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 - $\Pi$ interactions [ref]
CATIONPI	Cation-PI	Cation - $\Pi$ interactions [ref]
DONORPI	Donor-PI	Hydrogen Bond donor - $\Pi$ interactions [ref]
HALOGENPI	Halogen-PI	Halogen bond donors - $\Pi$ [ref]
METSULPHURPI	Sulphur-PI	Methionine sulphur - $\Pi$ 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"
    },