Nucleotide and amino acid composition of HIV genomes and 3D mapping of HIV-human protein interactions. (A) Nucleotide composition for HIV-1 and HIV-2. X-axis represents the HIV groups, subtypes and CRFs. Y-axis shows the average proportions of nucleotides (A, T, C, G) using the HIV genomic sequence datasets (one sequence per patient, Table 1). (B) Amino acid composition for HIV-1 and HIV-2. X-axis represents HIV groups, subtypes and CRFs. Y-axis shows the average proportions of amino acids using the HIV protein sequence datasets (one sequence per patient, Table 1). (C) Distribution plots of amino acid genetic diversity for 15 HIV-1 subtype B proteins. Each subplot demonstrates a viral protein. X- and y-axes indicate the amino acid diversity and the proportions of amino acid diversity, respectively. Red lines inside the distribution plots indicate the mean values of amino acid diversity at individual proteins. (D) Top and side views of 3D HIV-human protein interaction networks. HIV-1 proteins with protein names annotated are indicated by green spheres. Human proteins that interact with only one HIV-1 protein are indicated by blue spheres in the outer circle (one human protein one sphere). Human proteins that interact with more than one HIV-1 protein are indicated by purple spheres above the plane of HIV-1 proteins. The height of the layers above the plane indicates the number of HIV proteins that a human protein interacts with. Below, human proteins are clustered if they interact with a set of more than one HIV-1 protein. Abbreviation names have been described in the abbreviation list. Visualization software: Geomi V2.0(http://sydney.edu.au/engineering/it/~visual/geomi2/).