Figure 6

Analysis of eleven HIV-1 isolates. (a) Average physicochemical characteristics of the eleven HIV-1 isolates within the region of gp120 shown in Figure 5c. Four amino acid characteristics are considered: hydrophobicity, surface accessibility, flexibility, and propensity to be in a β-turn. Each scale was standardized to facilitate presentation in one plot [see Additional file 2]. Using the BM weights in Figure 5b, four average characteristics were calculated at each position 307–321 in the alignment of Figure 5c. To highlight the trend in these characteristics, the plot displays a moving average (window size 5) across the region. The center of the window is displayed on the x-axis, so that 309 corresponds on the y-axis to a smoothed value of amino acid positions 307 through 311. High values in the middle of the plot support the recently confirmed hypothesis that positions 312–315 form an exposed β-turn. (b) BM-weighted frequency of amino acids by position in the alignment of Figure 5c. For positions 307–321 (left to right), the amino acids in each column are ordered from top to bottom by decreasing frequency after weighting the contribution of each sequence by the BM weights in Figure 5b. By position, the height of each letter shows the weighted frequency of its corresponding amino acid, so that in total all columns have equal height one. The weighted consensus sequence reads across the top as QSITIGPGRAFYTTG, while the standard (unweighted) consensus is given by the sequence of letters in black. Note that the unweighted consensus in position 311 is not unique, as I and R appear four times each.