(LF). The interface of protein-protein complexes was described by
means of the interchain degree, i.e., the number of links nodes
establish with nodes pertaining to a chain different from that they
belong to (Fig. 7d). In this way, putative interface residues are
highlighted. Further, P and betweenness centrality profiles identify
probable allosteric sites (Fig. 7a, b). The closeness centrality reports
only a kind of “rigidity” map, useless to identify functional nodes
(Fig. 7c).
5 Notes
1. The distance cutoff to define links derives from chemicophysical considerations and statistical significance analysis
[30]; however, a recent study reports a simple cutoff of 5 Å
between residues center of mass as optimal for PCNs description [31]. This could be a useful option to define protein
contact networks.
Fig. 7 Ribbon maps of network descriptors for the anthrax trimeric complex (PA-EF-LF). (a) betweenness
centrality; (b) participation coefficient P; (c) closeness centrality; (d) interchain degree. The lethal factor LF is
marked by the red circle. Reprinted with permission from [29]
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Luisa Di Paola et al.