Table 3.
Interactions between amino acids in the RBDs of SARS-CoV-2 and SARS-CoV with ACE2.
| Region | Number | Amino Acid | Amino Acid ACE2 | Interactions | Details |
|---|---|---|---|---|---|
| TR1 | 1 | A475 | S19 | Strong polar contacts | H: A475(O)-S19(HG): 3.2 (6LZG) |
| P462 | - | No interactions | |||
| 2 | N487 | Q24 | Strong polar contacts | H: N487(ND2)-Q24(HE21): 2.2 (6LZG) H: N487(HD22)-Y83(OH): 2.3 (6LZG) |
|
| N473 | Q24,Y83 | Strong polar contacts | H: N473(ND2)-Q24(OE1): 2.5 (2AJF) H: N473(ND2)- Y83(HH): 2.5 (2AJF) |
||
| 3 | T486 | N330 | Hydrogen bonding | H: T486(O)-N330(HD22): 2.3 (2AJF) H: T486(OG1)-Y41(HH): 2.6 (2AJF) H: T486(O)-N330(HD22): 2.3 (2AJF) |
|
| F486 | Y83, M82 | Stacking and hydrophobic interactions | ST (Pi-Pi): F486-Y83: 5.2 (6LZG) D (Pi-alkyl): F486-M82: 4.6 (6LZG, 6M17) |
||
| 4 | Y489 | K31 | Hydrophobic and hydrogen interactions | ST (Pi-alkyl): Y489-K31: 4.8 (6LZG, 6M17) H: Y489(HH)-Y83(OH): 3.0 (6LZG) H: Y489(HH)-T27(O): 1.7 (6M17) |
|
| Y475 | K31 | Hydrophobic and hydrogen interactions | ST (Pi-alkyl): Y475- K31: 5.2 (2AJF) H: Y475(HH)-Y83(OH): 2.8 (2AJF) |
||
| 5 | E484 | K31 | Strong polar contacts | S: E484(OE2)-K31(NZ): 4.2 (6LZG) | |
| P470 | - | No interactions | - | ||
| Ridge and upper core region |
6 | K417 | D30 | Electrostatic interactions (Salt bridge) | HS: K417(HZ1)-D30(OD1): 2.1 (6LZG) HS: K417(HZ3)-D30(OD2): 3.0 (6LZG) |
| V404 | - | No interactions | - | ||
| 7 | L455 |
K31, H34 |
Hydrophobic interactions | D (Pi-alkyl): L455-H34: 3.5 (6LZG, 6M17) D: L455(CD2)-K31(CA): 4.3 (6LZG, 6M17) |
|
| Y442 | K31, H34 | - | ST: (Pi-Pi): Y442-H34: 6.0 (2AJF) D:Y442(CE1)-K31(CA): 4.1 (2AJF) |
||
| 8 | F456 | D30,K31 | Stacking | ST: (Pi-alkyl): F456-K31: 4.5(6M17) ST: (Pi-alkyl): F456-D30: 4.4 (6M17) |
|
| L443 | T27 | Hydrophobic interactions | D: L443(CD2)-T27(CG2): 4.2 (2AJF) | ||
| 9 | Q493 | K31, H34, E35 | Hydrogen bonding | H: Q493(HE22)-E35(OE2): 1.9 (6M17) H: Q493(HE21)-H34(O): 2.9 (6LZG) H: Q493(OE1)-K31(HZ2/HZ3): 3.0 (6M17) |
|
| N479 | H34 | - | H: N479(HD21)-H34(ND1): 3.1 (2AJF) | ||
| 10 | Y449 | D38, Q42 | Hydrogen bonding | H: Y449(HH)-D38(OD1): 2.8 ((6M17) H: Y449(OH)-Q42(OE1): 2.5 (6LZG) |
|
| Y436 | D38 | Hydrogen bonding | H: Y436(HH)-D38(OD1): 2.8 (2AJF) H: Y436(HH)-D38(OD2): 3.4 (2AJF) H: Y436(HH)-Q42(OE1): 3.4 (2AJF) |
||
| 11 | Y453 | H34 | Polar contacts | H: Y453(HH)-H34(NE2): 3.2 (6M17) | |
| Y440 | H34 | Polar contacts | H: Y440(HH)-H34(NE2): 3.3 (2AJF) | ||
