Table 2.
The structure-based classification of nonsynonymous mutations of SPIKE protein (S-protein) as increasing or decreasing in stability using CUPSAT, SDM 2.0, DUET Server.
| Domain | Mutation | CUPSAT |
SDM 2.0 |
DUET |
|||
|---|---|---|---|---|---|---|---|
| Predicted DDG (kcal/mol) | Prediction | DDG | Prediction | DDG | Prediction | ||
| SP | L5F | −0.29 | Destabilizing | 0.2 | Increased stability | −0.611 | Destabilizing |
| L8V | −3.18 | Destabilizing | −2.69 | Reduced stability | −2.13 | Destabilizing | |
| L8W | −8.17 | Destabilizing | −1.11 | Reduced stability | −2.003 | Destabilizing | |
| NTD | L18F | −2.64 | Destabilizing | −1.11 | Reduced stability | −1.72 | Destabilizing |
| H49Y | 0.96 | Stabilizing | 0.78 | Increased stability | 1.293 | Stabilizing | |
| S50L | 4.18 | Stabilizing | 1.2 | Increased stability | 0.734 | Stabilizing | |
| L54F | 4.41 | Stabilizing | −0.08 | Reduced stability | −0.866 | Destabilizing | |
| S71F | −0.53 | Destabilizing | −0.66 | Reduced stability | −1.772 | Destabilizing | |
| T76I | 1.1 | Stabilizing | 1.1 | Increased stability | −0.06 | Destabilizing | |
| V120I | 0.89 | Stabilizing | −0.65 | Reduced stability | −0.029 | Destabilizing | |
| D138Y | 1.71 | Stabilizing | −0.21 | Reduced stability | −1.505 | Destabilizing | |
| Y145H | −1.6 | Destabilizing | −0.29 | Reduced stability | −1.08 | Destabilizing | |
| M153T | −0.58 | Destabilizing | −0.09 | Reduced stability | −0.733 | Destabilizing | |
| F157S | −4.01 | Destabilizing | −0.83 | Reduced stability | −0.977 | Destabilizing | |
| L176F | −3.11 | Destabilizing | 0.2 | Increased stability | −0.537 | Destabilizing | |
| G181V | 3.27 | Stabilizing | −1.05 | Reduced stability | −0.466 | Destabilizing | |
| D215H | 1.17 | Stabilizing | 0.85 | Increased stability | 1.087 | Stabilizing | |
| S221L | −1.23 | Destabilizing | −0.08 | Reduced stability | 0.102 | Stabilizing | |
| S221W | −3.44 | Destabilizing | −0.74 | Reduced stability | −0.793 | Destabilizing | |
| Q239K | 6.79 | Stabilizing | −1.01 | Reduced stability | −1.223 | Destabilizing | |
| S247R | −3.25 | Destabilizing | −1.01 | Reduced stability | −1.155 | Destabilizing | |
| S254F | 0.11 | Stabilizing | −0.73 | Reduced stability | −1.638 | Destabilizing | |
| W258L | 0.71 | Stabilizing | −1.07 | Reduced stability | −1.932 | Destabilizing | |
| A262T | 1.51 | Stabilizing | 0.13 | Increased stability | −0.865 | Destabilizing | |
| CTD/RBD | V367F | −0.11 | Destabilizing | 0.14 | Increased stability | −0.636 | Destabilizing |
| S438F | 3.64 | Stabilizing | −0.38 | Reduced stability | −0.485 | Destabilizing | |
| G476S | −0.8 | Destabilizing | −4.37 | Reduced stability | −1.112 | Destabilizing | |
| V483A | −0.13 | Destabilizing | 0.12 | Increased stability | −0.317 | Destabilizing | |
| N501Y | 0.07 | Stabilizing | 0.91 | Increased stability | 0.207 | Stabilizing | |
| Linker | L611F | −1.01 | Destabilizing | −0.59 | Reduced stability | −1.308 | Destabilizing |
| D614G | 0.3 | Stabilizing | 0.87 | Increased stability | 0.173 | Stabilizing | |
| (S1/S2) | Q675H | −3.05 | Destabilizing | 0.33 | Increased stability | −0.71 | Destabilizing |
| Q675R | −0.87 | Destabilizing | 0.12 | Increased stability | 0.106 | Stabilizing | |
| A706V | 0.17 | Stabilizing | −0.12 | Reduced stability | −0.104 | Destabilizing | |
| FP | T791I | −2.58 | Destabilizing | 0.07 | Increased stability | 0.257 | Stabilizing |
| S2 | P809S | 2.16 | Stabilizing | −0.63 | Reduced stability | −0.236 | Destabilizing |
| A831V | −1.46 | Destabilizing | −0.84 | Reduced stability | −0.127 | Destabilizing | |
| D839Y | −0.98 | Destabilizing | 0.67 | Increased stability | −0.362 | Destabilizing | |
| A845S | 0.77 | Stabilizing | −0.14 | Reduced stability | −0.328 | Destabilizing | |
| A845V | 0.36 | Stabilizing | 1.16 | Increased stability | 0.119 | Stabilizing | |
| A846V | 1.47 | Stabilizing | −0.12 | Reduced stability | −0.018 | Destabilizing | |
| A852V | −0.5 | Destabilizing | −0.84 | Reduced stability | −0.55 | Destabilizing | |
| A879S | −1.52 | Destabilizing | −2.18 | Reduced stability | −1.393 | Destabilizing | |
| V1040F | −1.11 | Destabilizing | 0.14 | Increased stability | −0.781 | Destabilizing | |
| P1143L | 0.45 | Stabilizing | 1.45 | Increased stability | 0.358 | Stabilizing | |
| P1162L | 0.23 | Stabilizing | −0.58 | Reduced stability | −0.085 | Destabilizing | |
| HR1 | D936H | −0.91 | Destabilizing | 0.13 | Increased stability | −0.684 | Destabilizing |
| D936Y | −1.69 | Destabilizing | 0.77 | Increased stability | −0.434 | Destabilizing | |
| S939F | −0.37 | Destabilizing | 0.54 | Increased stability | −1.037 | Destabilizing | |
| S940F | −0.36 | Destabilizing | 0.54 | Increased stability | −0.89 | Destabilizing | |
| S940T | 0.06 | Stabilizing | −0.14 | Reduced stability | 0.342 | Stabilizing | |
| T941A | −1.07 | Destabilizing | 1.1 | Increased stability | −0.594 | Destabilizing | |
| S943P | 0.75 | Stabilizing | −0.48 | Reduced stability | −0.138 | Destabilizing | |
| HR2 | D1163G | −1.93 | Destabilizing | 0.87 | Increased stability | 0.411 | Stabilizing |
| TM | I1216T | 1.46 | Stabilizing | −1.06 | Reduced stability | −0.86 | Destabilizing |
| M1229I | −0.46 | Destabilizing | 0.11 | Increased stability | −0.18 | Destabilizing | |
| M1237L | −1.1 | Destabilizing | 0.54 | Increased stability | 0.498 | Stabilizing | |
| M1237I | −1.75 | Destabilizing | 0.11 | Increased stability | 0.439 | Stabilizing | |
| CT | C1247F | −1.53 | Destabilizing | −0.2 | Reduced stability | −0.369 | Destabilizing |
| C1254F | −1.24 | Destabilizing | −0.2 | Reduced stability | −0.424 | Destabilizing | |
| D1260 N | 0.27 | Stabilizing | −0.11 | Reduced stability | 0.616 | Stabilizing | |
| P1263L | −1.83 | Destabilizing | 2.24 | Increased stability | 0.394 | Stabilizing | |