Table 1 Main biochemical interactions of atoms and residues in the proteins[49, 51, 52]
From: A simple method for finding a protein’s ligand-binding pockets
Residue Name | Interactions |
|---|---|
THR | HBD: OG1 (OH) |
SER | HBD: OG (OH) |
GLN | HBA: NE2 (NH2) |
ASN | HBA: ND2 (NH2) |
TYR | HBA: O – HBD: N, OH – CR: CE1, CE2, CD1, CD2, CZ, CG |
CYS | Sul: SG (SH) |
MET | vdW: CE (CH3) – Sul: SD (S-CH3) |
ALA | vdW: CB (CH3) |
PRO | vdW: CB (CH2), CD (CH2), CG (CH2) |
LEU | vdW: CD1 (CH3), CD2 (CH3), CG (CH) |
VAL | vdW: CG1 (CH3), CG2 (CH3), CB (CH) |
ILE | vdW: CD1 (CH3) |
ASP | HBA: OD1(C = O) – Ion(−): OD2 (OH) |
GLU | HBA: OE1(C = O) – Ion(−): OE2 (OH) |
LYS | Ion(+): NZ (NH3) |
ARG | Ion(+): NH1 (NH2) trans, NH2 (NH2) cis |
HIS | Ion(+): NE1 (NH2) trans, NE2 (NH2) cis – CR: CD1, CE1, CD2, CE2, CG |
PHE | CR: CG, CD1, CE1, CZ, CE2, CD2 |
TRP | HBD: NE1 (NH) – CR: CD2, CE2, CZ2, CH2, CZ3, CE3 |
TYR | HBD: OH – CR: CD1, CE1, CE2, CZ, CD2, CG |
GLY | No participation |