REGULARITIES IN INTERACTION PATTERNS OF GLOBULAR-PROTEINS

The description of protein structure in the language of side chain con tact maps is shown to offer many advantages over more traditional appr oaches. Because it focuses on side chain interactions, it aids in the discovery, study and classification of similarities between interactio ns defining particular protein folds and offers new insights into the rules of protein structure. For example, there is a small number of ch aracteristic patterns of interactions between protein supersecondary s tructural fragments, which can be seen in various non-related proteins . Furthermore, the overlap of the side chain contact maps of two prote ins provides a new measure of protein structure similarity. As shown i n several examples, alignments based on contact map overlaps are a pow erful alternative to other structure-based alignments.