Structural families in loops of homologous proteins: automatic classification, modelling and application to...

Loop regions of polypeptide in homologous proteins may be classified into structural families. A method is described by which this classification may be performed automatically and "key residue" templates, which may be responsible for the loop adopting a given conformation, are defined. The technique has been applied to the hypervariable loops of antibodies and the results are compared with the previous definition of canonical classes. We have extended these definitions and provide complete sets of structurally determining residues (SDRs) for the observed clusters including the first set of key residues for seven-residue CDR-H3 loops.