Table 4.
Amino acid interactions of receptor nucleocapsid protein and their respective antimicrobial peptides
| Viral strain | APD3 ID | Binding affinity (kcal/mol) | Receptor amino acids | AMP ligand amino acids | Bond category | Distance (Å) |
|---|---|---|---|---|---|---|
| SARS-CoV | AP00180 | − 6.4 | ALA110 | GLU21 | Hydrogen bond; Electrostatic | 2.233 |
| LYS85 | ARG31 | Electrostatic | 4.476 | |||
| ARG241 | GLU21 | Electrostatic | 4.803 | |||
| ALA1 | ASP87 | Electrostatic | 4.792 | |||
| ALA1 | ASP834 | Electrostatic | 4.788 | |||
| ARG31 | GLU14 | Electrostatic | 3.488 | |||
| LYS85 | ARG13 | Conventional hydrogen bond | 1.759 | |||
| LYS88 | TYR4 | Conventional hydrogen bond | 2.270 | |||
| GLN129 | GLU21 | Conventional hydrogen bond | 2.177 | |||
| GLY132 | SER17 | Conventional hydrogen bond | 2.796 | |||
| ARG227 | THR7 | Conventional hydrogen bond | 3.086 | |||
| THR246 | GLY24 | Conventional hydrogen bond | 2.504 | |||
| GLN247 | GLY24 | Conventional hydrogen bond | 2.478 | |||
| LYS833 | CYS3 | Conventional hydrogen bond | 2.889 | |||
| LYS833 | CYS3 | Conventional hydrogen bond | 2.786 | |||
| ARG9 | CYS10 | Conventional hydrogen bond | 3.398 | |||
| ARG13 | ASP87 | Conventional hydrogen bond | 3.369 | |||
| LYS85 | CYS30 | Carbon hydrogen bond | 3.500 | |||
| LYS85 | ARG31 | Carbon hydrogen bond | 3.237 | |||
| ASP87 | ARG31 | Carbon hydrogen bond | 3.658 | |||
| PRO115 | THR2 | Carbon hydrogen bond | 3.468 | |||
| SER612 | THR12 | Carbon hydrogen bond | 3.393 | |||
| THR12 | SER612 | Carbon hydrogen bond | 3.005 | |||
| GLY18 | THR128 | Carbon hydrogen bond | 3.604 | |||
| GLY18 | GLN129 | Carbon hydrogen bond | 3.073 | |||
| SARS-CoV | AP00223 | − 6.1 | ARG13 | GLU111 | Hydrogen Bond; Electrostatic | 3.467 |
| LYS833 | GLU14 | Electrostatic | 4.564 | |||
| LYS85 | THR8 | Conventional hydrogen bond | 2.411 | |||
| ARG119 | GLU14 | Conventional hydrogen bond | 2.104 | |||
| ARG227 | VAL1 | Conventional hydrogen bond | 2.395 | |||
| GLN129 | ARG15 | Conventional hydrogen bond | 3.182 | |||
| TYR22 | GLU219 | Conventional hydrogen bond | 3.244 | |||
| ARG25 | PRO611 | Conventional hydrogen bond | 3.263 | |||
| LYS114 | PHE12 | Carbon hydrogen bond | 2.862 | |||
| ARG9 | CYS10 | Carbon hydrogen bond | 3.552 | |||
| SARS-CoV-2 | AP00549 | − 3.4 | ASN94 | GLN13 | Conventional hydrogen bond | 2.656 |
| ARG132 | GLY1 | Conventional hydrogen bond | 2.637 | |||
| ARG132 | PHE2 | Conventional hydrogen bond | 2.177 | |||
| ARG132 | ASN5 | Conventional hydrogen bond | 2.891 | |||
| ASN196 | ASN5 | Conventional hydrogen bond | 2.082 | |||
| GLN13 | ASN371 | Conventional hydrogen bond | 2.870 | |||
| THR197 | PRO198 | Hydrophobic | 5.198 | |||
| TRP8 | PRO179 | Hydrophobic | 5.431 | |||
| TRP8 | LEU170 | Hydrophobic | 5.338 | |||
| SARS-CoV-2 | AP01061 | − 3 | LYS1 | ASN1 | Conventional hydrogen bond | 2.945 |
| TYR29 | ASN91 | Conventional hydrogen bond | 2.803 | |||
| ARG132 | PRO3 | Conventional hydrogen bond | 2.855 | |||
| THR256 | GLY5 | Conventional hydrogen bond | 2.852 | |||
| THR370 | GLU24 | Carbon Hydrogen bond | 3.474 | |||
| ALA93 | VAL27 | Hydrophobic | 4.214 |