TABLE 2.
Covarying sites in the CD4 binding network for sensitive R5 viruses
| HXB2a | Degreeb | Selectionc | Sited | Domain | Protein | N-Gly motife |
|---|---|---|---|---|---|---|
| 173Y | 13 | Null | 151 | V2 | gp120 | |
| 238P | 15 | Null | 211 | C2 | gp120 | −3 |
| 363Q | 17 | 0.998267 | 331 | C3 | gp120 | N-X-S/T-Xf |
| 364S | 4 | Null | 332 | CD4 binding | gp120 | N-X-S/T-Xf |
| 365S | 4 | Null | 333 | CD4 binding | gp120 | N-X-S/T-Xf |
| 373T | 1 | Null | 341 | CD4 binding | gp120 | |
| 442Q | 21 | 0.999411 | 392 | C4 | gp120 | −2 |
| 502K | 7 | Null | 446 | C5 | gp120 | |
| 520L | 4 | Null | 464 | Fusion peptide | gp41 | |
| 620E | 24 | 1 | 564 | gp41_b | gp41 | |
| 658Q | 5 | Null | 602 | Coiled coil | gp41 | |
| 662E | 22 | Null | 606 | Coiled coil | gp41 |
HXB2 numbering is used as a reference.
Degree, number of covarying pairs with the site in the BLOSUM62 covariation network.
Selection indicates the results of positive-selection analysis (at 95% posterior probability); null indicates no positive selection.
Site indicates the position of the covarying site in the alignment.
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.
The sites are in the same N-X-S/T-X motif.