Table 3.
List of interacting residues at protein-protein interacting interface of SARS-CoV-2 NSP12 (Chain A) and NSP8 (Chain B), interface hotspot residues are predicted using three computational methods implemented in KFC server, HotRegion database and Robetta web server. The predicted hotspot residues contribute reasonably good binding energy which may help in the complexation process. The per-residue energy decomposition analysis was carried out using the last 10 ns MD trajectory.
| Residues | KFC | HotRegion | Robetta ΔΔG (kcal/mol) | Per-residue energy contribution (kcal/mol) |
|---|---|---|---|---|
| LEU-271A | HS | – | 2.16 | −14.06 |
| LYS-272A | – | – | – | −15.99 |
| TYR-273A | HS | HS | 0.75 | −4.67 |
| PRO-323A | – | – | – | −1.01 |
| THR-324A | – | – | 0.52 | 1.72 |
| SER-325A | – | – | – | −1.56 |
| PHE-326A | – | – | – | 3.48 |
| GLY-327A | – | – | – | 0.71 |
| PRO-328A | HS | – | – | −2.39 |
| LEU-329A | HS | HS | 0.60 | −9.92 |
| VAL-330A | HS | HS | 0.98 | −6.56 |
| ARG-331A | – | – | – | −28.16 |
| LYS-332A | – | – | – | −15.04 |
| VAL-335A | – | HS | – | −1.29 |
| ASP-336A | – | – | – | −15.88 |
| VAL-338A | – | – | – | −6.05 |
| PRO-339A | – | – | – | −1.58 |
| PHE-340A | HS | HS | 1.60 | −8.65 |
| VAL-341A | HS | HS | 0.72 | −7.46 |
| SER-343A | – | – | – | −0.13 |
| THR-344A | – | – | – | 0.63 |
| HIS-355A | – | – | – | −1.29 |
| LEU-366A | – | – | – | −5.89 |
| PHE-368A | – | – | 1.50 | −7.42 |
| LEU-371A | HS | HS | 1.81 | −9.57 |
| LEU-372A | – | – | – | −1.91 |
| TYR-374A | – | – | – | −1.12 |
| ALA-375A | – | – | – | −4.15 |
| PRO-378A | HS | – | – | −2.82 |
| ALA-379A | HS | HS | – | −1.64 |
| MET-380A | HS | HS | 1.33 | −11.68 |
| HIS-381A | – | – | – | 1.2 |
| ALA-382A | HS | HS | – | −0.38 |
| ALA-383A | HS | HS | – | −2.39 |
| SER-384A | – | – | – | 1.13 |
| GLY-385A | – | – | – | 0.69 |
| ASN-386A | – | – | – | −4.11 |
| LEU-387A | HS | HS | 2.81 | −19.69 |
| LEU-388A | HS | HS | 0.93 | −9.96 |
| LEU-389A | HS | HS | 1.59 | −13.88 |
| ASP-390A | – | – | – | 48.78 |
| LYS-391A | – | – | – | −60.14 |
| ARG-392A | – | HS | – | −54.46 |
| PHE-396A | – | – | – | −6.79 |
| SER-397A | – | – | – | 1.31 |
| VAL-398A | HS | HS | 0.84 | −2.42 |
| ALA-399A | HS | – | – | −3.18 |
| ALA-400A | – | – | – | −3.36 |
| LEU-401A | – | – | – | −2.86 |
| ASN-403A | – | – | – | 3.77 |
| ASN-404A | – | – | – | −2.07 |
| VAL-405A | HS | HS | 1.56 | −11.44 |
| PRO-505A | – | – | – | −2.81 |
| PHE-506A | – | – | – | −5.69 |
| TRP-509 | – | – | 2.29 | |
| LEU-514A | – | – | – | −5.26 |
| TYR-515A | HS | HS | – | −4.35 |
| ASP-517A | – | – | – | −39.5 |
| MET-666A | – | HS | – | −3.00 |
| ARG-80B | – | – | −84.85 | |
| VAL-83B | HS | HS | 1.14 | −13.05 |
| THR-84B | – | – | – | −2.6 |
| ALA-86B | – | – | – | −4.49 |
| MET-87B | HS | HS | 1.85 | −23.47 |
| MET-90B | HS | HS | 1.03 | −18.15 |
| LEU-91B | HS | HS | 2.32 | −15.16 |
| PHE-92B | – | HS | 1.09 | −9.56 |
| MET-94B | – | – | – | −10.42 |
| LEU-95B | HS | HS | 1.91 | −13.45 |
| ASN-108B | – | – | – | 1.23 |
| ASP-112B | – | – | – | 62.09 |
| GLY-113B | – | – | – | 0.60 |
| CYS-114B | HS | HS | −0.12 | −11.26 |
| VAL-115B | HS | HS | 0.55 | −6.58 |
| PRO-116B | HS | – | – | −21.44 |
| LEU-117B | HS | HS | 2.77 | −25.50 |
| ASN-118B | HS | – | 0.74 | 4.82 |
| PRO-121B | HS | – | – | −13.70 |
| ALA-125B | – | – | – | −4.57 |
| LYS-127B | – | – | – | −24.51 |
| LEU-128B | HS | HS | 1.40 | −12.3 |
| MET-129 | HS | – | 0.91 | −15.01 |
| VAL-130B | HS | HS | 0.84 | −9.71 |
| VAL-131B | HS | HS | 0.64 | −11.73 |
| PRO-133B | – | – | – | −8.7 |
| PRO-183B | – | – | – | −4.87 |
| ILE-185B | HS | HS | 1.43 | −10.92 |
| ARG-190B | – | – | – | −37.68 |
*HS: Hotspot.