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Figure 5 | Biology Direct

Figure 5

From: A new ensemble coevolution system for detecting HIV-1 protein coevolution

Figure 5

Intra-protein couplings of HIV-1 matrix and capsid predicted by CNPR. (A) Contact map of HIV-1 matrix protein and intra-protein coevolving pairs predicted by CNPR. Five helices (H1 to H5) and random-coil secondary structures are aligned to the x-axis. At the bottom right, protein contact map is colored according to the Euclidean distances between two amino acid positions in the 3D structure. Coevolving pairs are colored blue if Euclidean distances were less than 8 Å, otherwise gradient from yellow to red. At the upper left, the predicted coevolving residues are marked as asterisks. Green asterisks indicate true positive couplings falling within the black contours of protein contact map. (B) Cartoon representation of HIV-1 matrix structure. The predicted intra-subunit coupling between the residues A45 and E70 is annotated. PDB code: 1HIW. (C) Contact map of HIV-1 capsid protein and intra-protein coevolving pairs predicted by CNPR. Figure captions are the same as in (A). (D) Cartoon representation of HIV-1 capsid hexamer with 6 identical subunits. The predicted intra-subunit coupling between the residues A42 and T54 is annotated. PDB code: 3H4E. The intra-protein couplings predicted by all 28 methods in HIV-1 proteins are shown in Figure S4-S7. Visualization software: PyMOL V1.5 (http://www.pymol.org/).

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