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A Ala Alanine
Alanine is a small, hydrophobic
residue. Its side chain, R, is
just a methyl group. Alanine
likes to sit in an alpha helix,it
doesn’t like beta strand very
much, but it hates beta-turns.
If you want to mutate a
residue, but you don’t have a
good plan about what to
replace it with, take alanine.
©CMBI 2001
C Cys Cysteine
Cysteine is a small till
intermediately large
hydrophobic residue. It doesn’t
like the alpha helix, but doesn’t
mind strand and turn. It can
form Cys-Cys bridges with
other cysteines. It can bind
metals (especially Zn and Cu).
The S-H group is very reactive.
©CMBI 2001
D Asp Aspartic acid
Aspartic acid, or aspartate, is
an intermediately large,
hydrophilic, negatively charged
residue. Its side chain normally
titrates at pH 4.5. It likes to sit
near the N-terminus of a helix,
and in turns. It hates strands.It
often occurs in active sites. It
can bind ions (mainly Ca).
©CMBI 2001
E Glu Glutamic acid
Glutamic acid, or glutamate, is
a large, hydrophilic, negatively
charged residue. Its side chain
titrates at pH 4.6. It loves the
helix, doesn’t mind being in a
strand, but is not so good for a
turn.
©CMBI 2001
F Phe Phenylalanine
Phenylalanine is a large,
hydrophobic, aromatic residue.
It is good for a strand, it
doesn’t mind sitting in a helix,
but it hates the turn.
©CMBI 2001
G Gly Glycine
Glycine is the smallest residue.
It doesn’t have a side chain, so
its hydrophobicity is a bit
undetermined, but you can call
it hydrophobic or assign it an
intermediate hydrophobicity.
The fact that it doesn’t have a
side chain means that its
backbone is very flexible so
that it can make backbone
turns that other residues cannot
make. It is very bad for helix,
bad for strand, but it is the star of the turns.
©CMBI 2001
H His Histidine
Histidine is very special. It is
hydrophilic due to the two
nitrogens in its side chain. Both
nitrogens can titrate (the first
one at pH 6.2). It is a little bit
aromatic. It is often seen in
active sites.It is neutral at
physiological pH, but it can
easily become positive, and
occasionally even negative. It
can bind metal ions (mainly Zn,
Ni, Cu). It is not particularly
picky about its secondary structure.
©CMBI 2001
I Ile Isoleucine
Isoleucine is an intermediately
large, hydrophobic residue. It
is beta branched which means
that it likes to sit in a strand. It
doesn’t mind sitting in a helix
either, but it cries its eyes out
in a turn.
©CMBI 2001
K Lys Lysine
Lysine is a large, hydrophilic,
positively charged residue. It
is not a good strand residue,
but it doesn’t mind sitting in a
helix or in a turn. Its side chain
is very long and flexible.
©CMBI 2001
L Leu Leucine
Leucine is an intermediately
large, hydrophobic residue
that really loves to sit in a helix.
It is also good for a strand, but
it hates turns.
©CMBI 2001
M Met Methionine
Methionine is a large, sulphur
containing, hydrophobic
residue. It loves helices,
doesn’t mind sitting in a strand,
but it hates turns. Methionine
can bind metals with its sulphur,
but this sulphur is much less
reactive than the sulphur in
cysteine. It is often the first
residue of a molecule. The
N-terminus is mostly positive
and thus mostly at the surface.
Therefore, methionine, despite
being hydrophobic, is often at the surface.
We call this a forced marriage.
©CMBI 2001
N Asn Asparagine
Asparagine is an intermediately
large, polar residue. It hates the
helix, is mildly un-amused in a
strand, but it loves the turn. It
can bind metal ions (Ca), but
doesn’t do that as well as its
isosteric partner aspartic acid.
©CMBI 2001
P Pro Proline
In proline, the side chain is
connected to the backbone at
two places: the C and the N.
Therefore, it is not an amino
acid, but an imino acid. Unless
it is the N-terminal residue,
proline does not have a
backbone proton, and thus is
not good for helices and
strands. Due to the extra
covalent bond, proline is
already pre-bend, and thus
good for turns. Even though it is very hydrophobic, it often sits at
the surface
©CMBI 2001
Q Gln Glutamine
Glutamine is a large, polar
residue. It is not very picky
about its secondary structure.
It is isosteric with glutamic acid.
©CMBI 2001
R Arg Arginine
Arginine is a big, hydrophilic,
positively charged residue. Its
side chain contains a so-called
guadinium group that is rigid.
It is not picky about its
secondary structure.
©CMBI 2001
S Ser Serine
Serine is a small, alcoholic
residue of intermediate
hydrophobicity. It is not too
happy in helices and strands,
but it loves to sit in turns. It
often forms the active site of
an enzyme together with
histidine and aspartic acid. It
is occasionally involved in
metal (Ca) binding.
©CMBI 2001
T Thr Threonine
Threonine is a small, alcoholic
residue of intermediate
hydrophobicity. It is betabranched and thus good for
beta strands. It doesn’t care
about helices or turns. It is
occasionally involved in metal
(Ca) binding.
©CMBI 2001
V Val Valine
Valine is a small hydrophobic
residue. It is beta-branched
and thus good for beta strands.
It is isosteric with threonine.
Valine doesn’t care about
helices, but it hates turns.
©CMBI 2001
W Trp Tryptophan
Tryptophan is the biggest
residue. It is aromatic. Despite
that the nitrogen in the five-ring
is donor for hydrogen bonds, it
is very hydrophobic. It doesn’t
care about helices or turns, but
it loves strands.
©CMBI 2001
Y Tyr Tyrosine
Tyrosine is a large, aromatic,
alcoholic residue of
intermediate hydrophobicity. It
is not so happy in a helix,
indifferent about turns, and it
loves a strand.
©CMBI 2001