A.2 Amino Acid Codes
Amino acids are commonly referred to as the
"building blocks" of proteins. The
characteristics of each amino acid are dependent on their side chain,
and they can be divided into several classes. These classifications
are denoted as either polar, nonpolar, acidic, or basic. Figure A-1 shows the structure of an amino acid.
Although trying to recall all of the amino acid names and their
symbols may be a fun mental exercise, we've decided
to include a table of amino acids. Table A-2
includes the names, three- and single-letter codes, side chains, and
classification of each amino acid.
Table A-2. Amino acid codes
|
Alanine
|
Ala
|
A
|
|
nonpolar
|
|
Arginine
|
Arg
|
R
|
|
basic
|
|
Asparagine
|
Asn
|
N
|
|
polar
|
|
Aspartic Acid
|
Asp
|
D
|
|
acidic
|
|
Cysteine
|
Cys
|
C
|
|
polar
|
|
Glutamine
|
Gln
|
Q
|
|
polar
|
|
Glutamic Acid
|
Glu
|
E
|
|
acidic
|
|
Glycine
|
Gly
|
G
|
|
nonpolar
|
|
Histidine
|
His
|
H
|
|
basic
|
|
Isoleucine
|
Ile
|
I
|
|
nonpolar
|
|
Leucine
|
Leu
|
L
|
|
nonpolar
|
|
Lysine
|
Lys
|
K
|
|
basic
|
|
Methionine
|
Met
|
M
|
|
nonpolar
|
|
Phenylalanine
|
Phe
|
F
|
|
nonpolar
|
|
Proline
|
Pro
|
P
|
|
nonpolar
|
|
Selenocysteine
|
Sec
|
U
|
|
polar
|
|
Serine
|
Ser
|
S
|
|
polar
|
|
Threonine
|
Thr
|
T
|
|
polar
|
|
Tryptophan
|
Trp
|
W
|
|
polar
|
|
Tyrosine
|
Tyr
|
Y
|
|
polar
|
|
Valine
|
Val
|
V
|
|
nonpolar
|
|
Aspartic acid or Asparagine
|
Asx
|
B
|
See structures above.
|
-
|
|
Glutamic acid or Glutamine
|
Glx
|
Z
|
See structures above.
|
-
|
|
Unspecified Amino Acid
|
Xaa
|
X
|
-
|
-
|
A.2.1 Properties Summary
Although there are four main
classifications for amino acids, other characteristics may also be
used to describe them. This is best illustrated in the properties
diagram in Figure A-2. In the diagram,
tiny is used to describe very short side chains,
while small is used to denote small side chains.
The terms aliphatic,
aromatic and hydrophobic
commonly refer to the chemical composition of the side chain of an
amino acid. These types of side chains are typically composed of only
carbon and hydrogen atoms. The terms charged,
negative, positive, and
polar designate the electronic characteristics
of a side chain. The diagram is adapted from Livingstone &
Barton, CABIOS, 9, 745-756, 1993 (http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=8143162&form=6&db=m&Dopt=bPubMed).
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