380
VENT840101
381
VHEG790101
382
WARP780101
383
WEBA780101
384
WERD780101
385
WERD780102
386
WERD780103
387
WERD780104
388
389
390
391
392
WOEC730101
WOLR810101
WOLS870101
WOLS870102
WOLS870103
393
YUTK870101
394
YUTK870102
395
YUTK870103
396
YUTK870104
397
ZASB820101
398
ZIMJ680101
Normalized frequency of coil (Tanaka-Scheraga,
1977)
Normalized frequency of chain reversal
(Tanaka-Scheraga, 1977)
Relative population of conformational state A
(Vasquez et al., 1983)
Relative population of conformational state C
(Vasquez et al., 1983)
Relative population of conformational state E
(Vasquez et al., 1983)
Electron-ion interaction potential (Veljkovic et
al., 1985)
Bitterness (Venanzi, 1984)
Transfer free energy to lipophilic phase (von
Heijne-Blomberg, 1979)
Average interactions per side chain atom
(Warme-Morgan, 1978)
RF value in high salt chromatography
(Weber-Lacey, 1978)
Propensity to be buried inside (Wertz-Scheraga,
1978)
Free energy change of epsilon(i) to epsilon(ex)
(Wertz-Scheraga, 1978)
Free energy change of alpha(Ri) to alpha(Rh)
(Wertz-Scheraga, 1978)
Free energy change of epsilon(i) to alpha(Rh)
(Wertz-Scheraga, 1978)
Polar requirement (Woese, 1973)
Hydration potential (Wolfenden et al., 1981)
Principal property value z1 (Wold et al., 1987)
Principal property value z2 (Wold et al., 1987)
Principal property value z3 (Wold et al., 1987)
Unfolding Gibbs energy in water, pH7.0 (Yutani
et al., 1987)
Unfolding Gibbs energy in water, pH9.0 (Yutani
et al., 1987)
Activation Gibbs energy of unfolding, pH7.0
(Yutani et al., 1987)
Activation Gibbs energy of unfolding, pH9.0
(Yutani et al., 1987)
Dependence of partition coefficient on ionic
strength (Zaslavsky et al., 1982)
Hydrophobicity (Zimmerman et al., 1968)
54.14861
54.86893
52.32886
54.92309
54.09445
54.65230
53.16833
56.31499
61.66594
58.56261
57.52816
54.50607
55.30221
53.26581
57.39818
55.69216
55.49718
56.62912
61.99090
55.89796
55.91421
54.65771
54.63063
52.59424
56.27708
17
399
400
401
402
ZIMJ680102
ZIMJ680103
ZIMJ680104
ZIMJ680105
403
AURR980101
404
AURR980102
405
AURR980103
406
AURR980104
407
AURR980105
408
AURR980106
409
AURR980107
410
AURR980108
411
AURR980109
412
AURR980110
413
AURR980111
414
AURR980112
415
AURR980113
416
AURR980114
417
AURR980115
418
AURR980116
419
AURR980117
420
AURR980118
421
AURR980119
422
AURR980120
Bulkiness (Zimmerman et al., 1968)
Polarity (Zimmerman et al., 1968)
Isoelectric point (Zimmerman et al., 1968)
RF rank (Zimmerman et al., 1968)
Normalized positional residue frequency at helix
termini N4'(Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini N"' (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini N" (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini N'(Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini Nc (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini N1 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini N2 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini N3 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini N4 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini N5 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini C5 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini C4 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini C3 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini C2 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini C1 (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini Cc (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini C' (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini C" (Aurora-Rose,1998)
Normalized positional residue frequency at helix
termini C"' (Aurora-Rose,1998)
Normalized positional residue frequency at helix
53.23332
57.21404
62.94411
56.69952
54.96101
56.41248
53.03834
57.20862
54.04571
52.9896
51.56521
54.17569
