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

the type of contact
the two sets of atoms involved in the non-bonded contact
the distance between the two sets of atoms which determines that a contact is established.

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:

intramolecular
intermolecular
intramolecular or intermolecular

Intramolecular contact searches are faster than intermolecular since calculations involving symmetry-related molecules are unnecessary.
Normally in an intramolecular contact search you wish to exclude 1,3-interactions and perhaps 1,4-interactions also. A very powerful topological restraint is provided in QUEST3D whereby you can define the minimum path length between the two contact atoms, ie. the shortest route between the two atoms which follows a contiguous chain of covalent bond.
It should be noted that even for an intramolecular contact search you must define the query in terms of two discrete fragments. This condition may be relaxed in a later software release.
Intermolecular contacts between two molecules can involve the following pairs:
- different chemical molecules in the crystal structure, eg. a carbohydrate molecule and a water molecule
- two identical chemical molecules A and B, where B is related to A by crystallographic symmetry
- two identical chemical molecules A and B, where A and B are not related by crystallographic symmetry but rather the asymmetric unit contains more than one molecule, ie. Z'>1.

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:

a single atom
a group of atoms

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:

(i) A : A
- Set 1 consists of the 6 atoms of the aromatic ring.
- Set 2 consists of the 2 H atoms of the amino group.
The search process involves the calculation of the distance between each atom of set 1 and each atom of set 2, ie. 12 distances must be calculated.
If any one of these distances satisfies the specified distance criterion then a non-bonded contact is declared and a hit is registered.
(ii) C : A
- Set 1 consists of the centroid of the 6 atoms of the aromatic ring.
- Set 2 consists of the 2 H atoms.
In this case 2 distances must be tested for a non-bonded contact.
(iii) A : C
- Set 1 consists of the 6 atoms of the aromatic ring.
- Set 2 consists of the centroid of the 2 H atoms.
In this case 6 distances must be tested for a non-bonded contact.
(iv) C : C
- Set 1 consists of the centroid of the 6 atoms of the aromatic ring.
- Set 2 consists of the centroid of the 2 H atoms.
In this case 1 distance must be tested for a non-bonded contact.

Contact Distances

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

by using the standard van der Waals radii and tolerance limit stored in the QUEST3D program
by changing the standard van der Waals radii and/or tolerance limit, using the VDW-RAD command
by specifying the minimum and maximum values of the allowed distance between the two sets of atoms.

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:

the complete molecule containing the atoms of set 1 is displayed; this is termed the reference molecule
the atoms of set 2 in the neighbouring molecule are displayed, each atom having % appended to its label
a dotted blue line links the two atoms or centroids involved in the contact
if a set of atoms consists of more than one atom and it is represented by its constituent atoms rather than its centroid then the dotted blue line is drawn to that atom of the set which is involved in the shortest non-bonded contact distance

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.

Select CONTACT

In the dialogue area we now have:

Select or type atoms for CONTACT. If necessary reselect CONTACT to end input.
Select CANCEL to cancel command.

Select atom 4 and then atom 6

In the dialogue area we now have:

Type 1,2, or 3 to indicate type of contact:
          1 = INTRA-molecular contacts   2 = INTER-molecular contacts
          3 = ANY (ie, either INTRA or INTER-molecular contacts)  [Default = 3]

Type 2 <RETURN>

In the dialogue area we now have:

By default, a Van der Waals distance search will be used for this CONTACT.
To over-ride it with a minimum and maximum distance, enter the MIN. and MAX.
distances, separated by spaces or commas. Otherwise, press
<RETURN>.

Type 1.0 2.5 <RETURN>
On the diagram a blue line is drawn between atoms 4 and 6.
In the summary area we now have the line:
```
INTER 4 A 6 A 1.0 2.5
```
This line is displayed in blue to indicate that it is a non-bonded command.
In this line 4 A 6 A indicates that 4 and 6 are both atoms (A), as opposed to centroids (C).
In the dialogue area we now have the "home" prompt:
```
Search for ALL crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.
```
The resultant command in the instruction document is:
```
CONTACT INTER 4 A 6 A 1.0 2.5
```

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.

Select CONTACT

In the dialogue area we now have:

Select or type atoms for CONTACT. If necessary reselect CONTACT to end input.
Select CANCEL to cancel command.

Select atom 2 and then atom 4

In the dialogue area we now have:

Type 1,2, or 3 to indicate type of contact:
          1 = INTRA-molecular contacts   2 = INTER-molecular contacts
          3 = ANY (ie, either INTRA or INTER-molecular contacts)  [Default = 3]

Type 1 <RETURN>

For "INTRA" and "ANY" searches, you must specify the minimum and maximum number
of bonds allowed in the shortest path between INTRAMOLECULAR contact atoms.
Enter MIN. and MAX. numbers of bonds, separated by spaces or commas [4
999]

Type 9 9 <RETURN>

In the dialogue area we now have:

By default, a Van der Waals distance search will be used for this CONTACT.
To over-ride it with a minimum and maximum distance, enter the MIN. and MAX.
distances, separated by spaces or commas. Otherwise, press
<RETURN>.

Press <RETURN>
On the diagram a blue line is drawn between atoms 2 and 4.
In the summary area we now have the line:
```
INTRA  9  9  2  A  4  A
```
This line is displayed in blue to indicate that it is a non-bonded command.
In the dialogue area we now have the "home" prompt:
```
Search for ALL crystal fragments
OVERLAP of crystal fragments permitted
Select a menu command or TO-BUILD to return to the BUILD menu.
```
The resultant command in the instruction document is:
```
CONTACT INTRA  9  9  2  A  4  A
```

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 .