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pdb_atom_pairspdb_atom_pairs is the core table in piccolo. It describes all interacting pairs of atoms across a protein interface. Flags (1 or 0) indicate which interaction type criteria are fulfilled. The tables pdb_res_pairs, pdb_chain_pairs, pdb_atoms, pdb_residues and pdb_chains are essentially summaries of the contents of pdb_atom_pairs at different levels of abstraction.
pdb_atomsSummarizes the data in pdb_atom_pairs for each individual atom (each atom may interact with several others).
pdb_residue_pairsSummarizes the data in pdb_atom_pairs for each pair of interacting residues.
pdb_residuesSummarizes the data in pdb_atom_pairs for each individual residue.
pdb_chain_pairsSummarizes the data in pdb_atom_pairs for each pair of interacting chains.
pdb_chainsSummarizes the data in pdb_atom_pairs for each individual chain.
pdb_naccess_residuesSolvent accessibility data for each individual residue.
pdb_naccess_chainsSolvent accessibility data for each individual residue.

pdb_atom_pairs

idInternal serial ID
pdbPDB code
contact_idInternal interface serial ID
p1_chainChain ID for first atom
p1_residResidue number for first atom
p1_inscodeResidue insert code for first atom
p1_resnameResidue name for first atom
p1_atnameAtom name for first atom
p1_elementAtom element for first atom
p2_chainChain ID for second atom
p2_residResidue number for second atom
p2_inscodeResidue insert code for second atom
p2_resnameResidue name for second atom
p2_atnameAtom name for second atom
p2_elementAtom element for second atom
is_contactIs contact (atom pair meets at least one contact criteria excluding proximal interactions)
is_covIs covalent interaction
is_vdwIs van der Waal interaction
is_vdwclashIs van der Waal clash
is_hbIs hydrogen bond
is_mcmchbIs main chain to main chain hydrogen bond
is_scschbIs side chain to side chain hydrogen bond
is_mcschbIs main chain to side chain hydrogen bond
is_wmhbIs water-mediated hydrogen bonds interaction
is_mcmcwmhbIs main chain to main chain water-mediated hydrogen bonds interaction
is_scscwmhbIs side chain to side chain interaction
is_mcscwmhbIs main chain to side chain interaction
is_hydrophobeIs hydrophobic interaction
is_ionicIs ionic interaction
is_aromaromIs aromatic interaction
is_arom_facetofaceIs aromatic face-to-face interaction
is_arom_dispfacetofaceIs aromatic displaced face-to-face interaction
is_arom_edgetofaceIs aromatic edge-to-face interaction
is_disulphIs disulphide interaction
is_picatIs π-cation interaction
is_aromsulphIs aromatic sulphur interaction
is_proximalIs proximal interaction
distanceInteratomic distance (Ångstroms)

pdb_atoms

idInternal serial ID
pdbPDB code
p1_chainChain ID for first interface chain
p2_chainChain ID for second interface chain
chainChain ID
residResidue number
inscodeResidue insert code
resnameResidue name
atnameAtom name
elementAtom element
sum_contactNumber of contacts (atom pairs meeting at least one contact criteria excluding proximal interactions)
sum_covNumber of covalent interactions
sum_vdwNumber of van der Waal interactions
sum_vdwclashNumber of van der Waal clashes
sum_hbNumber of hydrogen bonds
sum_mcmchbNumber of main chain to main chain hydrogen bonds
sum_scschbNumber of side chain to side chain hydrogen bonds
sum_mcschbNumber of main chain to side chain hydrogen bonds
sum_wmhbNumber of water-mediated hydrogen bonds interactions
sum_mcmcwmhbNumber of main chain to main chain water-mediated hydrogen bonds interactions
sum_scscwmhbNumber of side chain to side chain interactions
sum_mcscwmhbNumber of main chain to side chain interactions
sum_hydrophobeNumber of hydrophobic interactions
sum_ionicNumber of ionic interactions
sum_aromaromNumber of aromatic interactions
sum_arom_facetofaceNumber of aromatic face-to-face interactions
sum_arom_dispfacetofaceNumber of aromatic displaced face-to-face interactions
sum_arom_edgetofaceNumber of aromatic edge-to-face interactions
sum_disulphNumber of disulphide interactions
sum_picatNumber of π-cation interactions
sum_aromsulphNumber of aromatic sulphur interactions
sum_proximalNumber of proximal interactions

