TABLE 3.
Mutation sites affecting binding affinity and stability in the epitope(s) and paratope(s) of spike–antibody interface
| Pdb id | Interface (chain) | Interface residues |
|---|---|---|
| 6WPT | Paratope (L) | D93 |
| Epitope (C) | N334 , L335 , P337 , G339 , E340 , N343 , A344, T345 , R346, N354, K356 , R357 , S359 , N360, C361 , L441 , R509 | |
| 6XC2 | Paratope | – |
| Epitope (A) | R403 , D405 , R408 , T415 , G416 , K417 , D420 , Y421 , Y453 , L455 , F456 , R457 , K458 , S459 , N460 , Y473 , Q474, A475 , G476 , F486 , N487 , Y489 , Q493 , S494, Y495 , G496 , Q498, T500 , N501 , G502, Y505 | |
| 6XC4 | Paratope | – |
| Epitope (A) | R403 , D405, T415 , G416 , K417 , D420 , Y421 , Y453, L455 , F456 , R457 , K458 , N460, Y473 , A475 , G476 , S477 , F486 , N487 , Y489 , Y495 , N501, Y505 | |
| 6XCN | Paratope (H,L) | G54, S56, G29, Y30, K31 |
| Epitope (C) | D405 , T415 , G416, K417 , Y421 , Y453 , F456 , R457 , K458 , N460, Y473 , A475 , G476, F486 , N487 , G502 , Y505 | |
| 6XE1 | Paratope (H,L) | D97, S27A |
| Epitope (E) | R403 , T415 , G416 , K417 , D420 , Y421 , Y453 , L455 , F456 , R457 , K458, N460, Y473 , A475 , G476 , F486 , N487 , Y489 , Q493 , N501 , G502, Y505 | |
| 6XEY | Paratope (J) | A99 |
| Epitope (C) | Y449 , L455 , F456 , V483 , E484 , G485 , F486 , Y489 , F490 , L492 , Q493 , S494 | |
| 6XKP | Paratope (H) | R96 |
| Epitope (A) | R346 , F347 , S349 , Y351 , K444 , V445 , G446 , G447 , N448 , Y449 , N450 , Y451 , L452 , T470 , E484 , F490 , L492 , Q493 , S494 , Q498 | |
| 6XKQ | Paratope (H,L) | M100E, D101, S27A, A29 |
| Epitope (A) | R403 , G446, Y449 , Y453, L455 , F456 , A475 , G476 , S477, T478 , G485, F486 , N487 , Y489 , Q493 , Y495 , Q498, N501 , Y505 | |
| 7B3O | Paratope (H,L) | N92, S31 , R97, A100 , D101 |
| Epitope (E) | R403 , D405 , E406, R408, Q409 , T415 , G416 , K417 , D420 , Y421 , Y453, L455 , F456 , R457 , K458, S459, N460, Y473 , Q474, A475 , G476, F486 , N487 , Y489 , Q493 , S494, Y495 , G496 , Q498, T500 , N501 , G502 , Y505 | |
| 7BWJ | Paratope (L) | G31 |
| Epitope (E) | R346 , K444 , G446, G447 , N448 , Y449 , N450 , L452 , V483 , E484 , G485, F490 , S494 | |
| 7BYR | Paratope (H) | S31, Y32, T53 , N54, D73, Q100, S103, W105 |
| Epitope (B) | G446, Y449, E484 , G485, F486 , Y489 , F490 , L492 , Q493 , G496 , Q498 , N501, Y505 | |
| 7BZ5 | Paratope | – |
| Epitope (A) | R403 , D405, E406, Q409 , T415 , G416 , K417 , D420 , Y421 , Y453 , L455 , F456 , R457 , K458, N460 , Y473 , Q474, A475 , G476 , E484 , F486 , N487 , Y489 , F490 , L492 , Q493 , Y495 , G496 , Q498, T500, N501 , G502 , Y505 | |
| 7C01 | Paratope (H,L) | D104, S30 |
| Epitope (A) | R403 , D405 , E406, R408 , Q409 , T415 , G416 , K417 , D420 , Y421 , L455 , F456 , R457 , K458, N460 , Y473 , Q474 , A475 , G476 , S477 , F486 , N487 , Y489 , Q493 , Y495 , G502, Y505 | |
| 7CAK | Paratope (D,E) | I2, S27, S30, N91, W93, D60, D102 , Y105 |
