Effects of gap regions for Si calculation and clustering. A) Two structures of the PTB domain differing in an insertion/deletion are displayed as green ribbons, and their respective ligands in orange (PDB entry codes: 1SHC and 1IRS). Interacting residues are coloured in red. The insertion/deletion is shown in white. Note that some of the red regions may be included in white ones. B) A section of the dendrogram obtained from the clustering of the PTB domain binding regions (more detailed in figure 4B) is shown for both cases, excluding and including gap regions. Two members of these clusters presenting different (peptide-binding, 1NMB:AB and crystal packing, 1QQG:AB) but overlapping binding regions are highlighted in blue and pink, respectively. A Si cut-off of 0.2 (dashed line) is shown for comparison.