HADDOCK – supported co-factors and modified amino acids

For co-factors, parameters are automatically obtained from the PRODRG server, unless they are in this list.

All supported modified amino acids are in this list. Other modified amino acids are not supported.

Amino acids must be defined in the PDB file using ATOM lines, co-factors using HETATM lines.

Modified amino acids:

• CYM: CYS with MTSL grouped.
  Atoms:
  CAC,CAS,CAD,NAQ,OAH,HAA,CAR,CAA,CAB,CAI,CAO,CAJ,SAL
  N,HN,CA,HA,CB,HB1,HB2,SG,C,O
• CSP: phosphorylated CYS.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,SG
  P,O1P,O2P,O3P,C,O
• CYF: CYS without the sulfur H (for coordinating metals).
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,SG,C,O
• CFE: CYS with an iron sulfur cluster.
  HADDOCK will automatically search for closeby CYF residues and created bonds with the iron cluster
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,SG,FE1,SF1,FE2,SF2,C,O
• NEP: NE phosphorylated HIS.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,CG,ND1,HD1,CD2,HD2,CE1,HE1,NE2
  P,O1P,O2P,O3P,C,O
• ALY: Acetylated LYS.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2
  NZ,HZ1,CZ,OZ,CM,HM1,HM2,HM3,C,O
• MLZ: monomethyl LYS.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2
  NZ,HZ1,HZ2,CM3,HM31,HM32,HM33,C,O
• MLY: dimethyl LYS.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2
  NZ,HZ1,HZ2,CM2,HM21,HM22,HM23,CM3,HM31,HM32,HM33,C,O
• M3L: trimethyl LYS.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2
  NZ,HZ1,HZ2,CM1,HM11,HM12,HM13,CM2,HM21,HM22,HM23,CM3,HM31,HM32,HM33,C,O
• HYP: 4R-hydroxyproline.
  Atoms:
  N,CA,HA,CB,HB1,HB2,CG,OG1,HG1,HG2,CD,HD1,HD2,C,O
• PTR: O-Phosphotyrosine.
  Atoms:
  N,CA,C,O,OXT,CB,CG,CD1,CD2,CE1,CE2,CZ,OH,P,O1P,O2P
  O3P,1HN,2HN,HA,HXT,1HB,2HB,HD1,HD2,HE1,HE2,PHO2,PHO3
• SEP: phosphorylated SER.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,OG
  P,O1P,O2P,O3P,C,O
• TOP: phosphorylated THR.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,OG
  P,O1P,O2P,O3P,CG2,HG21,HG22,HG23,C,O
• TYP or PTR: phosphorylated TYR.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,CG,CD1,HD1,CD2,HD2,CE1,HE1,CE2,HE2,CZ,OH
  P,O1P,O2P,O3P,C,O
• TYS: sulfonated TYR.
  Atoms:
  N,HN,CA,HA,CB,HB1,HB2,CG,CD1,HD1,CD2,HD2,CE1,HE1,CE2,HE2,CZ,OH
  S,O1S,O2S,O3S,C,O
• ACE: N-terminal acetyl group.
  Atoms:
  CA,HA1,HA2,HA3,C,O
• CTN: C-terminal amide group.
  Atoms:
  N,H1,H2

Co-factors:

None