| Epitope (A) | Y365 , Y369, A372 , S373 , F374 , S375 , T376 , F377 , K378 , S383 , P384 , T385 , R408 , P412 , G413, Q414 , N437, V503 | |
| 7CHB | Paratope (H,L) | G26, S31, A102, D106, Q27, S30 |
| Epitope (R) | R403 , T415 , G416 , K417 , D420 , Y421 , Y453 , L455 , F456 , R457 , K458, S459 , N460 , Y473 , A475 , G476 , F486 , N487 , Y489 , Q493 , Y495 , G496, Q498, T500 , N501 , G502 , V503, G504 , Y505 | |
| 7CHH | Paratope (D) | S25, D106 |
| Epitope (A) | K444, Y449 , N450, L452 , N481 , G482 , V483 , E484 , G485, F490 | |
| 7CJF | Paratope (A,B) | S30, F58, D106, S93 |
| Epitope (C) | R403 , D405, Q409 , T415 , G416, K417 , D420 , Y421 , Y453 , L455 , F456 , R457 , K458 , N460, Y473 , Q474, A475 , G476 , S477 , F486 , N487 , Y489 , Q493 , Y495 , G496 , Q498, T500 , N501 , G502 , Y505 | |
| 7CWO | Paratope (H) | S31 |
| Epitope (A) | L455 , T470, N481 , G482 , V483 , E484 , G485 , F486 , Y489 , F490 , L492 , Q493 | |
| 7JMW | Paratope (H) | P96 |
| Epitope (A) | Y369 , S371 , F377 , K378 , C379 , Y380 , G381, V382 , S383 , P384 , T385 , R408 , P412 , G413, Q414 , T415 , G416 , D427 , F429 | |
| 7JV2 | Paratope (H,L) | Y102, R63 |
| Epitope (A) | G446, Y449, N481 , G482, V483 , E484, G485 , F486 , F490 | |
| 7K43 | Paratope (H) | G31 , T74 |
| Epitope (A) | G446, Y449, L452 , L455 , F456 , E484, G485 , F486 , Y489 , F490 , L492 , Q493 , S494 , G496 | |
| 7K45 | Paratope (H) | G54, G104, S105 |
| Epitope (B) | L455 , Y473 , A475 , G476 , S477 , G485 , F486 , N487 , C488 , Y489 | |
| 7K8U | Paratope (H,L) | G26, S30, A31, Y92, G93, T95 |
| Epitope (A) | K444 , V483 , F486 , F490 | |
| 7K8V | Paratope (H) | D99, V100D, P100G |
| Epitope (A) | T345 , R346, L441 , D442 , N448 , Y449 , N450 , L452 , F490 , Q498 , P499 , T500 , R509 | |
| 7K8W | Paratope (H,L) | S58, D100B, Y100D, Y100E , K30, S92 |
| Epitope (A) | K444, V445, G446 , Y449, N450, E484, Q493 , S494, Q498, Y505 | |
| 7K8Y | Paratope (G) | T58, T74, G110 |
| Epitope (B) | K444 , Y449 , F456 , E484, G485 , F486 , N487 , Y489, F490 , Q498 | |
| 7K8Z | Paratope | – |
| Epitope (A) | T345 , R346 , S438 , N439 , N440 , P499 | |
| 7K90 | Paratope (H) | G54, G55, S56, K73, N76 |
| Epitope (B) | Y449 , L455 , F456 , V483, G485, F486 , N487 , Y489 , F490 , Q493 , S494 | |
| 7KFV | Paratope (H,L) | S98, S67 |
| Epitope (A) | R403 , T415 , G416 , K417 , D420 , Y421 , Y453 , L455 , F456 , R457 , K458, S459 , N460 , Y473 , A475 , G476 , F486 , N487 , Y489 , Q493 , S494, Y495 , G496 , Q498, T500 , N501 , G502 , G504, Y505 |
Note: (i) The residues shown in italics for paratope increase the binding affinity, bold residues increase the stability, while residues shown for epitope decrease the binding affinity and stability. (ii) The residues are highlighted if two out of three methods satisfy the criteria that at least 50% of the mutations in each residue increases (for paratope) or decreases (for epitope) the affinity and stability. (iii) Notation for residues; Wild type residue followed by residue number.