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Pages 1–8 1dl5 Evolutionary trace report by report maker November 15, 2009 4.4 4.5 4.6 4.7 1 4.3.1 Alistat 4.3.2 CE 4.3.3 DSSP 4.3.4 HSSP 4.3.5 LaTex 4.3.6 Muscle 4.3.7 Pymol Note about ET Viewer Citing this work About report maker Attachments 7 7 7 8 8 8 8 8 8 8 8 INTRODUCTION From the original Protein Data Bank entry (PDB id 1dl5): Title: Protein-l-isoaspartate o-methyltransferase Compound: Mol id: 1; molecule: protein-l-isoaspartate omethyltransferase; chain: a, b; ec: 2.1.1.77; engineered: yes Organism, scientific name: Thermotoga Maritima; 1dl5 contains a single unique chain 1dl5A (317 residues long) and its homologue 1dl5B. CONTENTS 1 Introduction 1 2 Chain 1dl5A 2.1 Q56308 overview 2.2 Multiple sequence alignment for 1dl5A 2.3 Residue ranking in 1dl5A 2.4 Top ranking residues in 1dl5A and their position on the structure 2.4.1 Clustering of residues at 25% coverage. 2.4.2 Overlap with known functional surfaces at 25% coverage. 2.4.3 Possible novel functional surfaces at 25% coverage. 1 1 1 1 2 2 2 4 3 Notes on using trace results 3.1 Coverage 3.2 Known substitutions 3.3 Surface 3.4 Number of contacts 3.5 Annotation 3.6 Mutation suggestions 6 6 6 6 7 7 7 4 Appendix 4.1 File formats 4.2 Color schemes used 4.3 Credits 7 7 7 7 2 CHAIN 1DL5A 2.1 Q56308 overview From SwissProt, id Q56308, 94% identical to 1dl5A: Description: Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) (Protein- beta-aspartate methyltransferase) (PIMT) (Protein L-isoaspartyl methyltransferase) (L-isoaspartyl protein carboxyl methyltransferase). Organism, scientific name: Thermotoga maritima. Taxonomy: Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga. Function: Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. Catalytic activity: S-adenosyl-L-methionine + protein L- isoaspartate = S-adenosyl-L-homocysteine + protein L-isoaspartate alphamethyl ester. Biophysicochemical properties: Kinetic parameters: Vmax=164 nmol/min/mg enzyme with KASA (isoD) LAKY as substrate at 85 degrees Celsius; Temperature dependence: Optimum temperature is 85 degrees Celsius. Highly thermostable, with no loss of activity after 60 min at 100 degrees Celsius. Enzyme activity is observed at temperatures as high as 93 degrees Celsius; Subunit: Monomer. Subcellular location: Cytoplasmic (By similarity). 1 Lichtarge lab 2006 Fig. 1. Residues 1-158 in 1dl5A colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Fig. 2. Residues 159-317 in 1dl5A colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) 2.4 Similarity: Belongs to the L-isoaspartyl/D-aspartyl protein methyltransferase family. About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are no restrictions on its use as long as its content is in no way modified and this statement is not removed. 2.2 Top ranking residues in 1dl5A and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 3 shows residues in 1dl5A colored by their importance: bright red and yellow indicate more conserved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Multiple sequence alignment for 1dl5A For the chain 1dl5A, the alignment 1dl5A.msf (attached) with 329 sequences was used. The alignment was downloaded from the HSSP database, and fragments shorter than 75% of the query as well as duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1dl5A.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 329 Total number of residues: Smallest: 129 Largest: 317 Average length: 194.7 Alignment length: 317 Average identity: 38% Most related pair: 99% Most unrelated pair: 15% Most distant seq: 38% 64060 Furthermore, <1% of residues show as conserved in this alignment. The alignment consists of 1% eukaryotic ( <1% vertebrata, <1% fungi, <1% plantae), 11% prokaryotic, and 4% archaean sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1dl5A.descr. 