Insights into Protein–DNA Interactions through Structure Network Analysis
Figure 5
P-p, P-S, and P-B clusters in the β-hairpin group protein Arc (1bdt).
In the Arc protein (1bdt), the P-p (yellow), P-S (green), and P-B (blue) clusters are shown. The β-hairpin that is interacting with the DNA is highlighted in red. A cluster of charged residues (Arg, Asn, and Gln) from the β-hairpin makes contact with successive bases of the DNA. These P-B clusters are flanked by the P-S and P-p clusters arising from other secondary structures (helices and loops) around the β-ribbon. A P-p hub (orange) in which the phosphate group of Ade4 interacts with Ser32, Val33 and Phe10 is also highlighted.