.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/gallery/structure/contacts/contact_sites.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_gallery_structure_contacts_contact_sites.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_examples_gallery_structure_contacts_contact_sites.py:


Contact sites of protein-DNA interaction
========================================

This script identifies which amino acids of the phage 434 repressor are
in contact with its corresponding DNA operator.
*In contact* is defined as a pairwise atom distance below a given
threshold (in this case 4.0 Å).

The identified contact residues are highlighted as sticks.

.. GENERATED FROM PYTHON SOURCE LINES 12-74



.. image-sg:: /examples/gallery/structure/contacts/images/sphx_glr_contact_sites_001.png
   :alt: contact sites
   :srcset: /examples/gallery/structure/contacts/images/sphx_glr_contact_sites_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Residues in contact with DNA:

    Asn16
    Gln17
    Gln28
    Gln29
    Glu32
    Gln33
    Asn36
    Lys38
    Thr39
    Lys40
    Arg41
    Pro42
    Arg43
    Phe44






|

.. code-block:: Python


    # Code source: Patrick Kunzmann
    # License: BSD 3 clause

    import numpy as np
    import biotite.database.rcsb as rcsb
    import biotite.structure as struc
    import biotite.structure.io.pdbx as pdbx

    # The maximum distance between an atom in the repressor and an atom in
    # the DNA for them to be considered 'in contact'
    THRESHOLD_DISTANCE = 4.0


    # Fetch and load structure
    pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("2or1", "bcif"))
    structure = pdbx.get_structure(pdbx_file, model=1)


    # Separate structure into the DNA and the two identical protein chains
    dna = structure[np.isin(structure.chain_id, ["A", "B"]) & ~structure.hetero]
    protein_l = structure[(structure.chain_id == "L") & ~structure.hetero]
    protein_r = structure[(structure.chain_id == "R") & ~structure.hetero]
    # Quick check if the two protein chains are really identical
    assert len(struc.get_residues(protein_l)) == len(struc.get_residues(protein_r))


    # Fast identification of contacts via a cell list:
    # The cell list is initiliazed with the coordinates of the DNA
    # and later provided with the atom coordinates of the two protein chains
    cell_list = struc.CellList(dna, cell_size=THRESHOLD_DISTANCE)

    # Sets to store the residue IDs of contact residues
    # for each protein chain
    id_set_l = set()
    id_set_r = set()

    for protein, res_id_set in zip((protein_l, protein_r), (id_set_l, id_set_r)):
        # For each atom in the protein chain,
        # find all atoms in the DNA that are in contact with it
        contacts = cell_list.get_atoms(protein.coord, radius=THRESHOLD_DISTANCE)
        # Only retain atoms in the protein with contact
        # to at least one atom of the DNA
        contact_indices = np.where((contacts != -1).any(axis=1))[0]
        # Get residue IDs for the atoms in the protein
        contact_res_ids = protein.res_id[contact_indices]
        # Put the residue IDs into the set,
        # duplicate IDs are automatically removed in this process
        res_id_set.update(contact_res_ids)

    # Only consider residues that show contacts in both peptide chains
    # -> intersection of sets
    common_ids = sorted(id_set_l & id_set_r)

    # Print output
    print("Residues in contact with DNA:")
    print()
    for res_id in common_ids:
        res_name = protein_l.res_name[protein_l.res_id == res_id][0]
        print(res_name.capitalize() + str(res_id))

    # Visualization with PyMOL...


.. _sphx_glr_download_examples_gallery_structure_contacts_contact_sites.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: contact_sites.ipynb <contact_sites.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: contact_sites.py <contact_sites.py>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_