Amino acid conservation in HIV-1 full-length gag. (A) Density plots of CI values are shown for 8 HIV-1 subtypes. Secondary structures are indicated for each protein region, with thick lines for helices and thin lines for coiled-coil structures. Positions conserved in all subtypes are colored blue (layer 1 in a small circle), known drug binding positions are colored red (layer 2) and regions where HIV-1 peptide inhibitors have been derived are colored green (layer 3). (B) Distributions of CI values at 500 gag positions across 8 HIV-1 subtypes and CRFs. Visualization software: Circos v0.64 (http://circos.ca/).