Figure 4

Network of non-covalent residue interactions for the NS3-4A protease and the corresponding list of protein-ligand interactions. (a) Network analysis of non-covalent residue interactions for the NS3-4A protease (PDB entry 1RTL). Nodes represent residues and colored edges represent different types of interactions: van der Waals interactions, backbone-side chain (blue), side chain-side chain (red); H-bond interactions, backbone-side chain (green), side chain-side chain (orange). Protein-ligand interactions for the 1RTL and 2FM2 ligands CPX and SCH 446211, respectively, as well as for VX-950 are tagged by brown Arabic numerals above each residue node (see (b)). Catalytic residues are yellow and the mutated residues are blue (V36), red (T54) and grey (R155, A156). (b) List of van der Waals interactions (vdW), H-bonds (HB) and covalent bonds (CB) for the 1RTL and 2FM2 ligands CPX and SCH 446211, respectively, and the VX-950 ligand docking result. Each dot or square represents one interaction of the ligand with an amino acid of the NS3-4A protease, and dots indicate interactions with the cyclopropyl group. Brown Arabic numerals refer to protein-ligand interactions in the network of non-covalent interactions (a).