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. 2021 Apr 2;16(4):e0248001. doi: 10.1371/journal.pone.0248001

Table 5. Non-bonding interactions of three T-cell epitope ligands and an Influenza Matrix Peptide with HLA-A*0201.

Legends Bonds [Donor. (Distance, Å). Acceptor] (Bond type)
Hydrogen Bond Electrostatic Bond Hydrophobic Bond
LLFGYPVYV A:ARG6:HH11 (2.300):LEU2:O (HB)
A:ARG6:HH12 (2.378):TYR5:OH (HB)
A:TYR27:HH (2.187):VAL7:O (HB)
A:GLN32:HN (2.147):VAL9:O1 (HB)
A:GLY237:HN (2.983):TYR8:O (HB)
A:GLY239:HN (2.319):TYR8:O (HB)
B:LYS458:HN (2.966):LEU1:O (HB)
B:TYR467:HH (2.328):TYR8:OH (HB)
:VAL9:O1 (3.381) A:ASP30:O (HB)
:TYR5:OH (3.319) A:ASP29:O (HB)
A:ARG6:CD (3.297):TYR5:OH (CHB)
A:THR31:CA (3.301):VAL9:O1 (CHB)		 A:ASP30:OD2 (3.789):PHE3 (Pi-Anion) :LEU1:CD2 (3.812) A:TYR113 (Pi-Sigma)
B:TYR467 (5.311):TYR8 (Pi-Pi Stacked)
A:ALA211 (4.904):PRO6 (A)
A:PRO235 (4.589):PRO6 (A)
A:PRO235 (4.365):VAL7 (A)
B:LYS458 (4.867):LEU1 (A)
B:LYS458 (4.180):LEU2 (A)
:VAL7 (4.979) B:LEU465 (A)
A:PHE241 (5.039):PRO6 (Pi-A)
B:TYR426 (5.412):PRO6 (Pi-A)
B:TYR463 (5.200):VAL7 (Pi-A)
ITWPLLPHV A:ARG6:HH11 (2.792):HIS8:O (HB)
A:TYR27:HH (2.216):TRP3:O (HB)
A:GLN32:HN (2.281):THR2:OG1 (HB)
A:GLU212:HN (2.545):VAL9:O2 (HB)
B:TYR463:HH (2.132):LEU6:O (HB)
:THR2:OG1 (3.371) A:ASP30:O (HB)
:VAL9:N (3.296) A:ASP30:OD1 (HB)
:VAL9:O2 (3.342) A:ASP30:OD1 (HB)
A:ASP30:CA (3.338):LEU5:O (CHB)
A:THR31:CA (3.542):THR2:OG1 (CHB)		 B:TYR467 (5.495):TRP3 (Pi-Pi Stacked)
:TRP3 (4.502) B:TYR467 (Pi-Pi Stacked)
A:ALA49 (5.108):ILE1 (A)
A:PRO50 (5.198):ILE1 (A)
A:ALA211 (5.155):LEU5 (A)
A:PRO235 (4.422):PRO4 (A)
A:PRO235 (5.145):LEU5 (A)
B:LYS458 (5.007):PRO7 (A)
:PRO4 (5.006) B:LEU465 (A)
A:TYR27 (5.433):LEU6 (Pi-A)
A:PHE241 (5.371):LEU5 (Pi-A)
B:TYR426 (5.493):PRO4 (Pi-A)
B:TYR463 (4.805):PRO4 (Pi-A)
B:TYR463 (5.333):LEU5 (Pi-A)
:HIS8 (4.403) A:ALA211 (Pi-A)
GLLPFHSTL A:GLY1:HT3 (2.059):LEU9:O2 (HB)
A:SER2:HN (1.961):LEU9:O2 (HB)
A:ARG6:HH12 (2.532):SER7:OG (HB)
A:THR233:HN (2.685):LEU2:O (HB)
A:THR233:HG1 (2.336):GLY1:O (HB)
A:LYS243:HZ3 (2.532):GLY1:O (HB)
B:SER457:HG (2.571):LEU3:O (HB)
B:LYS458:HN (2.406):HIS6:NE2 (HB)
:LEU3:N (3.215) A:GLU232:OE1 (HB)
:LEU9:O1 (3.365) A:ASP29:OD1 (HB)
:THR8:OG1 (3.190) A:ASP30:OD1 (HB)
A:TYR27:HH (3.000):PHE5 (Pi-Donor HB)
:SER7:OG (3.513):HIS6 (Pi-Donor HB)		 :GLY1:N (3.609) A:GLU212:OE2 (Salt Bridge) B:TYR463 (5.312):PHE5 (Pi-Pi Stacked)
A:PRO210 (4.398):LEU9 (A)
A:ALA211 (4.254):PRO4 (A)
:PHE5 (4.024) A:PRO235 (Pi-A)
Influenza Matrix Peptide A:TYR27:HH (1.971):ILE702:O (HB)
A:GLN32:HN (2.086):GLY701:O (HB)
B:SER452:HG (2.305):LEU703:O (HB)		 :GLY701:N (5.208) B:ASP453:OD1 (Attractive Charge) A:PRO235 (4.034):LEU703 (A)
B:LEU465 (4.753):ILE702 (A)
B:TYR426 (5.443):LEU703 (Pi-A)
B:TYR463 (4.861):LEU703 (Pi-A)

(Pose predicted by AutoDock Vina where, HB = Conventional Hydrogen Bond, CHB = Carbon hydrogen bond, A = alkyl, Pi-A = Pi-Alkyl).