Figure 4

Predicted Epitope Network Residues vs. Published Epitopes for PG9 (top panel) and PG16 (bottom panel). Residues predicted to be part of an interacting network are represented by ball-and-stick and are colored red. Residues reported by Walker et al. to impact PG9 and PG16 sensitivity [4] are colored blue. Overlap between predicted and published residues is indicated by blue residues which are also shown in ball-and-stick representation. The 3D models represent a theoretical view of full-length HXB2 gp120 as generated by the CPHmodels program [46]. A and B depict a hypothetical trimer seen from the top and side respectively, while C and D represent a monomer representation seen from the front and back respectively. Correct orientation of trimer subunits was obtained by aligning the Cα backbone of the predicted models with the corresponding chains of the trimer structure (PDB ID: 2NY7). Visualizations were generated using UCSF Chimera [49].