Figure 11.

Examples of folds that are better recognized by a contact definition different from the Cβ-Cβ distance 6.5Å. For each example, the tertiary structure and a contact map are presented. Contact maps are generated using CMView [47]. The chain color, blue to red, shows the orientation of the chain from the N- to the C-terminus. A, 1h6wA. In the contact maps, black are contacts detected by both the Cβ-Cβ 6.5 Å and the Cβ-Cβ 20 Å definitions; green and red are contacts dentified only by the latter definition. Contacts in red in the map correspond to the residue pairs connected by red lines in the structure. B, 1gyoA. Black are contacts detected by both the Cβ-Cβ 6.5 Å and the Cα-Cα 12 Å; green and red are contacts identified only by the latter definition. C, 1dq3A. Black are identified by both the Cβ-Cβ 6.5Å and the Cα-Cα 6.5Å; red and green contacts are identified only by the latter definition. Two residues in magenta in the structure are in contact using the definition of the Cα-Cα 6.5 Å but not by the Cβ-Cβ 6.5 Å. D, 1ogkE. Black are those which identified by both the Cβ-Cβ 6.5 Å and the Cα-Cα 6.5 Å. On the other hand, contacts in purple and red are detected only by the former definition. Contacts in green are unique to the latter definition

Yuan et al. BMC Bioinformatics 2012 13:292   doi:10.1186/1471-2105-13-292
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