2.3 Fig. 3. Residues in 1dl5A, colored by their relative importance. Clockwise: front, back, top and bottom views. 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.4 are composed of the residues listed in Table 1. Residue ranking in 1dl5A The 1dl5A sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 1dl5A can be found in the file called 1dl5A.ranks sorted in the attachment. 2 Table 2. continued res type subst’s (%) A(1) 135 G G(87) L(10)AE 85 G G(97) A(2) 88 Y Y(95) F(3) W(1) 81 E D(14) E(84)LV HN 107 E E(94) D(5) 152 V A(81) G(12) C(3)VP. SL 134 D D(88) P(6) N(1)T A(1)ESG 112 I L(89) V(1) M(2)PR I(3)FQW 59 S S(83) M(3) L(8) V(1)A.I T(1)PWN 151 T A(15) T(61) N(2) S(4) G(5) Q(4) E(3)DC W(1). 57 T T(81) F(1) V(5) S(2) W(1) .(1) P(1)M Y(1)IEA G 89 N A(8) Q(62) T(1) H(6)M L(4) Fig. 4. Residues in 1dl5A, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. cluster color red size 77 Table 1. member residues 18,21,22,25,26,27,28,30,31 56,57,58,59,60,61,62,63,64 65,67,71,79,80,81,82,83,84 85,86,87,88,89,90,91,92,93 94,103,105,106,107,108,109 112,116,120,123,127,128,133 134,135,138,139,143,144,145 146,147,148,150,151,152,153 154,158,161,164,165,168,169 170,171,174,175,176,205 Table 1. Clusters of top ranking residues in 1dl5A. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. SAH binding site. Table 2 lists the top 25% of residues at the interface with 1dl5SAH699 (sah). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). res type 87 83 G G Table 2. subst’s cvg noc/ dist (%) bb (Å) G(99)S 0.00 7/7 4.30 G(98) 0.01 31/31 3.14 continued in next column cvg noc/ bb dist (Å) 0.01 10/10 2.84 0.03 23/23 3.55 0.03 9/6 3.78 0.04 6/0 3.13 0.04 38/6 2.72 0.04 24/3 3.54 0.06 17/9 2.85 0.07 3/0 4.33 0.08 7/4 3.95 0.11 18/8 2.99 0.12 15/14 3.25 0.12 15/8 2.94 continued in next column 3 Table 2. continued res type subst’s (%) S(8) N(5)GC 108 Y R(68) C(2) I(9) Y(2) H(4) E(4) S(2)A D(2)FQ L(1)TV 84 G T(72) C(8) A(8)F S(8) G(1)DP 86 T S(71) T(6) C(13)Q L(3)E Y(2)F.P M 90 A A(57) T(33) S(6) G(1)C 58 S I(77) L(9) M(3) V(3) S(2)EP. R(1)TY 56 S .(16) Q(61) R(10) A(5) K(1)L S(3)VI 133 G A(8) G(79)R D(4)V E(1) S(2)TIN Q 82 I I(67) V(30) L(1) 109 S I(52) D(11) V(9) L(4)K F(2) cvg noc/ bb dist (Å) 0.12 45/15 3.21 0.13 21/21 3.33 0.14 4/3 3.94 0.14 1/1 4.67 0.15 8/5 3.92 0.16 15/4 2.88 0.17 6/6 3.72 0.18 4/2 4.55 0.19 2/1 4.35 Table 2. continued res type subst’s (%) Q(4)M Y(4) N(1) H(4)RSA T 106 V I(37) V(54) L(6) M(1)D cvg noc/ bb dist (Å) 0.20 9/6 3.57 Table 2. The top 25% of residues in 1dl5A at the interface with SAH.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the number of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) res type 87 83 135 85 88 81 107 152 134 112 59 151 57 89 108 84 86 90 58 56 133 82 109 106 G G G G Y E E V D I S T T N Y G T A S S G I S V Table 3. disruptive mutations (KR)(E)(FQMWH)(D) (KER)(QHD)(FYMW)(N) (R)(K)(H)(E) (KER)(QHD)(FYMW)(N) (K)(Q)(E)(M) (H)(FWR)(Y)(CG) (FWH)(R)(YVCAG)(T) (R)(K)(YE)(H) (R)(H)(FW)(KY) (Y)(R)(T)(H) (R)(K)(H)(Y) (R)(K)(H)(FW) (R)(K)(Q)(H) (Y)(H)(FW)(R) (K)(Q)(R)(M) (R)(K)(E)(QH) (R)(K)(H)(FW) (KR)(E)(YH)(Q) (R)(K)(H)(FW) (R)(YH)(K)(FW) (R)(K)(H)(E) (YR)(H)(T)(KE) (R)(K)(H)(FYW) (YR)(K)(H)(E) Table 3. List of disruptive mutations for the top 25% of residues in 1dl5A, that are at the interface with SAH. Figure 5 shows residues in 1dl5A colored by their importance, at the interface with 1dl5SAH699. continued in next column 