Package: pdbe-arpeggio
PDBe ArpeggioThis repository contains a refactored and expanded version of thearpeggiotool, modified and maintained by thePDBe teamto use as part of their weekly PDB release process.pdbe-arpeggiois a python library, that can be used to calculate interatomic contacts in a protein based on the rules defined inCREDO. This library only supports protein structures in mmCIF format.If you make use ofpdbe-arpeggio, please cite the following article:Harry C Jubb, Alicia P Higueruelo, Bernardo Ochoa-Montaño, Will R Pitt, David B Ascher, Tom L Blundell,Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.
Journal of Molecular Biology,
Volume 429, Issue 3,
2017,
Pages 365-371,
ISSN 0022-2836,DisclaimerThis is a refactored version of the originalarpeggioby Harry Jubb. Main changes are:Python 3 supportModular architecture to makearpeggioPIP installable.Support for mmCIF format to process also larger structures.Results in JSON format.pdbe-arpeggiodoesn't do any processing of input protein structure, other than what BioPython does by default. Alternate locations and missing density are not explicitly accounted for and may result in anomalous results. Please use with caution.Getting StartedWeb InterfaceIf you would like to run original version of arpeggio on a small number of individual structures, the easiest way to get started is to use theweb interface.InstallationThe easiest way to set up arpeggio is usingConda. Create a conda environment and install arpeggio dependencies:condacreate-narpeggio-envpython=3.9-cconda-forgegemmiopenbabelbiopython
condaactivatearpeggio-env
pipinstallpdbe-arpeggioDependenciesOpen Babel>= 3.0.0Biopython>= 1.80gemmi>= 0.5.8Running arpeggiopdbe-arpeggio 1tqn_h.cif [options]e.g.pdbe-arpeggio -s /A/508/ -o out/ 1tqn_h.cifUsepdbe-arpeggio -hfor available options.OutputAll the identified interactions are written in a JSON file.Interactionsatom-atom interactionsKeyInteractionDescriptionclashClashDenotes if the atom is involved in a steric clash.covalentCovalentDenotes if the atom appears to be covalently bonded.vdw_clashVdW ClashDenotes if the van der Waals radius of the atom is clashing with one or more other atoms.vdwVdWDenotes if the van der Waals radius of the the atom is interacting with one or more other atoms.proximalProximalDenotes if the atom is > the VdW interaction distance, but within 5 Angstroms of other atom(s).hbondHydrogen BondDenotes if the atom forms a hydrogen bond.weak_hbondWeak Hydrogen BondDenotes if the atom forms a weak hydrogen bond.xbondHalogen BondDenotes if the atom forms a halogen bond.ionicIonicDenotes if the atom may interact via charges.metalMetal ComplexDenotes if the atom is part of a metal complex.aromaticAromaticDenotes an aromatic ring atom interacting with another aromatic ring atom.hydrophobicHydrophobicDenotes hydrophobic interaction.carbonylCarbonylDenotes a carbonyl-carbon:carbonyl-carbon interaction.polarPolarLess strict hydrogen bonding (without angle terms).weak_polarWeak PolarLess strict weak hydrogen bonding (without angle terms).atom-plane interactionsKeyInteractionDescriptionCARBONPICarbon-PIWeakly electropositive carbon atom - $\Pi$ interactions[ref]CATIONPICation-PICation - $\Pi$ interactions[ref]DONORPIDonor-PIHydrogen Bond donor - $\Pi$ interactions[ref]HALOGENPIHalogen-PIHalogen bond donors - $\Pi$[ref]METSULPHURPISulphur-PIMethionine sulphur - $\Pi$ ring interactions[ref]plane-plane interactionsFollows nomenclature established byChakrabarti and Bhattacharyya (2007)group-group/plane interactionsKeyInteractionDescriptionAMIDEAMIDEamide - amide[ref]AMIDERINGamide - ring[ref]Interacting entitiesKeyMeaningINTERBetween an atom from the user's selection and a non-selected atomINTRA_SELECTIONBetween two atoms both in the user's selectionINTRA_NON_SELECTIONBetween two atoms that are both not in the user's selectionSELECTION_WATERBetween an atom in the user's selection and a water moleculeNON_SELECTION_WATERBetween an atom that is not in the user's selection and aWATER_WATERBetween two water moleculesExamplesatom-atom interaction{"bgn":{"auth_asym_id":"A","auth_atom_id":"CB","auth_seq_id":313,"label_comp_id":"VAL","label_comp_type":"P","pdbx_PDB_ins_code":" "},"contact":["proximal","hydrophobic"],"distance":4.02,"end":{"auth_asym_id":"A","auth_atom_id":"CBB","auth_seq_id":508,"label_comp_id":"HEM","label_comp_type":"B","pdbx_PDB_ins_code":" "},"interacting_entities":"INTER","type":"atom-atom"},atom-plane interaction{"bgn":{"auth_asym_id":"A","auth_atom_id":"O","auth_seq_id":523,"label_comp_id":"HOH","label_comp_type":"W","pdbx_PDB_ins_code":" "},"contact":["DONORPI"],"distance":3.9,"end":{"auth_asym_id":"A","auth_atom_id":"C1A,C2A,C3A,C4A,NA","auth_seq_id":508,"label_comp_id":"HEM","label_comp_type":"B","pdbx_PDB_ins_code":" "},"interacting_entities":"INTER","type":"atom-plane"},plane-plane interaction{"bgn":{"auth_asym_id":"A","auth_atom_id":"C1B,C2B,C3B,C4B,NB","auth_seq_id":508,"label_comp_id":"HEM","label_comp_type":"B","pdbx_PDB_ins_code":" "},"contact":["FT","ET"],"distance":4.72,"end":{"auth_asym_id":"A","auth_atom_id":"CD1,CD2,CE1,CE2,CG,CZ","auth_seq_id":435,"label_comp_id":"PHE","label_comp_type":"P","pdbx_PDB_ins_code":" "},"interacting_entities":"INTER","type":"plane-plane"},group-group interaction{"bgn":{"auth_asym_id":"A","auth_atom_id":"C,CA,N,O","auth_seq_id":308,"label_comp_id":"GLU","label_comp_type":"P","pdbx_PDB_ins_code":" "},"contact":["AMIDEAMIDE"],"distance":4.29,"end":{"auth_asym_id":"A","auth_atom_id":"C,CA,N,O","auth_seq_id":310,"label_comp_id":"THR","label_comp_type":"P","pdbx_PDB_ins_code":" "},"interacting_entities":"INTRA_BINDING_SITE","type":"group-group"},