Last modified 3rd April '95 © Birkbeck College 1995

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Ca-Ca distances between secondary structures are represented in the form of average values termed 'proximity indices' and the secondary structural organisation is indicated in the form of dendrograms. An example is shown for the case of calmodulin.

Specific nodes in these dendrograms are identified as tertiary structural clusters of the protein; these include supersecondary structures and domains. A ratio of the average proximity indices (ignoring inter-clusteral distances) to the average of all proximity indices, weighted for the aggregation of small sub-clusters and termed the disjoint factor, is employed as a discriminatory parameter to identify automatically clusters representing individual domains. An example of domains identified in glutathione reducatase is shown below :

The domains identified by this clustering method may not correspond to the functional domains proposed.

The "disjoint factor" gives a measure of the extent of interaction between domains and has been used to classify domains into one of the three types, disjoint, interacting and conjoint. Domains are classified as those with sparse inter-domain interfaces (disjoint), intermediate interactions (interacting) and elaborate interfaces (conjoint) based on the magnitude of the disjoint factor. An example of the three types is shown below :

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R. Sowdhamini