Find Clashes/Contacts

Find Clashes/Contacts identifies interatomic clashes and contacts based on VDW radii and user-specified criteria. Terminology:

• 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)

There are several ways to start Find Clashes/Contacts, a tool in the Structure Analysis and Surface/Binding Analysis categories. It is also implemented as the command findclash.

Atoms to Check are specified by selecting atoms, clicking Designate, and indicating which interactions should be found:

• themselves - interactions among the designated atoms
• all other atoms (default) - interactions between the designated atoms and all other atoms
• other atoms in same model - intra-model interactions between the designated atoms and all other atoms
• second set of designated atoms - interactions between the designated atoms and a second designated set (specified by selecting atoms and clicking Designate selection as second set)

The Clash/Contact Parameters control what will be considered a clash or contact. The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs:

overlap_ij = r_VDWi + r_VDWj – d_ij – allowance_ij

• Find atoms with VDW overlap >=[ cutoff ] angstroms - pairs of atoms with overlap ≥ cutoff will be identified. A larger positive cutoff restricts the results to more severe clashes, whereas a negative cutoff can also identify favorable contacts.
• Subtract [ allowance ] from overlap for potentially H-bonding pairs - 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 FindHBond, 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.

  For detecting clashes, cutoff values of 0.4-1.0 Å and allowance values of 0.2-0.6 Å are generally reasonable (default clash criteria 0.6 and 0.4 Å, respectively).

  For detecting contacts, negative cutoff values of 0.0-(–1.0) Å with an allowance of 0.0 Å are generally reasonable (default contact criteria –0.4 and 0.0 Å, respectively).

• Ignore contacts of pairs [ N ] or fewer bonds apart (N=4 by default)
• Include intra-residue contacts (default off)
• Include intra-molecule contacts (default on) - whether to include intramolecular interactions, where a molecule is defined as a covalently bonded set of atoms

• Select - whether to select atoms meeting the clash/contact criteria (and deselect all other atoms)
• Color [ color well ] (and color all other atoms [ color well ]) - whether to color atoms meeting and not meeting the clash/contact criteria (the default colors are red and No color, respectively; using No color reveals model-level colors)
• Draw pseudobonds of color [ color well ] and width [ linewidth ] - whether to draw pseudobonds of the specified color (default yellow) and linewidth (default 2.0) between pairs meeting the clash/contact criteria. These pseudobonds can be removed with the command ~findclash. The PseudoBond Panel can also be used to close the pseudobond group (named contacts) or alter its display.
• If endpoint atom hidden, show endpoint residue - turn on the display of residues containing a contact atom if that atom is not displayed initially (By default, if the atom on either end of a pseudobond representing a contact is not shown, the pseudobond itself is not shown, although it still exists; displaying the atom allows the contact pseudobond to be shown.)

  The following are only available for discontinuous checking (when OK/Apply clicked):

• Assign 'overlap' attribute - whether to assign the largest overlap per atom as an attribute named overlap and open the Render by Attribute tool
• Write information to file - whether to write clash/contact information to a text file. The dialog for saving the file includes a Naming style option to control how atoms will be listed:
  • simple (for example, HIS 16.A ND1)
  • command-line specifier (for example, :16.A@ND1)
  • serial number (for example, 126)
• Write information to reply log - whether to write clash/contact information to the Reply Log. The Atomspec display style setting in the Labels preferences controls how atoms will be listed.

• when OK/Apply clicked (default) - this option is compatible with all treatment options, including attribute assignment and writing out clash/contact information. Clicking OK runs the calculation and dismisses the dialog, whereas clicking Apply runs the calculation without dismissing the dialog.
• after relative motions (until dialog closed) - whenever relative motions are paused; only selection and display treatments are available. Relative motions include bond rotations and translations/rotations of one model relative to another, as opposed to translations/rotations of all models collectively.
• continuously (until dialog closed) - during motions; only selection and display treatments are available