Volume 2 Chapter 3 3D-Constrain Sub-menu CONTACT

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GROUP

Function

GROUP is used to define a set of atoms for use in a non-bonded contact search.

Full details of non-bonded contact searching are given in chapter 7 of Vol.1 and users must read that chapter before attempting to formulate such a search.

Remarks

Ex.1 Suppose we wish to find intermolecular contacts between the carbon, hydrogen atoms of a phenyl group and the oxygen atom of a ketone. In this example we will use the standard van der Waals radii so that hits will be registered for C...O < 4.42Å and H...O < 3.72Å.

An example of a hit registered by this search is shown below.

H8 is linked by a dotted blue line to O1%.

If you use MEASURE DIST the contact distance is displayed as 2.598Å.

Ex.2 Suppose we wish to find all intramolecular contacts in the range 1.9-2.9Å between the centroid of a benzene ring and the hydrogen atom of an NH group.

An example of a hit registered by this search is shown below.

H41, attached to N5, is linked by a dotted blue line to the centroid of a benzene ring.

In this case you cannot use MEASURE DIST to display the actual value of the non-bonded contact distance since a GROUP centroid is involved. To do this you would have to also SETUP CENTROID in the 3D-CONSTRAIN sub-menu.

Ex.3 This example has been chosen to illustrate the use of multiple CONTACT commands in a single search.

Consider the search query represented by 4 fragments:

Suppose we wish to find the following non-bonded contacts:

(i)
intramolecular contact between the centroid of the benzene ring and the sulfur atom

(ii)
intermolecular contact between the centroid of the benzene ring and the carbonyl oxygen atom

(iii)
intermolecular contact between the carbonyl oxygen atom and the hydrogen of the NH group

(iv)
intramolecular contact between the nitrogen of the NH group and the sulfur atom.

Using the standard dialogues, the following commands are constructed:

A search which satisfies all four CONTACT commands will hit, for example, the structure shown below.

The four contact distances are:

X1...S1   7.524Å  X1...O14% 4.591Å
O14%...H7 1.690Å  N7...S1   4.762Å

Related Commands

CONTACT, VDW-RAD

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Volume 2 Chapter 3 3D-Constrain Sub-menu VDW-RAD.