Properties Of Amino Acids Chart

Properties of amino acids

Occurrence

Accessible

Ranking of

Amino acid

pK

of ionizing

Average residue

Monoisotopic

in proteins

c

Percent buried

V

e

van der Waals surface

amino acid

a

r

residue

side chain

a

mass

b

(daltons)

mass (daltons)

b

(%)

residues

d

(%)

(Å

3

)

volume

f

(Å

3

)

area

g

(Å

2

)

polarities

h

Alanine

–

71.0788

71.03711

7.5

38 (12)

92

67

67

9 (7)

Arginine

12.5 (>12)

156.1876

156.10111

5.2

0

225

148

196

15 (19)

Asparagine

–

114.1039

114.04293

4.6

10 (2)

135

96

113

16 (16)

Aspartic acid

3.9 (4.4–4.6)

115.0886

115.02694

5.2

14.5 (3)

125

91

106

19 (18)

Cysteine

8.3 (8.5–8.8)

103.1448

103.00919

1.8

47 (3)

106

86

104

7 (8)

Glutamine

–

128.1308

128.05858

4.1

6.3 (2.2)

161

114

144

17 (14)

Glutamic acid

4.3 (4.4–4.6)

129.1155

129.04259

6.3

20 (2)

155

109

138

18 (17)

Glycine

–

57.0520

57.02146

7.1

37 (10)

66

48

11 (9)

Histidine

6.0 (6.5–7.0)

137.1412

137.05891

2.2

19 (1.2)

167

118

151

10 (13)

Isoleucine

–

113.1595

113.08406

5.5

65 (12)

169

124

140

1 (2)

Leucine

–

113.1595

113.08406

9.1

41 (10)

168

124

137

3 (1)

Lysine

10.8 (10.0–10.2)

128.1742

128.09496

5.8

4.2 (0.1)

171

135

167

20 (15)

Methionine

–

131.1986

131.04049

2.8

50 (2)

171

124

160

5 (5)

Phenylalanine

–

147.1766

147.06841

3.9

48 (5)

203

135

175

2 (4)

Proline

–

97.1167

97.05276

5.1

24 (3)

129

90

105

13 (–)

Serine

–

87.0782

87.03203

7.4

24 (8)

99

73

80

14 (12)

Threonine

–

101.1051

101.04768

6.0

25 (5.5)

122

93

102

12 (11)

Tryptophan

–

186.2133

186.07931

1.3

23 (1.5)

240

163

217

6 (6)

Tyrosine

10.9 (9.6–10.0)

163.1760

163.06333

3.3

13 (2.2)

203

141

187

8 (10)

Valine

–

99.1326

99.06841

6.5

56 (15)

142

105

117

4 (3)

a

The pK

values in most cases are at 25ºC. The expected pK

values in proteins, shown in parentheses, are determined from model compounds in which titration of side chains is decoupled from charge

a

a

effects of α-substituents. (Data from Cantor and Schimmel 1980.)

b

Data from Burlingame and Carr (1996).

c

Frequency of occurrence of each amino acid residue in the primary structures of 105,990 sequences in the nonredundant OWL protein database (release 26.0 e) (Trinquier and Sanejouand 1998).

d

This column represents the tendency of an amino acid to be buried (defined as <5% of residue available to solvent) in the interior of a protein and is based on the structures of nine proteins (total

of ~2000 individual residues studied, with 587 [29%] of these buried). Values indicate how often each amino acid was found buried, relative to the total number of residues of this amino acid found in

the proteins (values in parentheses indicate the number of buried residues of this amino acid found relative to all buried residues in the proteins). (Data from Schien 1990; for other calculation meth-

ods with similar results, see Janin 1979 and Rose at al. 1985.)

e

Average volume (V

) of buried residues, calculated from the surface area of the side chain (Richards 1977; Baumann et al. 1989).

r

f

Data from Darby and Creighton (1993).

g

Total accessible surface area (ASA) of amino acid side chain for residue X in a Gly-X-Gly tripeptide with the main chain in an extended conformation (Miller et al. 1987). The ASA or cavity surface

area is defined as the surface traced by the center of a sphere with the radius of a water molecule (0.15 mm) as it is rolled over the surface of a molecular model of the solution (Lee and Richards 1971).

h

Values shown represent the mean ranking of amino acids according to the frequency of their occurrence at each sequence rank for 38 published hydrophobicity scales (Trinquier and Sanejouand

1998). Although the majority of these hydrophobicity scales are derived from experimental measurements of chemical behavior or physicochemical properties (e.g., solubility in water, partition between

water and organic solvent, chromatographic migration, or effects on surface tension) of isolated amino acids, several “operational” hydrophobicity scales based on the known environment characteris-

tics of amino acids in proteins, such as their solvent accessibility or their inclination to occupy the core of proteins (based on the position of residues in the tertiary structures as observed by X-ray crys-

tallography or NMR) are included (Trinquier and Sanejouand 1998). The lower rankings represent the most hydrophobic amino acids, and higher values represent the most hydrophilic amino acids. For

comparative purposes, the hydrophobicity scale of Radzicka and Wolfenden is shown in parentheses. This scale was derived from the measured hydration potential of amino acids that is based on their

free energies of transfer from the vapor phase to cyclohexane, 1-octanol, and neutral aqueous solution (Radzicka and Wolfenden 1988).