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pdbearpeggio 1.4.4

PDBe Arpeggio
This repository contains a refactored and expanded version of the arpeggio tool, modified and maintained by the PDBe team to use as part of their weekly PDB release process.
pdbe-arpeggio is a python library, that can be used to calculate interatomic contacts in a protein based on the rules defined in CREDO. This library only supports protein structures in mmCIF format.
If you make use of pdbe-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,
Disclaimer
This is a refactored version of the original arpeggio by Harry Jubb. Main changes are:

Python 3 support
Modular architecture to make arpeggio PIP installable.
Support for mmCIF format to process also larger structures.
Results in JSON format.

pdbe-arpeggio doesn'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 Started
Web Interface
If 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 the web interface.
Installation
The easiest way to set up arpeggio is using Conda. Create a conda environment and install arpeggio dependencies:
conda create -n arpeggio-env python=3.9 -c conda-forge gemmi openbabel biopython
conda activate arpeggio-env
pip install pdbe-arpeggio

Dependencies

Open Babel >= 3.0.0
Biopython >= 1.80
gemmi >= 0.5.8

Running arpeggio
pdbe-arpeggio 1tqn_h.cif [options]
e.g.
pdbe-arpeggio -s /A/508/ -o out/ 1tqn_h.cif
Use pdbe-arpeggio -h for available options.
Output
All the identified interactions are written in a JSON file.
Interactions
atom-atom interactions

Key
Interaction
Description

clash
Clash
Denotes if the atom is involved in a steric clash.

covalent
Covalent
Denotes if the atom appears to be covalently bonded.

vdw_clash
VdW Clash
Denotes if the van der Waals radius of the atom is clashing with one or more other atoms.

vdw
VdW
Denotes if the van der Waals radius of the the atom is interacting with one or more other atoms.

proximal
Proximal
Denotes if the atom is > the VdW interaction distance, but within 5 Angstroms of other atom(s).

hbond
Hydrogen Bond
Denotes if the atom forms a hydrogen bond.

weak_hbond
Weak Hydrogen Bond
Denotes if the atom forms a weak hydrogen bond.

xbond
Halogen Bond
Denotes if the atom forms a halogen bond.

ionic
Ionic
Denotes if the atom may interact via charges.

metal
Metal Complex
Denotes if the atom is part of a metal complex.

aromatic
Aromatic
Denotes an aromatic ring atom interacting with another aromatic ring atom.

hydrophobic
Hydrophobic
Denotes hydrophobic interaction.

carbonyl
Carbonyl
Denotes a carbonyl-carbon:carbonyl-carbon interaction.

polar
Polar
Less strict hydrogen bonding (without angle terms).

weak_polar
Weak Polar
Less strict weak hydrogen bonding (without angle terms).

atom-plane interactions

Key
Interaction
Description

CARBONPI
Carbon-PI
Weakly electropositive carbon atom - Π interactions [ref]

CATIONPI
Cation-PI
Cation - Π interactions [ref]

DONORPI
Donor-PI
Hydrogen Bond donor - Π interactions [ref]

HALOGENPI
Halogen-PI
Halogen bond donors - Π [ref]

METSULPHURPI
Sulphur-PI
Methionine sulphur - Π ring interactions [ref]

plane-plane interactions
Follows nomenclature established by Chakrabarti and Bhattacharyya (2007)
group-group/plane interactions

Key
Interaction
Description

AMIDEAMIDE
amide - amide
[ref]

AMIDERING
amide - ring
[ref]

Interacting entities

Key
Meaning

INTER
Between an atom from the user's selection and a non-selected atom

INTRA_SELECTION
Between two atoms both in the user's selection

INTRA_NON_SELECTION
Between two atoms that are both not in the user's selection

SELECTION_WATER
Between an atom in the user's selection and a water molecule

NON_SELECTION_WATER
Between an atom that is not in the user's selection and a

WATER_WATER
Between two water molecules

Examples
atom-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"
},