Properties of Amino Acids Table

Properties of amino acids
Occurrence Accessible Ranking of
Amino acid pK
a
of ionizing Average residue Monoisotopic in proteins
c
Percent bur ied V
r
e
van der Waals surface amino acid
residue side chain
a
mass
b
(daltons) mass (daltons)
b
(%) residues
d
(%)
3
)volume
f
3
)area
g
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)
Tr yptophan 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
a
values in most cases are at 25ºC. The expected pK
a
values in proteins, shown in parentheses, are determined from model compounds in which titration of side chains is decoupled from charge
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
r
) of buried residues, calculated from the surface area of the side chain (Richards 1977; Baumann et al. 1989).
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).
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