Backbone Conformational Pattern Clustering of Three-Dimensional Peptide Fragments of Proteins

Motokazu KAMIMURA (
Yoshimasa TAKAHASHI (

Department of Knowledge-based Information Engineering,
Toyohashi University of Technology, Tempaku, Toyohashi 441, JAPAN


In this paper we aim to examine in detail the data distribution within each conformational pattern class and to identify some local common structural features among the fragments in a particular cluster (or subcluster). Backbone conformational pattern clustering was carried out for the three-dimensional peptide fragments where the phi-psi conformational pattern of the TA (target amino acid) belongs to class A (alpha-helix dominant class) or B (beta-sheet dominant class) as defined in our previous work. The analysis for the fragments of class A suggested that these fragments involve four representative local backbone conformational patterns, not only for typical alpha-helix fragments but also for fragments closely related to type I turn or the starting moieties of alpha-helices. On the other hand, the analysis for class B fragments showed that these have much more diversity than class A fragments with respect to their local backbone structures. The details of the methods and results of the analyses are discussed here.