53.26040
53.31456
53.20082
52.71339
52.90836
58.10225
54.60897
55.93588
58.57886
57.40901
56.28250
53.86157
18
termini C4' (Aurora-Rose,1998)
423
ONEK900101
424
ONEK900102
425
VINM940101
426
VINM940102
427
VINM940103
428
VINM940104
429
MUNV940101
430
MUNV940102
431
MUNV940103
432
MUNV940104
433
MUNV940105
434
WIMW960101
435
KIMC930101
436
MONM990101
437
BLAM930101
438
439
PARS000101
PARS000102
Delta G values for the peptides extrapolated to 0
M urea (O'Neil-DeGrado,1990)
Helix formation parameters (delta delta G)
(O'Neil-DeGrado, 1990)
Normalized flexibility parameters (B-values),
average (Vihinen et al., 1994)
Normalized flexibility parameters (B-values) for
each residue surrounded by none rigid neighbours
(Vihinen et al., 1994)
Normalized flexibility parameters (B-values) for
each residue surrounded by one rigid neighbours
(Vihinen et al., 1994)
Normalized flexibility parameters (B-values) for
each residue surrounded by two rigid neighbours
(Vihinen et al., 1994)
Free energy in alpha-helical conformation
(Munoz-Serrano, 1994)
Free energy in alpha-helical region
(Munoz-Serrano, 1994)
Free energy in beta-strand conformation
(Munoz-Serrano, 1994)
Free energy in beta-strand region
(Munoz-Serrano, 1994)
Free energy in beta-strand region
(Munoz-Serrano, 1994)
Free energies of transfer of AcWl-X-LL peptides
from bilayer interface to water (Wimley-White,
1996)
Thermodynamic beta sheet propensity
(Kim-Berg, 1993)
Turn propensity scale for transmembrane helices
(Monne et al., 1999)
Alpha helix propensity of position 44 in T4
lysozyme (Blaber et al., 1993)
p-Values of mesophilic proteins based on the
distributions of B values (Parthasarathy-Murthy,
2000)
p-Values of thermophilic proteins based on the
distributions of B values (Parthasarathy-Murthy,
2000)
55.67591
56.58037
58.52470
54.93393
54.53856
61.07561
51.99848
52.69714
54.62522
54.18111
53.44996
54.17028
53.12500
55.69757
51.95516
55.70841
55.61633
19
440
441
442
KUMS000101
KUMS000102
KUMS000103
443
KUMS000104
444
TAKK010101
445
FODM020101
446
447
448
449
450
451
NADH010101
NADH010102
NADH010103
NADH010104
NADH010105
NADH010106
452
NADH010107
453
MONM990201
454
KOEP990101
455
KOEP990102
Distribution of amino acid residues in the 18
non-redundant families of thermophilic proteins
(Kumar et al., 2000)
Distribution of amino acid residues in the 18
non-redundant families of mesophilic proteins
(Kumar et al., 2000)
Distribution of amino acid residues in the
alpha-helices in thermophilic proteins (Kumar et
al., 2000)
Distribution of amino acid residues in the
alpha-helices in mesophilic proteins (Kumar et
al., 2000)
Side-chain contribution to protein stability
(kJ/mol) (Takano-Yutani, 2001)
Propensity of amino acids within pi-helices
(Fodje-Al-Karadaghi, 2002)
Hydropathy scale based on self-information
values in the two-state model (5% accessibility)
(Naderi-Manesh et al., 2001)
Hydropathy scale based on self-information
values in the two-state model (9% accessibility)
(Naderi-Manesh et al., 2001)
Hydropathy scale based on self-information
values in the two-state model (16% accessibility)
(Naderi-Manesh et al., 2001)
Hydropathy scale based on self-information
values in the two-state model (20% accessibility)
(Naderi-Manesh et al., 2001)
Hydropathy scale based on self-information
values in the two-state model (25% accessibility)
(Naderi-Manesh et al., 2001)
Hydropathy scale based on self-information
values in the two-state model (36% accessibility)
(Naderi-Manesh et al., 2001)
Hydropathy scale based on self-information
values in the two-state model (50% accessibility)
(Naderi-Manesh et al., 2001)
Averaged turn propensities in a transmembrane
helix (Monne et al., 1999)
Alpha-helix propensity derived from designed
sequences (Koehl-Levitt, 1999)
Beta-sheet propensity derived from designed