| 12 | Y505 | - | - | H: Y505(HH)-E37(OE1): 2.6 (6LZG, 6M17) H: Y505(OH)-R393(HH22): 3.4 (6LZG, 6M17) ST: (Pi-amid): Y505-K353/Gly354: 4.0 (6LZG, 6M17) ST (Pi-alkyl):Y505-K353: 4.6 (6LZG, 6M17) |
|
| Y491 | - | - | H: Y491(HH)-E37(OE1): 2.4 (2AJF) H: Y491(OH)-R393(HH22): 3.4 (2AJF) ST: (Pi-amid): Y491-K353/Gly354: 4.1 (2AJF) ST: (Pi-alkyl): Y491-K353: 4.3 (2AJF) |
||
| TR2 | 13 | G496 | K353 * | Hydrogen bonding | H: G496(O)-K353(HZ2/HZ3): 2.3 (6LZG, 6M17) |
| G482 | K353 * | Hydrogen bonding | H: G482(O)-K353(HZ2/HZ3): 3.9 (2AJF) | ||
| 14 | Q498 | Q48 | Hydrogen bonding | H: Q498(HE22)-Q42(OE1): 2.2 (6LZG) | |
| Y484 | Y41 | Stacking | ST (Pi-Pi): Y484-Y41: 5.3 (2AJF) | ||
| 15 | T500 | Y41 | Hydrogen bonding | H: T500(OG1)-Y41(HH): 2.8 (6LZG, 6M17) | |
| T486 | N330 | Hydrogen bonding | H: T486(O)-N330(HD22): 2.3 (2AJF) H: T486(OG1)-Y41(HH): 2.6 (2AJF) H: T486(O)-N330(HD22): 2.3 (2AJF) |
||
| 16 | N501 | Y41 | Hydrogen bonding | H: N501(HD21)- Y41(OH): 2.3 (6LZG) | |
| T487 | Y41 | Hydrogen bonding | H: T487(HG1)- Y41(HH): 4.0 (2AJF) | ||
| 17 | G502 | K353 * | Hydrogen bonding | H: G502(HN)-K353(O): 1.7 (6LZG, 6M17) | |
| G488 | K353 * | Hydrogen bonding | H: G488(HN)-K353(O): 1.5 (2AJF) | ||
| 18 | N439 | - | No interactions | - | |
| R426 | E329, Q325 | - | S: R426(NH2)-E329(OE2): 3.0 (2AJF) H: R426(HH21)-Q325(OE1): 3.5 (2AJF) H: R426(HH12)-E329(OE2): 3.1 (2AJF) H: R426(HH22)-E329(OE2): 2.0 (2AJF) |
H: hydrogen bonding. S: Electrostatic interaction. HS: hydrogen and electrostatic interaction. D: hydrophobic interaction. ST: stacking interaction. Details include bond type: RBD amino acids (interacting atom)-ACE2 (interacting amino acids): distance in angstrom and (PDB IDs). Measured distance is based on PDB ID: 2AJF for SARS-CoV, and based on PDB IDs: 6LZG and 6M17 (if the contact is not found in 6LZG) for SARS-CoV-2. Orange colour indicates identical residues, cyan indicates different residues with partial conserved interactions, while grey indicates different residues between SARS-CoV-2 and SARS-CoV that have different contacts. For each amino acid, the upper cell corresponds to SARS-CoV-2, while the lower one corresponds to SARS-CoV. Residues in red font are non-conserved ACE2 amino acids in different mammals [1]. * A single K353A mutation was sufficient to abolish the polar contacts mediated by hydrophilic residues which dominate the virus-receptor engagement [2].