Volume 2 Chapter 3 3D-Constrain Sub-menu MANUAL MODE

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CONTACT

Function

CONTACT is used to search for non-bonded contacts between two sets of atoms in terms of certain contact distance criteria.

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.

Components of the Command

The construction of a CONTACT command involves the specification of the following components:

For most applications only one CONTACT will be required but for certain types of search it will be necessary to define more than one CONTACT command. This will be illustrated later.

Types of Contact

The following types of contact are available:

Sets of Atoms and the Search Process

The non-bonded contact search is made between two sets of atoms.

A set of atoms can be either:

If the set consists of a group of atoms then this set must be defined using the NON-BONDED GROUP command before the CONTACT command is constructed.

If a set of atoms is a group then it is represented

either
by its constituent atoms
or
by the centroid of the constituent atoms.

Consider the interaction between an aromatic ring and the hydrogen atoms of an amino group.

The four sets of contacts are illustrated below:

Contact Distances

In formulating a non-bonded search the contact distance criterion can be specified in 3 ways:

Suppose that:
the distance between two non-bonded atoms i and j is dij
the van der Waals radii for atoms are ri and rj

The two atoms are considered to be in contact if:
dij < ri + rj +t
where t is a tolerance limit, set by default to 1.0Å

The default van der Waals radii are taken from A. Bondi (1964) "van der Waals Volumes and Radii "

J.Phys.Chem. 68, 441-451. These values are shown in the table below (all values in Å). If an element does not appear in the table it is assigned a value of 2.0Å.

Ag    1.72       Ar    1.88       As     1.85       Au     1.66
Br    1.85       C     1.70       Cd     1.58       Cl     1.75
Cu    1.40       F     1.47       Ga     1.87       H      1.20
He    1.40       Hg    1.55       I      1.98       In     1.93
K     2.75       Kr    2.02       Li     1.82       Mg     1.73
N     1.55       Na    2.27       Ne     1.54       Ni     1.63
O     1.52       P     1.80       Pb     2.02       Pd     1.63
Pt    1.72       S     1.80       Se     1.90       Si     2.10
Sn    2.17       Te    2.06       Tl     1.96       U      1.86
Xe    2.16       Zn    1.39
If either set of atoms is represented by a centroid then the distance must specified explicitly in terms of the minimum and maximum values.

Display of Hits

When a hit is registered for an intermolecular contact the display is as follows:

When a hit is registered for an intramolecular contact the display is simply one molecule with a dotted blue line linking the two atoms or centroids involved in the contact.

Ex.1 Suppose we wish to find all intermolecular contacts in the range 1.0 - 2.5Å between a keto-oxygen atom and the hydrogen atom of a secondary amine.

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

The keto-oxygen (O12) of the acetyl group is linked by a dotted blue line to the hydrogen atom on the ring N of a neighbouring molecule.

The H atom is labelled H1% and the other atoms of the second fragment are labelled N1%, C2%, C5%.

Use of MEASURE DIST indicates that the actual value of the non-bonded contact distance O12-H1% is 2.029Å.

Ex.2 Suppose we wish to find all intramolecular contacts between a carbonyl oxygen and the hydrogen of an NH group in peptide structures.

We will use standard van der Waals radii so that contacts will be declared for O-H less than 3.72Å

We will also require that the minimum path length between the O and H atoms be exactly 9.

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

The carbonyl oxygen O1 is linked by a dotted blue line to the hydrogen H23 attached to N3.

Use of MEASURE DIST indicates that the actual value of the non-bonded contact distance is 2.051Å.

Related Commands

GROUP, VDW-RAD

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Volume 2 Chapter 3 3D-Constrain Sub-menu GROUP.