sequences (Koehl-Levitt, 1999)
54.22444
54.13237
54.61438
54.31109
54.48440
54.48982
55.69216
63.08492
60.84272
59.32084
56.97032
55.74632
54.05113
53.24415
53.53661
56.59662
20
456
CEDJ970101
457
CEDJ970102
458
CEDJ970103
459
CEDJ970104
460
CEDJ970105
461
462
FUKS010101
FUKS010102
463
FUKS010103
464
FUKS010104
465
FUKS010105
466
FUKS010106
467
FUKS010107
468
FUKS010108
469
470
471
472
FUKS010109
FUKS010110
FUKS010111
FUKS010112
Composition of amino acids in extracellular
proteins (percent) (Cedano et al., 1997)
Composition of amino acids in anchored proteins
(percent) (Cedano et al., 1997)
Composition of amino acids in membrane
proteins (percent) (Cedano et al., 1997)
Composition of amino acids in intracellular
proteins (percent) (Cedano et al., 1997)
Composition of amino acids in nuclear proteins
(percent) (Cedano et al., 1997)
Surface composition of amino acids in
intracellular proteins of thermophiles (percent)
(Fukuchi-Nishikawa, 2001)
Surface composition of amino acids in
intracellular proteins of mesophiles (percent)
(Fukuchi-Nishikawa, 2001)
Surface composition of amino acids in
extracellular proteins of mesophiles (percent)
(Fukuchi-Nishikawa, 2001)
Surface composition of amino acids in nuclear
proteins (percent) (Fukuchi-Nishikawa, 2001)
Interior composition of amino acids in
intracellular proteins of thermophiles (percent)
(Fukuchi-Nishikawa, 2001)
Interior composition of amino acids in
intracellular proteins of mesophiles (percent)
(Fukuchi-Nishikawa, 2001)
Interior composition of amino acids in
extracellular proteins of mesophiles (percent)
(Fukuchi-Nishikawa, 2001)
Interior composition of amino acids in nuclear
proteins (percent) (Fukuchi-Nishikawa, 2001)
Entire chain composition of amino acids in
intracellular proteins of thermophiles (percent)
(Fukuchi-Nishikawa, 2001)
Entire chain composition of amino acids in
intracellular proteins of mesophiles (percent)
(Fukuchi-Nishikawa, 2001)
Entire chain composition of amino acids in
extracellular proteins of mesophiles (percent)
(Fukuchi-Nishikawa, 2001)
Entire chain compositino of amino acids in
nuclear proteins (percent) (Fukuchi-Nishikawa,
2001)
54.35984
53.90490
54.13237
54.15945
55.52968
60.08990
58.12933
58.09142
63.23657
54.16486
53.65576
56.23375
55.88713
55.96295
54.68479
53.23332
54.85810
21
473
AVBF000101
474
AVBF000102
475
AVBF000103
476
AVBF000104
477
AVBF000105
478
AVBF000106
479
AVBF000107
480
AVBF000108
481
AVBF000109
482
YANJ020101
483
MITS020101
484
TSAJ990101
485
TSAJ990102
486
COSI940101
487
PONP930101
488
WILM950101
489
WILM950102
490
WILM950103
491
WILM950104
492
493
KUHL950101
GUOD860101
494
JURD980101
495
BASU050101
Screening coefficients gamma, local (Avbelj,
2000)
Screening coefficients gamma, non-local (Avbelj,
2000)
Slopes tripeptide, FDPB VFF neutral (Avbelj,
2000)
Slopes tripeptides, LD VFF neutral (Avbelj,
2000)
Slopes tripeptide, FDPB VFF noside (Avbelj,
2000)
Slopes tripeptide FDPB VFF all (Avbelj, 2000)
Slopes tripeptide FDPB PARSE neutral (Avbelj,
2000)
Slopes dekapeptide, FDPB VFF neutral (Avbelj,
2000)
Slopes proteins, FDPB VFF neutral (Avbelj,
2000)
Side-chain conformation by gaussian
evolutionary method (Yang et al., 2002)
Amphiphilicity index (Mitaku et al., 2002)
Volumes including the crystallographic waters
using the ProtOr (Tsai et al., 1999)
Volumes not including the crystallographic
waters using the ProtOr (Tsai et al., 1999)
Electron-ion interaction potential values (Cosic,
1994)
Hydrophobicity scales (Ponnuswamy, 1993)
Hydrophobicity coefficient in RP-HPLC, C18
with 0.1%TFA/MeCN/H2O (Wilce et al. 1995)
Hydrophobicity coefficient in RP-HPLC, C8 with
0.1%TFA/MeCN/H2O (Wilce et al. 1995)
Hydrophobicity coefficient in RP-HPLC, C4 with
0.1%TFA/MeCN/H2O (Wilce et al. 1995)
Hydrophobicity coefficient in RP-HPLC, C18
with 0.1%TFA/2-PrOH/MeCN/H2O (Wilce et al.
