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Canonical loops and structural alignment

An automated loop clustering program[Martin & Thornton, 1996] was used to assign each CDR from the dataset to one of a number of distinct backbone conformations. The first step in the protocol employs Ward's minimum variance method[Ward, 1963,Wishart, 1969] to cluster `loop vectors' derived from backbone torsion angles. A second `post-clustering' step merges clusters which are similar in cartesian space. In most cases the conformational clusters match the canonical classes described by Chothiachothia:HVRegions, but additional conserved backbone conformations have also been identified[Martin & Thornton, 1996].

CDRs were aligned for the `through-space' contact analysis using the program ProFit, fitting on three framework residues either side of the loop residues (see Table 2.3). In the figures, single representatives for multiply populated CDR conformations were chosen arbitrarily by PDB code (alphabetically).