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HADDOCK2.4 library
Supported carbohydrates
- A2G: 2-N-acetyl-alpha-D-glucopyranose, different stereochemistry at C4
- BGC: beta-D-glucopyranose
- BMA: beta-D-mannopyronose
- FCA: alpha-D-fucopyranose
- FCB: beta-D-fucopyranose
- FUC: alpha-L-fucopyranose
- FUL: beta-L-fucopyranose
- GAL (GLB): beta-D-galactopyranose
- GLA: alpha-D-galactopyranose
- GLC: alpha-D-glucopyranose
- MAN: alpha-D-mannopyranose
- NAG: 2-N-acetyl-beta-D-glucopyranose
- NDG: 2-N-acetyl-alpha-D-glucopyranose
- NGA: 2-N-acetyl-beta-D-galactopyranose
- SIA: alpha-N-acetyl neuraminic acid
- SIB: beta-N-acetyl neuraminic acid
- XYP: beta-D-xylopyranose
HETAM
, example:
HETATM 9 C1 NAG B 102 171.992 99.750 236.168 1.00 10.00 C
Supported ions
- AG: Silver
- AL: Aluminium
- AU: Gold
- BR: Bromine
- CA: Calcium
- CD: Cadmium
- CL: Chlore
- CO: Cobalt
- CR: Chromium
- CS: Cesium
- CU: Copper
- F: Fluor
- FE: Iron
- HG: Mercury
- HO: Holmium
- I: Iodine
- IR: Iridium
- K: Potassium
- KR: Krypton
- LI: Adenine
- MG: Magnesium
- MN: Manganese
- MO: Molybdenum
- NA: Sodium
- NI: Nickel
- OS: Osmium
- PB: Lead
- PT: Platinum
- SR: Strontium
- U: Uranium
- V: Vanadium
- YB: Ytterbium
- ZN: Zinc
HETAM
flag. Residue name should contain the absolute
charge (e.g. ZN2) while atom name should have the exact charge (e.g. ZN+2), example:
HETATM 3833 ZN+2 ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN
Supported multi atom ions
- PO4: Phosphate
- SO4: Sulphate
- WO4: Tungstate
Supported co-factors:
The following will use HADDOCK's internal parameters, other co-factors will try to be automatically obtained from the PRODRG server.
- HEB: Heme B
Atoms: download an example PDB file - HEC: Heme C
Atoms: download an example PDB file
HETAM
, example:
HETATM 1 FE HEB 500 3.565 0.487 0.949 1.00 15.00
Supported nucleic acid bases
-
DNA
- DA: Adenine
- DC: Cytosine
- DG: Guanidine
- DT: Thymidine
- A: Adenine
- C: Cytosine
- G: Guanidine
- U: Uridine
Modified amino acids recognized by HADDOCK
All supported modified amino acids are in this list and must be defined as ATOM. Modified amino acids not present on this list are not supported.
Modified amino acids:
- ACE: N-terminal acetyl group.
Atoms:
CA,HA1,HA2,HA3,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 - ASH: protonated ASP.
Atoms:
N,HN,CA,HA,CB,HB1,HB2,CG,OD1,OD2,HD2,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 - CSP: phosphorylated CYS.
Atoms:
N,HN,CA,HA,CB,HB1,HB2,SG,P,O1P,O2P,O3P,C,O - CTN: C-terminal amide group.
Atoms:
N,H1,H2 - CYC: special for covalent docking - vdw of Sulphur reduced.
Atoms:
N,HN,CA,HA,CB,HB1,HB2,SG,C,O - CYF: CYS without the sulfur H (for coordinating metals).
Atoms:
N,HN,CA,HA,CB,HB1,HB2,SG,C,O - 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 - DDZ: 3,3,-dihydroxy ALA.
Atoms:
N,HN,CA,HA,CB,HB1,OG1,HG1,OG2,HG2 - GLH: protonated GLU.
Atoms:
N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,OE1,OE2,HE2,C,O - HY3: 3-hydroxyproline.
Atoms:
N,CA,HA,CB,OB1,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,C,O - HYP: 4R-hydroxyproline.
Atoms:
N,CA,HA,CB,HB1,HB2,CG,OG1,HG1,HG2,CD,HD1,HD2,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 - 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 - 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 - MSE: Selenomethionine
Atoms:
N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,SE,CE,HE1,HE2,HE3,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 - NME: C-terminal N-Methyl
Atoms:
N,HN,CA,HA1,HA2,HA3 - PNS: Phosphopanthetine Serine.
Atoms:
N,HN,CA,HA,CB,HB1,HB2,OG,P,O1P,O2P,O3P,C,O,C28,H28,H29,C29,C30,H31,H32,H30,C31,H34,H35,H33,C32,H36,O33,H46,C34,O35,N36,H48,C37,H37,H38,C38,H39,H4A,C39,O40,N41,H41,C42,H42,H43,C43,H44,H45,S44,H47 - 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