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.

Figure A-1. Amino acid structure
figs/seq_appa01.gif

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

Name

Three-letter code

Single-letter code

Side chain

classification

Alanine

Ala

A

figs/seq_appatab1a.gif

nonpolar

Arginine

Arg

R

figs/seq_appatab1b.gif

basic

Asparagine

Asn

N

figs/seq_appatab1c.gif

polar

Aspartic Acid

Asp

D

figs/seq_appatab1d.gif

acidic

Cysteine

Cys

C

figs/seq_appatab1e.gif

polar

Glutamine

Gln

Q

figs/seq_appatab1f.gif

polar

Glutamic Acid

Glu

E

figs/seq_appatab1g.gif

acidic

Glycine

Gly

G

figs/seq_appatab1h.gif

nonpolar

Histidine

His

H

figs/seq_appatab1i.gif

basic

Isoleucine

Ile

I

figs/seq_appatab1j.gif

nonpolar

Leucine

Leu

L

figs/seq_appatab1k.gif

nonpolar

Lysine

Lys

K

figs/seq_appatab1l.gif

basic

Methionine

Met

M

figs/seq_appatab1m.gif

nonpolar

Phenylalanine

Phe

F

figs/seq_appatab1n.gif

nonpolar

Proline

Pro

P

figs/seq_appatab1o.gif

nonpolar

Selenocysteine

Sec

U

figs/seq_appatab1p.gif

polar

Serine

Ser

S

figs/seq_appatab1q.gif

polar

Threonine

Thr

T

figs/seq_appatab1r.gif

polar

Tryptophan

Trp

W

figs/seq_appatab1s.gif

polar

Tyrosine

Tyr

Y

figs/seq_appatab1t.gif

polar

Valine

Val

V

figs/seq_appatab1u.gif

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).

Figure A-2. Summary diagram of amino acid properties
figs/seq_appa02.gif


Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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