pdb_residue_pairs

idInternal serial ID
pdbPDB code
p1_chainChain ID for first residue
p1_residResidue number for first residue
p1_inscodeResidue insert code for first residue
p1_resnameResidue name for first residue
p2_chainChain ID for second residue
p2_residResidue number for second residue
p2_inscodeResidue insert code for second residue
p2_resnameResidue name for second residue
sum_contactNumber of interactions (atom pairs meeting at least one contact criteria exclusing proximal interactions)
sum_covNumber of covalent interactions
sum_vdwNumber of van der Waal interactions
sum_vdwclashNumber of van der Waal clashes
sum_hbNumber of hydrogen bonds
sum_mcmchbNumber of main chain to main chain hydrogen bonds
sum_scschbNumber of side chain to side chain hydrogen bonds
sum_mcschbNumber of main chain to side chain hydrogen bonds
sum_wmhbNumber of water-mediated hydrogen bonds interactions
sum_mcmcwmhbNumber of main chain to main chain water-mediated hydrogen bonds interactions
sum_scscwmhbNumber of side chain to side chain interactions
sum_mcscwmhbNumber of main chain to side chain interactions
sum_hydrophobeNumber of hydrophobic interactions
sum_ionicNumber of ionic interactions
sum_aromaromNumber of aromatic interactions
sum_arom_facetofaceNumber of aromatic face-to-face interactions
sum_arom_dispfacetofaceNumber of aromatic displaced face-to-face interactions
sum_arom_edgetofaceNumber of aromatic edge-to-face interactions
sum_disulphNumber of disulphide interactions
sum_picatNumber of π-cation interactions
sum_aromsulphNumber of aromatic sulphur interactions
sum_proximalNumber of proximal interactions

pdb_residues

idInternal serial ID
pdbPDB code
p1_chainChain ID for first interface chain
p2_chainChain ID for second interface chain
chainChain ID for residue
residResidue number
inscodeResidue insert code
resnameResidue name
sum_contactNumber of interactions (atom pairs meeting at least one contact criteria exclusing proximal interactions)
sum_covNumber of covalent interactions
sum_vdwNumber of van der Waal interactions
sum_vdwclashNumber of van der Waal clashes
sum_hbNumber of hydrogen bonds
sum_mcmchbNumber of main chain to main chain hydrogen bonds
sum_scschbNumber of side chain to side chain hydrogen bonds
sum_mcschbNumber of main chain to side chain hydrogen bonds
sum_wmhbNumber of water-mediated hydrogen bonds interactions
sum_mcmcwmhbNumber of main chain to main chain water-mediated hydrogen bonds interactions
sum_scscwmhbNumber of side chain to side chain interactions
sum_mcscwmhbNumber of main chain to side chain interactions
sum_hydrophobeNumber of hydrophobic interactions
sum_ionicNumber of ionic interactions
sum_aromaromNumber of aromatic interactions
sum_arom_facetofaceNumber of aromatic face-to-face interactions
sum_arom_dispfacetofaceNumber of aromatic displaced face-to-face interactions
sum_arom_edgetofaceNumber of aromatic edge-to-face interactions
sum_disulphNumber of disulphide interactions
sum_picatNumber of π-cation interactions
sum_aromsulphNumber of aromatic sulphur interactions
sum_proximalNumber of proximal interactions

