Figure 6

Intra-protein couplings of HIV-1 protease and Gag cleavage sites in the protein structures. (A) HIV-1 protease coevolving pairs predicted by CNPR. The contact map of HIV-1 protease (bottom right) and the predicted coevolving pairs (top left) are illustrated. Green dots indicate true positive predictions in the protein contact map. The random-coil (e.g. L1-L2), beta-strand (e.g. β1-β8) and helix (e.g. H1) secondary structures are shown along the x- and y-axes. (B) Top and side views of the residue positions (T4, L10, I54, L63, V8, L90) in HIV-1 protease. One helix (e.g. H1) and eight beta-strand (e.g. β1-β8) secondary structures are also shown. (C) Gag cleavage sites in the 3D protein structure of Gag proteins. Gag cleavage sites are annotated in boxes and amino acid positions (V128, S373-T375, V431, F448-P453) are colored in red. PDB code: 1HIW (matrix), 3NTE (capsid), 1U57 (p2), 2M3Z (nucleocapsid), 2C55 (p6). Visualization: PyMOL V1.5 (http://www.pymol.org/).