Hydrophobic character of amino acid residues in globular proteins

Abstract

PREDICTIVE studies on the secondary structure of globular proteins aimed at locating ordered structural segments have provided little information about spatial orientations or even as to whether residues are exposed or buried. However, the physico-chemical properties¹ of residues can be used to obtain such information. In particular the hydrophobic character², is a useful parameter in these studies. The hydrophobic character as defined by the indices given by Tanford³ and Jones⁴ does not reflect hydrophobic environment within protein structures, but we introduce here a new parameter, the ‘bulk hydrophobic character’ obtained from an analysis of the surrounding hydrophobic environment of amino acid residues in protein crystals. This is a better index of protein hydrophobicity, showing very good correlation with the extent to which residues are buried⁵ (correlation coefficient r = 0.9) compared with the hydrophobic indices used previously, and it could be used to characterise tertiary structures.