Stereochemical criteria for polypeptide and protein chain conformations. III. Helical and hydrogen-bonded polypeptide chains

Abstract

The previous study, for a pair of peptide units, of the conformations which are allowed on the basis of stereochemical criteria of van der Waals contacts has been extended to the analysis of possible conformations of helical polypeptide chains. Computer methods have been developed which select conformations on the basis of both satisfactory interatomic contacts as well as the formation of good intramolecular hydrogen bonds. Such programs have been used to map the allowed dihedral angle pairs (ϕ, ψ) for helical polypeptide chains. This survey has been made for values of the N—C^α—C' angle (τ) of 105°, 110°, and 115°, from which the significant influence of this angle in determining allowed helical conformations can be demonstrated. Calculations have also been carried out using potential energy functions for the interaction between nonbonded atoms. The potential energy contour maps obtained in this manner are basically similar to the conformational maps calculated by the first method.