Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins.
The radial distributions of the Calpha and side-chain atoms in a sample of 13 native proteins have been examined. It is found that there are substantial differences in behavior between different atoms of the same amino acid. In particular, the Calpha atoms of polar residues show no particular preference for being far from the center of mass. In light of these results, a new criterion for hydrophobicity and hydrophilicity is proposed--namely, the orientational preference of the side chain. The distribution of this property is shown, and it is suggested that this provides a basis for incorporating hydrophobic interactions into a protein folding algorithm.
D000596:Amino Acids; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003201:Computers; D011487:Protein Conformation; D011506:Proteins; D012995:Solubility
D000596:Amino Acids; D011506:Proteins
Macromolecules. 1977 Mar-Apr;10(2):291-304
192953
Q Rev Biophys. 1977 Aug;10(3):239-52
335427
Macromolecules. 1976 Nov-Dec;9(6):945-50
1004017
J Mol Biol. 1976 Jul 25;105(1):1-12
994183
J Mol Biol. 1976 Oct 5;106(4):983-94
978745
Nature. 1974 Mar 22;248(446):338-9
4819639
J Mol Biol. 1973 Sep 15;79(2):351-71
4760134
Nature. 1975 Mar 27;254(5498):304-8
1118010
J Mol Biol. 1971 Feb 14;55(3):379-400
5551392