Tool: Clashes, Contacts

Clashes and Contacts are two separate tools with nearly identical options. Some of the default parameters are different, as meant to detect:

• clashes – unfavorable interactions where atoms are too close together; close contacts
• contacts – all kinds of direct interactions: polar and nonpolar, favorable and unfavorable (including clashes)

The corresponding commands are clashes and contacts. See also: zone atom specification, Select Contacts, Rotamers, H-Bonds, Distances, Crystal Contacts, interfaces, select by pseudobond length, measurements, Protein-Ligand Binding Sites tutorial

Clashes and Contacts can be opened from the Structure Analysis section of the Tools menu and manipulated like other panels (more...). Clicking Apply (or OK, which also dismisses the dialog) runs the calculation. Several of the dialog settings are remembered as preferences when the calculation is run. Clicking Reset restores the dialog to factory default settings. Help opens this page in the Help Viewer.

Interaction parameters:

• Find pairs of atoms with:
  • VDW overlap ≥ [ cutoff ] Å (initial default on) – identify pairs of atoms with VDW overlap ≥ cutoff. The VDW overlap between two atoms is defined as the sum of their VDW radii minus the distance between their centers. An overlap of 0 means the VDW surfaces are just touching. A positive overlap is how far the VDW surfaces interpenetrate, whereas a negative overlap is the distance of separation between the VDW surfaces. A larger positive cutoff restricts the results to more severe clashes, whereas a negative cutoff can also identify pairs of atoms that are farther apart.
    ...for Clashes only: after subtracting [ allowance ] for H-bonding – an allowance > 0 reflects the observation that atoms sharing a hydrogen bond can come closer to each other than would be expected from their VDW radii. The allowance is only subtracted for pairs comprised of a donor (or donor-borne hydrogen) and an acceptor. This is equivalent to using smaller radii to characterize hydrogen-bonding interactions (for example, see Li and Nussinov, Proteins 32:111 (1998)). As in H-Bonds, possible donor groups are hydrogen-bearing nitrogen, oxygen, and sulfur atoms, and possible acceptor groups are nitrogen, oxygen, and sulfur atoms with a lone pair.

    tool	cutoff (Å)		allowance (Å)
    	initial default	usual range	initial default	usual range
    Clashes	0.6	0.4-1.0	0.4	0.2-0.6
    Contacts	−0.4	0.0-(−1.0)	not applicable

    – OR –
  • center-center distance ≤ [ d ] Å (initial default off, with d=4.0) – instead of VDW overlap, use a simple distance cutoff to identify interactions
• Limit by selection (initial default off) – whether to limit the results by the current selection according to one of the following choices in the pulldown menu:
  • with at least one end selected
  • with exactly one end selected
  • with both ends selected
  • between selection and atom spec... [atom-spec] The two sets of atoms may overlap, but will not overrule other restrictions.
• Ignore interactions between atoms [ N ] or fewer bonds apart (initial default N=4)
• Ignore interactions between residues < [ M ] apart in sequence (initial default off, with M=5)
• Include intermodel (initial default on)
• Include intramodel (initial default on)
• Include intramolecule (initial default on) – whether to include intramolecular interactions, where a molecule is defined as a covalently bonded set of atoms
• Include intraresidue (initial default off)
• Ignore hidden models (initial default on) – ignore models that are hidden at the model level (e.g., with Model Panel show/hide checkbox unchecked)

Calculate:

• when OK/Apply clicked (default)
• continuously (until tool closed) – during motions

Treatment of results:

• Select (initial default off) – whether to select the interacting atoms
• Reveal residues (initial default off) – since a pseudobond is only shown when both of its endpoint atoms are shown, whether to ensure all showing all H-bonds by displaying all of the endpoint atoms. To avoid showing disconnected atoms, the entire residues will be shown, except that amino acid and nucleic acid residues are split into sidechain and backbone moieties separately displayed by this option. Displayed backbone atoms may still be invisible where cartoon is shown, unless their simultaneous display has been enabled with cartoon suppress false.
• Assign attribute named [name] (initial default off) – whether to assign the largest overlap per atom as an attribute with the specified name (default overlap) and open the Render by Attribute tool; this option is disallowed with continuous monitoring
• Display as pseudobonds (initial default on) – whether to show the interactions as pseudobonds, with related settings:
  • Color (initial default medium orchid for clashes, forest green for contacts) – pseudobond color
  • Radius (initial default 0.15 for clashes, 0.075 for contacts) – pseudobond radius in Å
  • Dashes (initial default 4 for clashes, 6 for contacts) – pseudobond number of dashes; currently, odd numbers are rounded down to give an even number of dashes.
  • Distance label (initial default off) – whether to show Å distances as bond labels; the number of decimal places and whether to show the Å symbol can be changed with distance style or set beforehand in the Distances preferences, and label height in Å can be changed with label height or set beforehand in the Labels preferences. The distances (pseudobond lengths) can also be plotted as a histogram with crosslinks histogram.
  • Group name (initial default clashes or contacts according to which tool is being used) – name for the since a pseudobond group. Pseudobonds with group name clashes can be removed with the command clashes delete or ~clashes, and those with group name contacts removed with contacts delete or ~contacts. A pseudobond model can also be closed with the Model Panel or the close command.

Write information to: Where to write clash/contact information, including atom pair specifications (see the Labels preferences for specifier style), overlaps, and center-center distances; disallowed with continuous monitoring.

• Log (initial default off) – show the information in the Log
• File (initial default off) – save the information to a text file