DETERMINANTS OF BACKBONE PACKING IN GLOBULAR-PROTEINS - AN ANALYSIS OF SPATIAL NEIGHBORS

This study attempts to examine the pattern and variability of backbone packing density in protein structures. A carefully selected non-redun dant data set of known protein structures is analyzed in terms of amin o-acid composition and the preference of individual amino acids to fal l into regions of low, medium or high density depending on the number of observed non-sequence spatial neighbours. The relationship of the b ackbone packing density to a number of properties such as the hydropho bicity, non-bonded energies and secondary structural features of the a mino acids are examined. The correlation between the average percentag e composition and the percentage composition in regions corresponding to different levels of packing density of the proteins is evaluated. T hese studies are extended to the family of globins whose amino-acid se quences have diverged retaining the same three-dimensional structure d uring 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 reg ions of globin proteins follows the same pattern found for the general data set.