Figure 2

Step-by-step diagram production. Figure 2 shows the diagram production for epoxy succinyl inhibitor (EPO) in PDB entry 1CSB [6]. a shows the partitioning of EPO into structural elements. Chains are boxed in green, rings in blue, isolated atoms in red. The simple orthographic projection of the 3D structure of EPO is shown in b. c presents the ligand layout after the first step of the ligand layout algorithm. A conflict occurs with several atom overlaps and bond crossings. d shows the ligand layout (in black) obtained after the conflict resolution step and the processing of the explicit residue (Cystein 29 - chain A). The explicit residue appears in grey and the connection in red. e is the diagram obtained after the interaction layout algorithm. Hydrogen bonds are in blue and nearby residues are represented by ovals coloured depending on hydrophobic properties (polar residues in pink, non-polar in green and other in grey). For each residue the chain ID encoding in the PDB file is given in brackets. f is the final diagram produced by LeView, containing the residue names.