Table 3.
Residues pairs that have low commute times, (C(i,j)) < 0.20, in the GPO1, GPO2, and GPO3 X-ray structures as determined by GNM fluctuation profiles are sorted by communication hub in the bridging sheet, inner domain and outer domain. Residues that also exhibit GNM slow mode minima or maxima are in bold or underlined font, respectively. Residues that are conserved in HIV sequences are indicated in italics (G258, P270, R469, G471, G472, T458. Residues pairs with efficient communication propensities as determined by MD simulation are colored in blue. The amino-acid residue is given for YU2/GPO3 only.
| Hub | (i) | Hub | (j) 1 | Hub | (j) 2 | Hub | (j) 3 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Bridging
Sheet |
P118 | C119 | K121 | L122 | A433 | M434 | ||||||||||||
|
Inner
Domain |
A219 | A224 | I225 | |||||||||||||||
| A224 | I225 | L226 | K227 | C228 | V242 | T244 | V245 | K487 | V488 | |||||||||
| C239 | V242 | |||||||||||||||||
|
Outer
Domain |
T257 | Q258 | L259 | L260 | L261 | N262 | H374 | S375 | F376 | I449 | T450 | L453 | L454 | P470 | G471 | G472 | ||
| T257 | I371 | |||||||||||||||||
| L265 | A266 | Q287 | L288 | N289 | ||||||||||||||
| A266 | I270 | |||||||||||||||||
| I270 | V271 | I272 | Q287 | L288 | N289 | |||||||||||||
| I284 | I285 | V286 | Q287 | L288 | T450 | G451 | L453 | L454 | T455 | |||||||||
| V293 | I449 | |||||||||||||||||
| I294 | N295 | N332 | S447 | N448 | I449 | |||||||||||||
| N295 | N332 | |||||||||||||||||
| C296 | H330 | |||||||||||||||||
| H330 | C385 | |||||||||||||||||
| H330 | C331 | N332 | L333 | I414 | L416 | C418 | ||||||||||||
| I359 | I360 | F361 | N362 | E466 | I467 | F468 | R469 | |||||||||||
| F361 | N362 | P363 | F391 | |||||||||||||||
| I371 | T373 | H374 | S375 | |||||||||||||||
| H374 | S375 | F376 | F383 | Y384 | C385 | N386 | ||||||||||||
| F383 | Y384 | C385 | L416 | C418 | I420 | |||||||||||||
| L453 | L454 | T455 | R456 | F468 | R469 | P470 | G471 | G472 |