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Figure 8 | BMC Evolutionary Biology

Figure 8

From: The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes

Figure 8

(A + B) CBP profiles of the hydrophobic amino acids (Leu, Ile, Phe, and Trp) of the same two HIV-1 NEF sequences as profiled in Fig. 3A and Fig. 3B. Hydrophobic amino acids (black dots) and hydrophobic areas (orange blocks) are depicted above the running average (window size 15) of hydrophobic amino acid density (black line) and of the epitope C-terminal density (grey line). (A) Both the fraction of the sequence that is part of a hydrophobic region (14%), and the H&S index score (1.48) are likely to occur at random (CBP: p rich = 0.099, H&S: p = 0.095). (B) Both the fraction of the sequence that is part of a hydrophobic region (15%), and the H&S index score (0.758) are likely to occur at random (CBP: p rich = 0.047, H&S: p = 0.576). (C) An overlay of HIV-1 proteins on top of the human proteome. The degree of clustering of hydrophobic amino acids is determined by the H&S index and plotted against protein length. Significant sequences (i.e. p < 0.001, permutation test) are plotted as red dots for HIV-1 (only 5 out of 11039), and yellow dots for Human (1195 out of 70269).

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