2.4.3 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 1dl5A surface, away from (or susbtantially larger than) other functional sites and interfaces recognizable in PDB entry 1dl5. It is shown in Fig. 6. The right panel 4 Table 4. continued res type substitutions(%) cvg 164 Q Q(94)R(1).L(1)S 0.03 CE 107 E E(94)D(5) 0.04 V A(81)G(12)C(3)V 0.04 152 P.SL 165 L L(96)V(1).TMC 0.04 D D(88)P(6)N(1)T 0.06 134 A(1)ESG 144 P P(94)EKL(1)TRQ. 0.06 I L(89)V(1)M(2)PR 0.07 112 I(3)FQW 59 S S(83)M(3)L(8) 0.08 V(1)A.IT(1)PWN 64 M V(77)L(9)T(1) 0.09 I(2)H(4)F(2)E M(2)QCA 26 P P(82)E(1)D(9)G 0.10 A(1)TK(1)NR.SQ 60 Q Q(60)E(8)A(16) 0.11 K(6)RHTV(1)S(1) D(2).I 146 D D(86)A(1)N(5) 0.11 S(1)E(2)KQMH. 151 T A(15)T(61)N(2) 0.11 S(4)G(5)Q(4) E(3)DCW(1). 57 T T(81)F(1)V(5) 0.12 S(2)W(1).(1) P(1)MY(1)IEAG 89 N A(8)Q(62)T(1) 0.12 H(6)ML(4)S(8) N(5)GC 108 Y R(68)C(2)I(9) 0.12 Y(2)H(4)E(4) S(2)AD(2)FQL(1) TV 84 G T(72)C(8)A(8)F 0.13 S(8)G(1)DP 143 S A(68)G(24)KS(3) 0.13 MLREIV. 86 T S(71)T(6)C(13)Q 0.14 L(3)EY(2)F.PM 120 V L(78)F(13)M(2) 0.14 S(1)CV(1)I(2)A 58 S I(77)L(9)M(3) 0.15 V(3)S(2)EP.R(1) TY 168 G G(83)P(2)KQN(4) 0.15 D(2)HET.LSRM 56 S .(16)Q(61)R(10) 0.16 A(5)K(1)LS(3)VI 71 V L(71)A(16)I(3) 0.16 continued in next column Fig. 5. Residues in 1dl5A, at the interface with SAH, colored by their relative importance. The ligand (SAH) is colored green. Atoms further than 30Å away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1dl5A.) shows (in blue) the rest of the larger cluster this surface belongs to. Fig. 6. A possible active surface on the chain 1dl5A. The larger cluster it belongs to is shown in blue. The residues belonging to this surface ”patch” are listed in Table 4, while Table 5 suggests possible disruptive replacements for these residues (see Section 3.6). res 83 135 138 85 88 type G G G G Y Table 4. substitutions(%) cvg G(98)A(1) 0.01 G(87)L(10)AE 0.01 G(96)L(1)IAEKV 0.02 G(97)A(2) 0.03 Y(95)F(3)W(1) 0.03 continued in next column 5 Table 4. continued res type substitutions(%) M(1)V(6)QRGTN 28 E E(39)NH(44)A(3) G(3)R(1)D(1)S. K(1)Y(1)Q(1)LP 127 N Q(2)N(77)EG(2) P(3)R(5)A(1)K S(1)T(1)H(1) D(1)MYI 133 G A(8)G(79)RD(4)V E(1)S(2)TINQ 63 L I(30)P(3)M(27) V(15)AT(15)D L(3).RKS 82 I I(67)V(30)L(1) 109 S I(52)D(11)V(9) L(4)KF(2)Q(4)M Y(4)N(1)H(4)RSA T 31 L V(68)L(12)I(7) A(3)M(3)F(3)T.S C 106 V I(37)V(54)L(6) M(1)D 25 I V(62)L(6)I(15)G T(11)KRS.EYC 94 S A(57)S(31)G(2)F L(1)C(3)YD(1)IH TMVQ 128 V V(62)I(22)K(3) A(4)L(3)TFMQRNC P 170 R R(62)V(11)I(13) K(6)LSG.T(1)HQE CFN 13 G G(66).(17)I(5) L(1)DPA(1)ENY V(3)M(1) 123 L T(2)L(74)YA(7) V(1)I(2)H(2)NWE Q(1)M(2).F(1)S 69 E E(62)Q(16)D(12) S(2)HA(2)LK.NRV MT 205 F F(66).(19)V(3) H(1)SI(1)LY(3)W MPT Table 5. continued res type disruptive mutations 135 G (R)(K)(H)(E) G (R)(KEH)(Y)(FW) 138 G (KER)(QHD)(FYMW)(N) 85 88 Y (K)(Q)(E)(M) Q (Y)(FWH)(T)(VCAG) 164 E (FWH)(R)(YVCAG)(T) 107 V (R)(K)(YE)(H) 152 165 L (R)(Y)(H)(K) D (R)(H)(FW)(KY) 134 P (Y)(HR)(T)(CG) 144 112 I (Y)(R)(T)(H) S (R)(K)(H)(Y) 59 M (Y)(H)(R)(T) 64 26 P (Y)(R)(H)(T) Q (Y)(FWH)(T)(CG) 60 D (R)(FWH)(Y)(CG) 146 T (R)(K)(H)(FW) 151 57 T (R)(K)(Q)(H) N (Y)(H)(FW)(R) 89 Y (K)(Q)(R)(M) 108 84 G (R)(K)(E)(QH) S (R)(H)(K)(Y) 143 T (R)(K)(H)(FW) 86 V (R)(KY)(E)(H) 120 58 S (R)(K)(H)(FW) G (R)(FWH)(E)(K) 168 S (R)(YH)(K)(FW) 56 71 V (Y)(R)(E)(H) E (FWH)(Y)(R)(CG) 28 N (Y)(H)(FW)(T) 127 133 G (R)(K)(H)(E) L (Y)(R)(H)(T) 63 I (YR)(H)(T)(KE) 82 S (R)(K)(H)(FYW) 109 31 L (R)(Y)(H)(K) V (YR)(K)(H)(E) 106 I (R)(Y)(H)(K) 25 94 S (R)(K)(H)(Q) V (Y)(E)(R)(K) 128 R (D)(T)(Y)(E) 170 13 G (R)(K)(H)(E) L (R)(Y)(H)(T) 123 E (H)(FW)(Y)(R) 69 F (K)(E)(Q)(DR) 205 cvg 0.17 0.17 0.17 0.18 0.18 0.19 0.20 0.20 