1995)
Hydrophilicity scale (Kuhn et al., 1995)
Retention coefficient at pH 2 (Guo et al., 1986)
Modified Kyte-Doolittle hydrophobicity scale
(Juretic et al., 1998)
Interactivity scale obtained from the contact
matrix (Bastolla et al., 2005)
53.94281
52.98419
54.41941
52.71880
55.32929
57.31694
54.53856
55.63258
56.55329
52.55091
60.36070
54.80394
54.91768
54.66313
56.23917
59.90576
57.93436
61.42223
52.58341
55.39970
60.43111
57.57691
54.27318
22
496
BASU050102
497
BASU050103
498
SUYM030101
499
PUNT030101
500
PUNT030102
501
GEOR030101
502
GEOR030102
503
GEOR030103
504
GEOR030104
505
506
GEOR030105
GEOR030106
507
GEOR030107
508
GEOR030108
509
GEOR030109
510
ZHOH040101
511
ZHOH040102
512
513
ZHOH040103
BAEK050101
514
HARY940101
Interactivity scale obtained by maximizing the
mean of correlation coefficient over
single-domain globular proteins (Bastolla et al.,
2005)
Interactivity scale obtained by maximizing the
mean of correlation coefficient over pairs of
sequences sharing the TIM barrel fold (Bastolla
et al., 2005)
Linker propensity index (Suyama-Ohara, 2003)
Knowledge-based membrane-propensity scale
from 1D_Helix in MPtopo databases
(Punta-Maritan, 2003)
Knowledge-based membrane-propensity scale
from 3D_Helix in MPtopo databases
(Punta-Maritan, 2003)
Linker propensity from all dataset
(George-Heringa, 2003)
Linker propensity from 1-linker dataset
(George-Heringa, 2003)
Linker propensity from 2-linker dataset
(George-Heringa, 2003)
Linker propensity from 3-linker dataset
(George-Heringa, 2003)
Linker propensity from small dataset (linker
length is less than six residues) (George-Heringa,
2003)
Linker propensity from medium dataset (linker
length is between six and 14 residues)
(George-Heringa, 2003)
Linker propensity from long dataset (linker length
is greater than 14 residues) (George-Heringa,
2003)
Linker propensity from helical (annotated by
DSSP) dataset (George-Heringa, 2003)
Linker propensity from non-helical (annotated by
DSSP) dataset (George-Heringa, 2003)
The stability scale from the knowledge-based
atom-atom potential (Zhou-Zhou, 2004)
The relative stability scale extracted from
mutation experiments (Zhou-Zhou, 2004)
Buriability (Zhou-Zhou, 2004)
Linker index (Bae et al., 2005)
Mean volumes of residues buried in protein
interiors (Harpaz et al., 1994)
54.30026
55.78964
52.84337
58.20516
55.95212
54.44649
55.12348
54.24068
54.27318
64.54376
53.35789
54.76603
53.92656
53.54744
53.95906
53.60702
58.25932
55.65425
54.90685
23
515
PONJ960101
516
DIGM050101
517
518
WOLR790101
OLSK800101
519
KIDA850101
520
GUYH850102
521
GUYH850103
522
GUYH850104
523
GUYH850105
524
ROSM880104
525
ROSM880105
526
JACR890101
527
COWR900101
528
BLAS910101
529
CASG920101
530
531
532
533
534
535
536
537
CORJ870101
CORJ870102
CORJ870103
CORJ870104
CORJ870105
CORJ870106
CORJ870107
CORJ870108
538
MIYS990101
539
MIYS990102
540
MIYS990103
541
MIYS990104
Average volumes of residues (Pontius et al.,
1996)
Hydrostatic pressure asymmetry index, PAI (Di
Giulio, 2005)
Hydrophobicity index (Wolfenden et al., 1979)
Average internal preferences (Olsen, 1980)
Hydrophobicity-related index (Kidera et al.,
1985)
Apparent partition energies calculated from
Wertz-Scheraga index (Guy, 1985)
Apparent partition energies calculated from
Robson-Osguthorpe index (Guy, 1985)
Apparent partition energies calculated from Janin
index (Guy, 1985)
Apparent partition energies calculated from
Chothia index (Guy, 1985)
Hydropathies of amino acid side chains, neutral
form (Roseman, 1988)
Hydropathies of amino acid side chains, pi-values
in pH 7.0 (Roseman, 1988)
Weights from the IFH scale (Jacobs-White, 1989)
Hydrophobicity index, 3.0 pH (Cowan-Whittaker,
1990)
Scaled side chain hydrophobicity values
(Black-Mould, 1991)
Hydrophobicity scale from native protein
structures (Casari-Sippl, 1992)
NNEIG index (Cornette et al., 1987)
SWEIG index (Cornette et al., 1987)
PRIFT index (Cornette et al., 1987)
PRILS index (Cornette et al., 1987)
ALTFT index (Cornette et al., 1987)
ALTLS index (Cornette et al., 1987)
TOTFT index (Cornette et al., 1987)
TOTLS index (Cornette et al., 1987)
Relative partition energies derived by the Bethe
approximation (Miyazawa-Jernigan, 1999)
Optimized relative partition energies - method A
(Miyazawa-Jernigan, 1999)
Optimized relative partition energies - method B
(Miyazawa-Jernigan, 1999)
Optimized relative partition energies - method C
(Miyazawa-Jernigan, 1999)
53.67743
54.68479
55.76256
59.0338
60.17114
57.38735
55.3672
64.18284
59.33167
56.37998
56.94866
58.51928
60.73982
55.32929
57.46317
56.76993
53.96989
56.24458
56.06044
58.87673
58.46512
57.84770
57.33860
57.53358
57.88020
59.98159
60.23614
24
542
MIYS990105
543
544
ENGD860101
FASG890101
Optimized relative partition energies - method D
(Miyazawa-Jernigan, 1999)
Hydrophobicity index (Engelman et al., 1986)
Hydrophobicity index (Fasman, 1989)
60.06282
58.34055
61.21101
25