Figure 5

Probability (%) maps of C5aR:PMX53 intermolecular contacts and hydrogen bonds, computed from the MD simulation trajectory of binding mode 22. Panels A, B, C and D, show, respectively, protein side-chain – ligand side-chain, protein mainchain – ligand mainchain, protein side-chain – ligand mainchain, and protein mainchain – ligand side-chain contacts. A contact was considered present in a trajectory snapshot, if the distance betweeen the geometric center of the corresponding moieties was smaller than 6.5 Å. Panel E displays a probability map (%) of C5aR:PMX53 hydrogen bonds. A hydrogen bond among two heavy atoms was considered present if the donor-acceptor distance was smaller than 3.5 Å and the D-H – A angle was larger than 90°.