Determinants of backbone packing in globular proteins: an analysis of spatial neighbours

Abstract

This study attempts to examine the pattern and variability of backbone packing density in protein structures. A carefully selected non-redundant data set of known protein structures is analyzed in terms of amino-acid composition and the preference of individual amino acids to fall into regions of low, medium or high density depending on the number of observed non-sequence spatial neighbours. The relationship of the backbone packing density to a number of properties such as the hydrophobicity, non-bonded energies and secondary structural features of the amino acids are examined. The correlation between the average percentage composition and the percentage composition in regions corresponding to different levels of packing density of the proteins is evaluated. These studies are extended to the family of globins whose amino-acid sequences have diverged retaining the same three-dimensional structure during evolution. The significance of high-backbone-density regions in this family has become apparent as due to helix/helix packing. Further, the variation in the amino-acid composition in different contact regions of globin proteins follows the same pattern found for the general data set.