Table 8.
CTL epitopes and HLA-A*0201 interactions.
| Peptide | Global energy (kcal/mol)a | Attractive vdW energy (kcal/mol) | H-bond energy (kcal/mol) | H-bond interaction | ||
|---|---|---|---|---|---|---|
| Epitope-MHC atom pairb | Distance initialc (Å) | Distance after MDd (Å) | ||||
| STVAYEDLY | −55.57 | −23.35 | −1.64 | SER 1 N-GLU 53 OE2 | 3.16 | nd |
| SER 1 OG-GLU 53 OE1 | 2.45 | nd | ||||
| SER 1 N-GLU 53 OE1 | 3.68 | nd | ||||
| TYR 5 OH-ARG 181 NH2 | 3.22 | nd | ||||
| TYR 9 OH-TRP 51 NE1 | 2.69 | nd | ||||
| GLU 6 OE2-ARG 48 HH22 | nd | 2.31 | ||||
| GLU 6 OE2-ARG 48 HH12 | nd | 1.73 | ||||
| ASP 7 OD1-ARG 48 HE | nd | 1.87 | ||||
| ASP 7 OD1-ARG 48 HH11 | nd | 2.15 | ||||
| ASP 7 OD2-ARG 48 HH11 | nd | 1.87 | ||||
| SER 1 H3-GLU 53 OE1 | nd | 1.74 | ||||
| ILVPGAWKY | −56.90 | −26.02 | −3.82 | LEU 2 N-TYR 99 OH | 3.02 | nd |
| ILE 1 O-LYS 66 NZ | 3.72 | nd | ||||
| ILE 1 N-GLU 63 OE1 | 3.96 | nd | ||||
| ILE 1 H3-GLU 63 OE1 | nd | 1.59 | ||||
| QIGSIPFTY | −48.99 | −23.86 | −1.41 | GLN 1 N-ASP 30 O | 2.12 | nd |
| THR 8 OG1-ASP 30 OD2 | 2.11 | nd | ||||
| GLN 1 OE1- TYR 27 OH | 2.86 | nd | ||||
aFireDock energy for the best ranked complex.
bInteracting pair of atoms and residues between epitope and HLA-A*0201.
cInitial distance between the H-bond acceptor and the donor.
dDistance between the H-bond acceptor and the donor after the MD simulation. nd = H-bond not detected.