Skip to main content

Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Table 1 The designation of the 18 atom types 1

From: Designing coarse grained-and atom based-potentials for protein-protein docking

Atom type Amino acid Atom3 Atom type Amino acid Atom Atom type Amino acid Atom
N BKBN2 N   Glu CD   Leu CG
BKBN CA   Glu OE1   Lys CG
C BKBN C   Glu OE2   Met CG
O BKBN O RNη Arg CZ   Met SD
GCα Gly CA   Arg NH1   Phe CG
Ala CB   Arg NH2   Phe CD1
  Arg CB NNδ Asn CG   Phe CD2
  Asn CB   Asn OD1   Phe CE1
  Asp CB   Asn ND2   Phe CE2
  Cys CB   Gln CD   Phe CZ
  Gln CB   Gln OE1   Thr CG2
  Glu CB   Gln NE2   Trp CG
  His CB RNε Arg CD   Trp CD1
  Ile CB   Arg NE   Trp CD2
  Leu CB SOγ Ser CB   Trp CE2
  Lys CB   Ser OG   Trp CE3
  Met CB   Thr OG1   Trp CZ2
  Phe CB   Tyr OH   Trp CZ3
  Pro CB HNε His CG   Trp CH2
  Pro CG   His ND1   Tyr CG
  Pro CD   His CD2   Tyr CD1
  Thr CB   His CE1   Tyr CD2
  Trp CB   His NE2 LCδ Ile CG2
  Tyr CB   Trp NE1   Ile CD
  Val CB YCξ Tyr CE1   Leu CD1
KNξ Lys CE   Tyr CE2   Leu CD2
  Lys NZ   Tyr CZ   Met CE
KCδ Lys CD FCξ Arg CG   Val CG1
DOδ Asp CG   Gln CG   Val CG2
  Asp OD1   Glu CG CSγ Cys SG
  Asp OD2   Ile CG1    
  1. 1. Atom types were taken from the work of Zhang et al. [13].
  2. 2. BKBN designate main chain backbone atoms.
  3. 3. Atom names are according to the PDB nomenclature.