When to use

DynDom Description

Bending Residues

  Determination of Dynamic Domains

The program initially determines the "dynamic domains." First, a whole protein best fit of the two conformations is made. Then, rotation vectors of short main-chain segments are determined. A clustering algorithm is then used to identify clusters of rotation vectors. Residues from segments in an individual cluster form a possible dynamic domain.

  Determination of Hinge Axes

Groups of residues are only accepted for the analysis of hinge axes if they satisfy a criterion based on the ratio of the interdomain displacement to intradomain displacement with another group of residues with which there exists a physical connection. If this is the case the two groups of residues form dynamic domains and their interdomain motion is meaningful. The axes determined are in fact interdomain screw axes. This is based on the theorem of Chasles which states that the general displacement of a rigid body is a screw motion. The location of the interdomain screw axis tells us something about the kind of motion allowed by the interdomain connections. It is possible for the interdomain screw axis to be located far away from the interdomain connections if they are very flexible. Only if the interdomain screw axis is located near to those residues involved in the interdomain bending (defined below) can we think of the axis as a hinge axis. In such a case we call the axis an, "effective hinge axis" and the residues are said to be acting as "mechanical hinges."

When to use

(Table of Contents)

Bending Residues

For further details email : sjh@cmp.uea.ac.uk

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