Relationships between protein sequence and structure patterns based on residue contacts

The identification of correlations between sequence patterns and structural motifs is a prerequisite in the development of protein structure prediction methods. The prediction accuracy indicates whether these correlations are discerned. We present an approach to identify long-range relationships between sequence patterns and structural motifs by varying 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 neighboring residues and described by vectors whose components express contact strengths on an atomic level. Through testing various classification schemes, including their resolution and optimizing parameters, discernible relationships between sequences and folds are explored. About ten structural contact states, together with information from noncontacting regions, could improve the accuracy of contact prediction. (C) 1998 Wiley-Liss, Inc.