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. 2010 May 20;6(5):e1000789. doi: 10.1371/journal.pcbi.1000789

Figure 4. Topological clustering of peptide-mediated interactions.

Figure 4

(A) Alignment of BRCA1 C Terminus (BRCT) sequences to the domain's HMM profile; interface residues are highlighted. The colour corresponds to the “rainbow” colouring scheme used for the domain visualisation in panel B. Lowercase letters refer to amino acids that do not match the domain's profile, - to positions in the profile that do not occur in the given sequence. (B) Clustering of the interaction topologies, based on shared interface residues. Domains with the same or highly similar topologies are grouped together. In the structural representation, all three BRCT domains have the same orientation. Note that the BRCT domain usually forms dimers that bind the peptide, using the interfaces from clusters (3,4,5,6) and (1,2,9), respectively (cf. Figure 5).