cC

78

Chapter 3 Amino Acids, Peptides, and Proteins

TABLE 3 1 Properties and Conventions Associated with the Common Amino Acids Found in
-

Proteins

pk, values
Amino
acid

Abbreviation/ pK1
Mr
symbol

R groups Glycine Alanine Proline Valine

Leucine Isoleucine
Gly
7
Methionine
G Ala
5
89
Aromatic R groups A Pro
P Val
11
Phenylalanine
V Leu
5
Tyrosine
L He
11
Tryptophan
I Met
7
M
Polar, uncharged
R groups
Serine
Phe F
165
Threonine Cysteine
Tyr Y
181
Aspa ragine
Tip
204
Glutamine
W
Positively charged R
groups
Ser
10
Lysine
S
5
Histidine
Thr
Arginine
T
11
Negatively charged Cys
9
C
R groups

pK2

PKR
( COON) (--N11,1) (R group)
-

Hydropathy Occurrence in
index*
proteins (%)I
Nonpolar, aliphatic

2.3
4
2.3
4
1.9
9
2.3
2

9.6
0
9.6
9
10.9
6
9.6
2

1.83
2.20
2.38

9.13
9.11
9.39

,10.07

5.97
6.01
6.48
5.97
5.98
6.02
5.74

-OA
1.8
1.6
4.2
3.8
4.5
1.9

5.48
5.66
5.89

2.8
-1.3
-0.9

7.
2
7.8
5.2
6.6
9.1
5.3
3.
9
3.

2.2
1
2.1
1
1.9

9.1
5
9.6
2
10.2
8

5.6
8
5.8
7
5.0
7

0.
8
-0.
7
2.
5

6.
8
59
1_
9
4.

Lys K
14
2.1
8.9
10.5
9.7
6
His H
8
5
3
4
.A scale combining hydrophobicity and
hydrophilicity of R groups; it can be used to measure the tendency of an amino acid to
Arg
6.00
7.59
seek an aqueous environment (- values) or a hydrophobic environment (4 values). See Chapter 11, Fmrn Kyte, J. & Doolittle.,
15
1.8
R
9.1
R.F. (1982) A simple method for displaying the hydropathic character of a protein. I, Mot Biol. 157, 105-132.

-3.9

5.
9

8.1
8

Aspartate
Glutamate

3.2
-4.5

'Average occurrence in more than 1,150 proteins. From Doolittle, R f. (1989) Redundancies in protein sequences, In Prediction of

Protein Stoic Lure and the Principles of Protein Conformation (Tasman, 0.0 ed ), pp 599-623, Plenum Press, New York,

Asp
D

133
147

1.88
2.19

9.60
9.67

3.6
5
4.2

2.7
7
3.2
2

-3.5
3.5

5.
3
6.
3

Amino Acids Can Be Classified by R Group

Knowledge of the chemical properties of the counon
amino acids is central to an understandilig of biochemistry. The topic can be simplified by groupitig the amino
acids into five main classw; based on the properties of
their R groups (Table 1 ), in part it I heir polarity,
or tendency to interact s,vith water ai biological p1 l (nom.
pH 7.0). The polarity of the R groups varied idely, from
nonpolar and hydrophobic Oval erinsolul )It') to highly
polar and hydrophilic (water-soluble).
The structures of the 20 common amino acids are
shown in Figure 3-5, and some of their properties are

listed in Table 3-1. Within each class there are

gradations of polarity, size, and shape Of the R

groups.
Nonpolar, Aliphatic R Groups The R. groups in this class of

aniino acids are nonpolar and hydrophobic. The

side chains of Marline, valine, 'endue, and
isoleucine I( nd to cluster together wilhin proteins,
stabilwag
pro
_
100
h\
riicmr:
or
h y d r o p h o b i c m i e r a m o u s wycine has the
simplest structure. Although it is formally nonpolar,

its very small side chain makcs mu) real col itribution
to hydrophobic interactions, Mettionitne, ow' of
the

INVO snl fur-containing amino acids, has a non