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. 2014 Jan 28;9(1):e85940. doi: 10.1371/journal.pone.0085940

Figure 5. Diverse interaction modes of NBD-analogue Region III with gp120.

Figure 5

Close-up views of NBD-557 (A, B), AS-II-37 (C, D), AS-I-261 (E, F), MAE-II-167 (G, H), and MAE-II-188 (I, J) in the Phe 43 cavity. Region I and II reside inside the Phe 43 cavity. The Region III of the analogues protrudes outside the cavity in diverse conformations. All atoms on gp120 within 5 Å distance to the Region III of the analogues are shown with dotted lines; hydrogen bonds in red and two atoms within the van der Waals radius in green dotted lines. (B, D, F, H, and J) NBD analogues in 2fo-fc electron density map colored by the B-factor. The color scale ranges from blue to red for B-factors of >40 to <150 Å2.