Protein Interaction Analysis — Advanced Options Dialog Box

Advanced Options Dialog Box Features

• List closest interaction neighbors within box
• Ignore interactions between backbone atoms option
• Hydrogen bonds settings
• Salt bridges setting
• Pi stacking setting
• Van der Waals clashes setting
• Reset button

List closest interaction neighbors within box

Set the cutoff for determining the closest interaction neighbors for the interaction analysis. Any residue that has any atom within the specified distance of the target residue is considered a neighbor of that residue.

Ignore interactions between backbone atoms option

Do not include backbone–backbone interactions in the interaction analysis.

Hydrogen bonds settings

Specify the criteria for determining whether a hydrogen bond exists. The four atoms involved in the hydrogen bond are designated D-H...A-X, where D is the donor atom and A is the acceptor atom. The default values are the Maestro defaults (see the Non-bonded interactions section of the Preferences panel topic for a discussion).

Minimum acceptor angle box

Set the minimum acceptor angle H...A–X, in degrees. The default is 90°.

Minimum donor angle box

Set the minimum donor angle D–H...A, in degrees. The default is 120°.

Maximum distance box

Set the maximum H...A distance, in angstroms. The default is 2.8 Å.

Salt bridges setting

Specify the criterion for a salt bridge, designated here as A...B...C, where B is the bridging ion and A and C are the bridged atoms (which must have a substantial partial charge).

Maximum distance box

Set the maximum A..B or B..C distance. The default is 4.0 Å.

Pi stacking setting

Specify the distance criterion for a pi-pi stacking interaction.

Maximum centroid distance box

Set the maximum distance between the centroids of the two aromatic rings. The default is 4.0 Å.

Van der Waals clashes setting

Specify the overlap criterion for determining whether two atoms clash, based on their van der Waals radii.

Allowable overlap box

Set the maximum overlap distance of the van der Waals spheres of any two atoms. If R_A+R_B−R_AB is greater than the allowable overlap, the atoms are considered to clash, where R_A and R_B are the van der Waals radii, and R_AB is the distance between atoms A and B. The default is 0.4 Å.

Reset button

Reset the panel to its default settings.