RELATIONSHIPS BETWEEN PROTEIN-SEQUENCE AND STRUCTURE PATTERNS BASED ON RESIDUE CONTACTS

The identification of correlations between sequence patterns and struc tural motifs is a prerequisite in the development of protein structure prediction methods. The prediction accuracy indicates whether these c orrelations are discerned. We present an approach to identify long-ran ge relationships between sequence patterns and structural motifs by va rying the granulation of the structure description. Since interaction among residues is a major determinant in protein folding, we consider contact environments formed by two triplets of three sequentially neig hboring residues and described by vectors whose components express con tact strengths on an atomic level. Through testing various classificat ion schemes, including their resolution and optimizing parameters, dis cernible relationships between sequences and folds are explored. About ten structural contact states, together with information from noncont acting regions, could improve the accuracy of contact prediction. (C) 1998 Wiley-Liss, Inc.