HIV-1 Immune Escape Maps Figure 1. Gag Immune Escape Map. Escape maps indicate the locations, specific residues and HLA restrictions of HLA-associated polymorphisms. The HIV-1 consensus B amino acid sequence is used as a reference. Alternating black and brown letters in the consensus amino acid sequence distinguish the different proteins in HIV-1 Gag (p17, p24, p2, p7, p1, p6). One hundred amino acids are displayed per line. Shaded vertical bars separate blocks of 10 amino acids. ‘‘Adapted’’ amino acids (those enriched in the presence of the HLA allele) are red. ‘‘Non-adapted’’ amino acids (those depleted in the presence of the HLA allele) are blue. UPPERCASE letters distinguish polymorphisms that survive correction for HIV codon covariation (‘‘direct’’ associations), while lowercase letters distinguish polymorphisms that do not survive correction for codon covariation (‘‘indirect’’ associations). Polymorphisms associated with the same HLA allele that occur in proximity to one another are grouped together in yellow boxes. Optimally-defined CTL epitopes containing HLA-associated polymorphisms are indicated above the consensus sequence. Note that the escape map does not list the locations of all published CTL epitopes. This is available at http://www.hiv.lanl.gov/content/immunology. The escape maps show all HLA-associated polymorphisms with q#0.05. A complete listing of all HLA-associated polymorphisms with q#0.2 is provided in Table S1. doi:10.1371/journal.pone.0006687.g001 PLoS ONE | www.plosone.org 5 August 2009 | Volume 4 | Issue 8 | e6687