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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 strands
very much, but it hates betaturns.
If you want to mutate a residue,
but you don’t have a good plan
about what to replace it with,
take alanine because it is a
subset of all other amino acids
(Gly is special).
C Cys Cysteine
Cysteine is a small
hydrophobic residue.
It doesn’t like the alpha helix,
but doesn’t mind strands.
It can form bridges with other
cysteines (Cys-Cys bridges).
It can bind metals (especially
Zn and Cu).
The S-H group is very reactive
and can easily be oxidised.
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 Nterminus of a helix, and in turns.
It hates strands.
It often occurs in active sites. It
can bind ions (mainly Ca).
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 turns.
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.
G Gly Glycine
Glycine is the smallest residue.
It doesn’t have a side chain, so
its hydrophobicity is a bit
undetermined.
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.
H His Histidine
Histidine is very special. It is a
large hydrophilic residue. Both
its side chain nitrogens can
titrate (the first one at pH 6.2). It
is a little bit aromatic.
It is not particularly picky about
its secondary structure.
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).
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.
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.
L Leu Leucine
Leucine is an intermediately
large, hydrophobic residue.
It really loves to sit in a helix.
It is also good for a strand, but
it hates turns.
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 not
reactive.
It is often the first residue of a
molecule. The N-terminus is
mostly positive and thus mostly at
the surface.
Therefore, the hydrophobic
methionine is often at the surface.
We call this a forced marriage.
N Asn Asparagine
Asparagine is an intermediately
large, polar residue.
It hates the helix, is mildly unamused 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.
P Pro Proline
Proline is small and hydrophobic.
In proline, the side chain is
connected to the backbone at
two places: the C and the N.
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. And turns tend
to be at the surface. So, even
though it is very hydrophobic, Pro
often sits at the surface.
We call this a forced marriage.
*Except when at the N-terminus
of the chain, of course.
Q Gln Glutamine
Glutamine is a large, polar
residue.
It is not very picky about its
secondary structure but has a
mild preference for the helix.
It is isosteric with glutamic
acid.
R Arg Arginine
Arginine is a big, hydrophilic,
positively charged residue.
It is not picky about its
secondary structure.
Its side chain contains a socalled guadinium group that is
rigid.
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.
T Thr Threonine
Threonine is a small, alcoholic
residue of intermediate
hydrophobicity.
It is beta- branched and thus
good for beta strands. It
doesn’t care about helices or
turns.
It is occasionally involved in
metal (Ca) binding.
V Val Valine
Valine is a small hydrophobic
residue.
It is beta-branched and thus
good for beta strands. Valine
doesn’t care about helices, but
it hates turns.
It is isosteric with threonine.
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.
Size matters. Its size determines
that Trp is the most conserved of
all residues.
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.