FIG. 1.

Occurrence of insertions and deletions in the V1V2 domain. Distributions of insertions (A) and deletions (B) are shown for HIV-1 reference strain HxB2 positions from 126 to 196. The most frequently occurring side chains at each position corresponding to the HxB2 numbering are labeled on the x-axis. A linear secondary structure diagram of the V1V2 domain is provided at the bottom of each histogram. (C) Two clusters of high length polymorphism (colored in red) are mapped on the three-dimensional structure of the gp140 trimer. Note that the structure of the second cluster has not been resolved in the crystallographic study of the gp140 trimer and thus is shown as a dashed red line (arrow). The structure of V1V2 is shown in ribbon and stick representation (colors correspond to those on the secondary structure diagram in the top and middle panels), while the rest of the trimer is shown in skin representation. The space occupied by glycans is shown by gray dot-envelopes. Color images available online at www.liebertpub.com/aid