THE INFLUENCE OF SHORT-RANGE INTERACTIONS ON PROTEIN CONFORMATION, III. DIPEPTIDE DISTRIBUTIONS IN PROTEINS OF KNOWN SEQUENCE AND STRUCTURE

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Abstract
A statistical analysis is made of the distribution into α-helical and non-α-helical regions of the various dipeptide types appearing in a sample of seven proteins of known sequence and structure. By considering as a group all dipeptide types occurring at a given location relative to the reported helix-coil boundaries and examining the percentage of cases in which these appear in non-α-helical regions throughout the protein sample , we find a sharp change in the nature of the observed dipeptide types when the helix-coil boundary is crossed. Furthermore, we find that dipeptide types which occur in the coil region near the C-terminal end of helical segments are non-α-helical in almost 90 per cent of the cases in which they appear throughout the sample. No similar effect is found in the coil region near the N-terminal end of helical segments. These results give evidence for the importance of short-range interactions in determining protein conformation. They are also consistent with predictions based on a model for helix formation given in the second paper of this series. 1