0.21 0.21 0.23 0.23 0.24 0.24 0.25 0.25 Table 5. Disruptive mutations for the surface patch in 1dl5A. Table 4. Residues forming surface ”patch” in 1dl5A. res type 83 G Table 5. disruptive mutations (KER)(QHD)(FYMW)(N) continued in next column 3 3.1 NOTES ON USING TRACE RESULTS Coverage Trace results are commonly expressed in terms of coverage: the residue is important if its “coverage” is small - that is if it belongs to some small top percentage of residues [100% is all of the residues in a chain], according to trace. The ET results are presented in the 6 form of a table, usually limited to top 25% percent of residues (or to some nearby percentage), sorted by the strength of the presumed evolutionary pressure. (I.e., the smaller the coverage, the stronger the pressure on the residue.) Starting from the top of that list, mutating a couple of residues should affect the protein somehow, with the exact effects to be determined experimentally. V 3.2 COVERAGE Known substitutions 3.3 V [W F Y HR], hydrophobic [LP V AM W F I], polar [GT CY ]; positively [KHR], or negatively [DE] charged, aromatic [W F Y H], long aliphatic chain [EKRQM ], OH-group possession [SDET Y ], and NH2 group possession [N QRK]. The suggestions are listed according to how different they appear to be from the original amino acid, and they are grouped in round brackets if they appear equally disruptive. From left to right, each bracketed group of amino acid types resembles more strongly the original (i.e. is, presumably, less disruptive) These suggestions are tentative - they might prove disruptive to the fold rather than to the interaction. Many researcher will choose, however, the straightforward alanine mutations, especially in the beginning stages of their investigation. Surface 4 APPENDIX 4.1 File formats Files with extension “ranks sorted” are the actual trace results. The fields in the table in this file: Number of contacts • alignment# number of the position in the alignment • residue# residue number in the PDB file • type amino acid type • rank rank of the position according to older version of ET • variability has two subfields: 1. number of different amino acids appearing in in this column of the alignment Annotation If the residue annotation is available (either from the pdb file or from other sources), another column, with the header “annotation” appears. Annotations carried over from PDB are the following: site (indicating existence of related site record in PDB ), S-S (disulfide bond forming residue), hb (hydrogen bond forming residue, jb (james bond forming residue), and sb (for salt bridge forming residue). 3.6 5% Fig. 7. Coloring scheme used to color residues by their relative importance. Another column worth noting is denoted “noc/bb”; it tells the number of contacts heavy atoms of the residue in question make across the interface, as well as how many of them are realized through the backbone atoms (if all or most contacts are through the backbone, mutation presumably won’t have strong impact). Two heavy atoms are considered to be “in contact” if their centers are closer than 5Å. 3.5 30% RELATIVE IMPORTANCE To detect candidates for novel functional interfaces, first we look for residues that are solvent accessible (according to DSSP program) by at least 10Å2 , which is roughly the area needed for one water molecule to come in the contact with the residue. Furthermore, we require that these residues form a “cluster” of residues which have neighbor within 5Å from any of their heavy atoms. Note, however, that, if our picture of protein evolution is correct, the neighboring residues which are not surface accessible might be equally important in maintaining the interaction specificity - they should not be automatically dropped from consideration when choosing the set for mutagenesis. (Especially if they form a cluster with the surface residues.) 