Superposition of c.58 and c.78 domain pairs, by DALI alignment. Panel (a): one intra-cluster, cluster 1, pair of c.58, d1edza2 (146 residues, red) and d1b0aa2 (121 residues, blue), 118 residues aligned, RMSD = 2.7Å, and Zscore = 14.4. Panel (b): another intra-cluster, cluster 2, pair of c.58, d1c1da2 (148 residues, yellow) and d1leha2 (134 residues, magenta), 130 residues aligned, RMSD = 1.4Å and Zscore = 21.3. Panel (c): inter-cluster pair of c.58, between cluster 1 and cluster 2, d1b0aa2 (blue) and d1c1da2 (yellow), 81 residues aligned, RMSD = 4.7Å and Zscore = 4.5. Panel (d): inter-fold domain pair between d1b74a1 (c.78, 105 residues, green) and d1b0aa2 (c.58, 121 residue, blue), 75 residues aligned, RMSD = 3.3Å, Zscore = 6.2. Both c.58 and c.78 folds are characterized by having a core of 3 layers a/b/a with a parallel beta-sheet of 4 strands, ordered 2134. Under hierarchical clustering, fold c.58 is comprised of two homogeneous clusters (Figure 4).
Sam et al. BMC Bioinformatics 2008 9:74 doi:10.1186/1471-2105-9-74