Skip to main content

Advertisement

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) cisCR: 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
  1. Abbreviations used: HBA: Hydrogen bond acceptor, HBD: Hydrogen bond donor, vdW: van der Waals interaction, Ion: Ionic interaction, Sul: Sulfur interaction.