3.4 50% 100% One of the table columns is “substitutions” - other amino acid types seen at the same position in the alignment. These amino acid types may be interchangeable at that position in the protein, so if one wants to affect the protein by a point mutation, they should be avoided. For example if the substitutions are “RVK” and the original protein has an R at that position, it is advisable to try anything, but RVK. Conversely, when looking for substitutions which will not affect the protein, one may try replacing, R with K, or (perhaps more surprisingly), with V. The percentage of times the substitution appears in the alignment is given in the immediately following bracket. No percentage is given in the cases when it is smaller than 1%. This is meant to be a rough guide - due to rounding errors these percentages often do not add up to 100%. 2. their type • rho ET score - the smaller this value, the lesser variability of this position across the branches of the tree (and, presumably, the greater the importance for the protein) • cvg coverage - percentage of the residues on the structure which have this rho or smaller Mutation suggestions • gaps percentage of gaps in this column Mutation suggestions are completely heuristic and based on complementarity with the substitutions found in the alignment. Note that they are meant to be disruptive to the interaction of the protein with its ligand. The attempt is made to complement the following properties: small [AV GST C], medium [LP N QDEM IK], large 4.2 Color schemes used The following color scheme is used in figures with residues colored by cluster size: black is a single-residue cluster; clusters composed of 7 4.3.7 Pymol The figures in this report were produced using Pymol. The scripts can be found in the attachment. Pymol is an open-source application copyrighted by DeLano Scientific LLC (2005). For more information about Pymol see http://pymol.sourceforge.net/. (Note for Windows users: the attached package needs to be unzipped for Pymol to read the scripts and launch the viewer.) more than one residue colored according to this hierarchy (ordered by descending size): red, blue, yellow, green, purple, azure, turquoise, brown, coral, magenta, LightSalmon, SkyBlue, violet, gold, bisque, LightSlateBlue, orchid, RosyBrown, MediumAquamarine, DarkOliveGreen, CornflowerBlue, grey55, burlywood, LimeGreen, tan, DarkOrange, DeepPink, maroon, BlanchedAlmond. The colors used to distinguish the residues by the estimated evolutionary pressure they experience can be seen in Fig. 7. 4.3 4.4 Credits Note about ET Viewer Dan Morgan from the Lichtarge lab has developed a visualization tool specifically for viewing trace results. If you are interested, please visit: 4.3.1 Alistat alistat reads a multiple sequence alignment from the file and shows a number of simple statistics about it. These statistics include the format, the number of sequences, the total number of residues, the average and range of the sequence lengths, and the alignment length (e.g. including gap characters). Also shown are some percent identities. A percent pairwise alignment identity is defined as (idents / MIN(len1, len2)) where idents is the number of exact identities and len1, len2 are the unaligned lengths of the two sequences. The ”average percent identity”, ”most related pair”, and ”most unrelated pair” of