Input

As an input, the VoroContacts server accepts a single structure file in PDB or mmCIF format. An input structure can contain multiple chains, biological assemblies in PDB format are also accepted.

When a structure is submitted, the VoroContacts server calculates all its interatomic and solvent contacts, and then displays a summary of the processed structure and all the calculated contacts.

Once all the contacts are calculated and summarized, the server provides an interface to query subsets of the calculated contacts.

Output querying

Querying is possible after the server calculates all the interatomic contacts.

Querying is done by clicking the "Query contacts" button after providing (or not providing) query parameters in the selection form. Below is an overview of querying possibilities:

• Left and right selection forms can be left fully blank: in this case the server returns all available contacts.
• If you are interested in contacts between X and anything else, define X in the left selection form.
• If you are interested in contacts between X and Y, define X in the left selection form and define Y in the right selection form.
• Selection forms can be filled partially, leaving some entries blank.
• Both single values and comma-separated lists are accepted in selection forms.
• Integer intervals, denoted using ':' (or '-') symbol, are accepted in selection forms. a:b (or a-b) means an inclusive interval [a, b].
• Artificial chain name "solvent" can be used to query solvent-accessible areas.
• Multiple tags can be specified using logical operators '|' and '&'.
• 'Exclude intra-chain contacts' checkbox can be used to discard contacts between atoms of the same chain.
• 'Exclude polymerization bonds' checkbox can be used to discard contacts corresponding to bonds between residues adjacent in sequence: peptide bonds in proteins and phosphodiester bonds in nucleic acids.

The aforementioned tags are markers that indicate some contacts with specific properties. Currently, three tags are used:

• 'hb' indicates a hydrogen bond. It is identified using the HBPLUS software.
• 'sb' indicates a salt bridge. It is identified when a contact is between ASP or GLU oxygen atoms (OD1, OD2 ,OE1, OE2, OXT) and ARG, HIS or LYS nitrogen atoms (NH1, NH2, ND1, NE2, NZ), with an additional condition for the distance between the atom centers to be no more than 4.0 angstroms.
• 'ds' indicates a disulfide bridge. It is identified when a contact is between two CYS sulfur atoms (SG), with an additional condition for the distance between the atom centers to be no more than 3.0 angstroms.

Output viewing

After a successful query, the VoroContacts server displays:

• A brief summary of the selected contacts.
• An interactive table of contacts, where columns can be sorted by value.
• A link to download a table of contacts in TSV (tab separated values) format. This table file can be opened and analyzed using various software tools, e.g, R, Excel, LibreOffice Calc, etc.
• A link to download a Bash script to recreate the VoroContacts server results offline using the standalone Voronota software. This script can be executed on Linux and macOS. It can also be executed on Windows OS with an available Bash shell.

In addition, if the computation of graphics was requested, the VoroContacts server displays:

• A link to view the selected contacts using a WebGL-based viewer.
• A link to view the selected contacts using JSmol (provided if the scene is not too big for JSmol to handle).
• A link to download a Python script for PyMol. This script can be opened with PyMol to produce a high-quality rendering of the contacts graphics. For example, running "pymol input.pdb draw.py" opens both a molecular structure and contacts graphics in the same scene.

Context help

Job submission and querying pages contain a "Show help" button. It can be clicked to view the appropriate instructions and hints for the page.