Structural Compromise of Disallowed Conformations in Peptide and Protein Structures

C. Ramakrishnan; B. Lakshmi; A. Kurien; D. Devipriya; N. Srinivasan

doi:10.2174/092986607781483921

Abstract

Using a data set of 454 crystal structures of peptides and 80 crystal structures of non-homologous proteins solved at ultra high resolution of 1.2 Å or better we have analyzed the occurrence of disallowed Ramachandran (φ, Ψ) angles. Out of 1492 and 13508 non-glycyl residues in peptides and proteins respectively 12 and 76 residues in the two datasets adopt clearly disallowed combinations of Ramachandran angles. These examples include a number of conformational points which are far away from any of the allowed regions in the Ramachandran map. According to the Ramachandran map a given (φ, Ψ) combination is considered disallowed when two non-bonded atoms in a system of twolinked peptide units with ideal geometry are prohibitively proximal in space. However, analysis of the disallowed conformations in peptide and protein structures reveals that none of the observations of disallowed conformations in the crystal structures correspond to a short contact between non-bonded atoms. A further analysis of deviations of bond lengths and angles, from the ideal peptide geometry, at the residue positions of disallowed conformations in the crystal structures suggest that individual bond lengths and angles are all within acceptable limits. Thus, it appears that the rare tolerance of disallowed conformations is possible by gentle and acceptable deviations in a number of bond lengths and angles, from ideal geometry, over a series of bonds resulting in a net gross effect of acceptable non-bonded inter-atomic distances.

Keywords: Contact criteria, Peptide geometry, Peptide structures, Protein structures, Ramachandran map, Stereochemistry

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