the alignment are the average, maximum, and minimum of all (N)(N-1)/2 pairs, respectively. The ”most distant seq” is calculated by finding the maximum pairwise identity (best relative) for all N sequences, then finding the minimum of these N numbers (hence, the most outlying sequence). alistat is copyrighted by HHMI/Washington University School of Medicine, 1992-2001, and freely distributed under the GNU General Public License. http://mammoth.bcm.tmc.edu/traceview/ The viewer is self-unpacking and self-installing. Input files to be used with ETV (extension .etvx) can be found in the attachment to the main report. 4.5 Citing this work The method used to rank residues and make predictions in this report can be found in Mihalek, I., I. Reš, O. Lichtarge. (2004). ”A Family of Evolution-Entropy Hybrid Methods for Ranking of Protein Residues by Importance” J. Mol. Bio. 336: 1265-82. For the original version of ET see O. Lichtarge, H.Bourne and F. Cohen (1996). ”An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families” J. Mol. Bio. 257: 342-358. report maker itself is described in Mihalek I., I. Res and O. Lichtarge (2006). ”Evolutionary Trace Report Maker: a new type of service for comparative analysis of proteins.” Bioinformatics 22:1656-7. 4.3.2 CE To map ligand binding sites from different source structures, report maker uses the CE program: http://cl.sdsc.edu/. Shindyalov IN, Bourne PE (1998) ”Protein structure alignment by incremental combinatorial extension (CE) of the optimal path . Protein Engineering 11(9) 739-747. 4.6 About report maker report maker was written in 2006 by Ivana Mihalek. The 1D ranking visualization program was written by Ivica Reš. report maker is copyrighted by Lichtarge Lab, Baylor College of Medicine, Houston. 4.3.3 DSSP In this work a residue is considered solvent accessible if the DSSP program finds it exposed to water by at least 10Å2 , which is roughly the area needed for one water molecule to come in the contact with the residue. DSSP is copyrighted by W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995, CMBI version by [email protected] November 18,2002, 4.7 Attachments The following files should accompany this report: http://www.cmbi.kun.nl/gv/dssp/descrip.html. • 1dl5A.complex.pdb - coordinates of 1dl5A with all of its interacting partners 4.3.4 HSSP Whenever available, report maker uses HSSP alignment as a starting point for the analysis (sequences shorter than 75% of the query are taken out, however); R. Schneider, A. de Daruvar, and C. Sander. ”The HSSP database of protein structuresequence alignments.” Nucleic Acids Res., 25:226–230, 1997. • 1dl5A.etvx - ET viewer input file for 1dl5A • 1dl5A.cluster report.summary - Cluster report summary for 1dl5A • 1dl5A.ranks - Ranks file in sequence order for 1dl5A http://swift.cmbi.kun.nl/swift/hssp/ • 1dl5A.clusters - Cluster descriptions for 1dl5A 4.3.5 LaTex The text for this report was processed using LATEX; Leslie Lamport, “LaTeX: A Document Preparation System AddisonWesley,” Reading, Mass. (1986). • 1dl5A.msf - the multiple sequence alignment used for the chain 1dl5A 4.3.6 Muscle When making alignments “from scratch”, report maker uses Muscle alignment program: Edgar, Robert C. (2004), ”MUSCLE: multiple sequence alignment with high accuracy and high throughput.” Nucleic Acids Research 32(5), 1792-97. • 1dl5A.ranks sorted - full listing of residues and their ranking for 1dl5A • 1dl5A.descr - description of sequences used in 1dl5A msf • 1dl5A.1dl5SAH699.if.pml - Pymol script for Figure 5 • 1dl5A.cbcvg - used by other 1dl5A – related pymol scripts http://www.drive5.com/muscle/ 8