Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism
Fig 3
Diagrams of the top selected interactions for the cases of all rules + interactions and interactions only.
(A) Interaction map for the 11 interactions selected in combination with all rules. V3-loop is shown as an idealized loop with 35 amino acids where grey circles indicate positions for which no interactions were selected (inactive), while green circles indicate V3-loop positions with interactions selected (active). Red triangles represent residues of CCR5 and blue squares represent residues of CXCR4, with dashed lines representing interactions with V3-loop residues. Ordered lists of observed amino acids (based on occurrence with a minimum of 5%) in one-letter code for each active V3-loop residue are provided. Observed amino acids for CCR5 tropic sequences are in red and those observed for CXCR4 tropic sequences in blue. Bolded letters in the ordered list of observed amino acids indicate an amino acid that is observed in at least 50% of sequences at a given position. (B) Interaction map for the 18 interactions selected without rules. Color scheme and layout is the same as in (A). Faded triangles/squares indicate interactions that were also selected when including all rules. The crossed out interaction was selected when including rules, but not when using interactions only.