PACKING OF SECONDARY STRUCTURAL ELEMENTS IN PROTEINS - ANALYSIS AND PREDICTION OF INTER-HELIX DISTANCES

Interacting helix pairs were defined as those in which each member has one residue which undergoes a fractional loss of 0.10 solvent accessible contact area on association. Analysis of 1095 such pairs of helices, selected from the Brookhaven Data Bank, confirms that helix pairs in proteins can pack interactively at all angles with preferential packing observed in the angle intervals (Ω), -160° to -140°, -100° to -20°, 10° to 40°, and 50° to 160°. The distance (d) between the helix axes in the contact region of two interactively packed helices is linearly correlated with the volume-dependent function, log(V/nda), of the residues in this region. The correlation is used to predict inter-helix distances in equivalent helix pairs of homologous proteins and is therefore of value in comparative modelling of protein three-dimensional structures. © 1993 Academic Press Limited.