Estimated Secondary Structure Propensities within V1/V2 Region of HIV gp120 Are an Important Global Antibody Neutralization Sensitivity Determinant
Figure 3
Multiple alignment of 106 sequences of V1/V2 domains in HIV gp120.
Sequence profile is shown above the alignment: stack of amino-acid residue letter codes above each position indicates frequencies (taller letters – more frequent), with most frequent one at the bottom of the stack. Secondary structure cartoon is shown below the alignment as assigned in the X-ray structure (PDB 3U4E). Also indicated at the bottom are the three 5-residue segments (red intervals) that represent BSP/NS ‘hotspots’.