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. 2015 Sep 2;89(22):11457–11472. doi: 10.1128/JVI.01384-15

TABLE 3.

Covarying sites in the CD4 binding network for resistant R5 viruses

HXB2a Degreeb Selectionc Sited Domain Protein N-Gly motife
99D 16 Null 98 C1 gp120
365S 9 0.968434 333 CD4 binding gp120 N-X-S/T-X
373T 10 0.986405 341 CD4 binding gp120
415T 17 Null 365 V4 gp120
444R 15 0.999052 394 C4 gp120
471G 14 0.972233 415 V5 gp120
514G 13 Null 458 Fusion peptide gp41
620E 16 0.999999 564 gp41_b gp41 +1
621Q 23 0.999999 565 gp41_b gp41 +2
636N 22 0.971159 580 Coiled coil gp41 −1
644S 10 0.999716 588 Coiled coil gp41 +4
658Q 10 Null 602 Coiled coil gp41
659E 19 Null 603 Coiled coil gp41
662E 12 Null 606 Coiled coil gp41
734E 26 Null 678 gp41_d gp41
746I 24 Null 690 gp41_d gp41
750N 18 0.978824 694 gp41_d gp41
754A 27 Null 698 gp41_d gp41
792A 18 0.999976 736 gp41_d gp41
804S 17 Null 748 gp41_d gp41
817A 20 Null 761 gp41_d gp41 N-X-S/T-X
a

HXB2 numbering is used as a reference.

b

Degree, number of covarying pairs with the site in the BLOSUM62 covariation network.

c

Selection indicates the results of positive-selection analysis (at 95% posterior probability); null indicates no positive selection.

d

Site indicates the position of the covarying site in the alignment.

e

N-Gly motif, the position of the covarying site in the N-linked glycosylation motif N-X-S/T-X. The position is highlighted in boldface and underlined, and positive/negative numbers indicate the position of the covarying site relative to its closest N-X-S/T-X motif in the sequence. Negative (−) means the covarying site is located on the left side of the motif, while positive (+) means the site is located on the right side of the motif.