pdb_chain_pairs

idInternal serial ID
pdbPDB code
p1_chainChain ID for first interface chain
p2_chainChain ID for second interface chain
sum_contactNumber of interactions (atom pairs meeting at least one contact criteria exclusing proximal interactions)
sum_covNumber of covalent interactions
sum_vdwNumber of van der Waal interactions
sum_vdwclashNumber of van der Waal clashes
sum_hbNumber of hydrogen bonds
sum_mcmchbNumber of main chain to main chain hydrogen bonds
sum_scschbNumber of side chain to side chain hydrogen bonds
sum_mcschbNumber of main chain to side chain hydrogen bonds
sum_wmhbNumber of water-mediated hydrogen bonds interactions
sum_mcmcwmhbNumber of main chain to main chain water-mediated hydrogen bonds interactions
sum_scscwmhbNumber of side chain to side chain interactions
sum_mcscwmhbNumber of main chain to side chain interactions
sum_hydrophobeNumber of hydrophobic interactions
sum_ionicNumber of ionic interactions
sum_aromaromNumber of aromatic interactions
sum_arom_facetofaceNumber of aromatic face-to-face interactions
sum_arom_dispfacetofaceNumber of aromatic displaced face-to-face interactions
sum_arom_edgetofaceNumber of aromatic edge-to-face interactions
sum_disulphNumber of disulphide interactions
sum_picatNumber of π-cation interactions
sum_aromsulphNumber of aromatic sulphur interactions
sum_proximalNumber of proximal interactions

pdb_chains

idInternal serial ID
pdbPDB code
p1_chainChain ID for first interface chain
p2_chainChain ID for second interface chain
chainChain ID
sum_contactNumber of interactions (atom pairs meeting at least one contact criteria exclusing proximal interactions)
sum_covNumber of covalent interactions
sum_vdwNumber of van der Waal interactions
sum_vdwclashNumber of van der Waal clashes
sum_hbNumber of hydrogen bonds
sum_mcmchbNumber of main chain to main chain hydrogen bonds
sum_scschbNumber of side chain to side chain hydrogen bonds
sum_mcschbNumber of main chain to side chain hydrogen bonds
sum_wmhbNumber of water-mediated hydrogen bonds interactions
sum_mcmcwmhbNumber of main chain to main chain water-mediated hydrogen bonds interactions
sum_scscwmhbNumber of side chain to side chain interactions
sum_mcscwmhbNumber of main chain to side chain interactions
sum_hydrophobeNumber of hydrophobic interactions
sum_ionicNumber of ionic interactions
sum_aromaromNumber of aromatic interactions
sum_arom_facetofaceNumber of aromatic face-to-face interactions
sum_arom_dispfacetofaceNumber of aromatic displaced face-to-face interactions
sum_arom_edgetofaceNumber of aromatic edge-to-face interactions
sum_disulphNumber of disulphide interactions
sum_picatNumber of π-cation interactions
sum_aromsulphNumber of aromatic sulphur interactions
sum_proximalNumber of proximal interactions

pdb_naccess_residues

idInternal serial ID
pdbPDB code
p1_chainChain ID for first interface chain
p2_chainChain ID for second interface chain
chainChain ID
res_idResidue number
inscodeResidue insert code
resnameResidue name
apo_abs_asaResidue absoulute accessible surface area for unbound chain
apo_rel_asaResidue relative accessible surface area for unbound chain
bound_abs_asaResidue absoulute accessible surface area for bound complex
bound_rel_asaResidue relative accessible surface area for bound complex
delta_asaChange in residue accessible surface area upon binding

pdb_naccess_chains

idInternal serial ID
pdbPDB code
p1_chainChain ID for first interface chain
p2_chainChain ID for second interface chain
p1_chain_asaAccessible surface for first unbound chain
p2_chain_asaAccessible surface for second unbound chain
bound_abs_asaSum of accessible surface area for both unbound chains
bound_asaAccessible surface area for bound complex
delta_asaChange in accessible surface area upon binding