Figure 5. Predicted ranking of the CDR amino acids in the antibody-VEGF complex interfaces.

Panel (a) to (e) shows the complex structure for 1BJ1, 2FJH, 2QR0, 1TZH, and 1TZI respectively. In each of the panels, the atoms of the antigen VEGF are shown in spheres; the VEGF atoms colored in magenta are core interface atoms and the VEGF atoms colored in cyan are rim interface atoms. The core-rim assignment follows the definition previously published [54]. The CDR atoms in the core interface are shown in thick stick model and the CDR atoms in the rim interface are shown in thin stick model. The ranking of the CDR amino acids in the structures are color-coded according to the color bar shown at the bottom of the figure: Better ranking is shown with increasing depth in red; worse ranking is shown with increasing depth in blue. The CDR residues colored in yellow are not in contact with the antigen.