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. 2012 May 18;7(5):e37530. doi: 10.1371/journal.pone.0037530

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Yokoyama et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Full-length gp120 sequences of the HIV-1 CRF01_AE [42] were extracted from a public database, and divided into subgroups on the basis of the net charge of the V3 loop (+2∼+8). The divided sequences were used to calculate the Shannon entropy, H(i) [63], within each subpopulation, and the H(i) values were plotted on the 3-D structure of gp120 (PDB code: 2B4C [1]). The results for the gp120 subgroups that have V3 loops with +7 (left panel) and +3 (right panel) charges are shown as representative. The numbers of sequences used to calculate the H(i) were 9 and 81 for +7 and +3, respectively. (A) Distribution of H(i) in the gp120 monomer. (B) Distribution of H(i) around the CD4 binding site.