Figure 2
From: Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties
Electrostatic clustering analysis of the HIV-1 subtypes, using the year 2009 consensus sequences and structural template derived from the gp120 structure with PDB Code 2QAD. The horizontal axis of the dendrogram represents electrostatic similarity distance. Electrostatic potentials were calculated using ionic strength corresponding to 0 mM salt concentration. Isopotential contours are presented in four different orientations, corresponding to rotations about the vertical axis (indicated in the figure). Isopotential contours are plotted at ± 1 kBT/e, with blue and red corresponding to positive and negative electrostatic potentials, respectively. The net charge, global prevalence, geographic distribution, and coreceptor selectivity are indicated in the figure for each subtype. N/A denotes that information was not available. The orange boxes highlight clusters with HIV-1 subtypes that have similar electrostatic potential and same charge. Green circles in the branches of the dendrogram denote intersection points between net charges or infected population. The symbol # refers to the global prevalence of Subtype D, which includes D and D35 combined.