Volume 1 Chapter 7 The CSD Reference Molecules and the Extended Crystal Structure

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7.14.2 Searching for Specific Contact Types

The main command for defining a non-bonded search between two sets of atoms is CONTACT. The following components of the command must be provided by the user:

Ex.1 Suppose we wish to find all intermolecular contacts between a carbonyl oxygen and the hydrogen of an NH group in peptide structures.

We will consider the two groups to be in contact when the O-H distance is less than 3.1Å.

The resultant command in the instruction document is: The 3D CONSTRAIN sub-menu with the defined CONTACT is shown below.

Note that there are two separate fragments on the screen - the line between the H and O is not a bond but merely indicates that we have defined a contact between these two atoms. Whenever a CONTACT command is used there must be at least two fragments on the screen. No CONTACT commands are allowed between atoms in the same fragment.

An example of a hit, AAGAGG10, registered by this search is shown below.

Although a CONTACT command cannot accept two sets of atoms from the same fragment that does not mean we cannot search for intramolecular contacts. To conduct the same search again, but for intramolecular contacts, we proceed as follows:

Ex.2

The resultant command in the instruction document is: An example of a hit registered by this search is shown below.

A new question has appeared, asking about the shortest bond path between the two atoms. By giving the values 1 999 as the endpoints of the allowed range, this option has been "turned off". Examination of the results reveals that some "hydrogen bonds" within amide groups were located. These atoms satisfy the distance criteria but only because the two groups are chemically adjacent. The shortest bond path option provides a way to avoid these unwanted results.

Ex. 3 If the search is conducted again with:

CONTACT INTRA 5 999 2 A 4 A 0.0 3.1

the desired result is obtained, as shown below.

Finally, it is possible to conduct non-bonded searches that accept both intramolecular and intermolecular contacts.

Ex. 4 If the command is altered to

CONTACT ANY 5 999 2 A 4 A 0.0 3.1

all hydrogen bonds are located. Note that the shortest bond path range must still be given in case any intramolecular contacts are encountered. The results of the search are shown below.

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Volume 1 Chapter 7 Using van der Waals Radii for Distance Testing.