Properties of intraglobular contacts in proteins: An approach to prediction of tertiary structure

Matrices of intraglobular contacts and vectors of coordination numbers derived from the amino acid sequence form the basis for computer procedures for the analysis and prediction of the tertiary structure of proteins. Three main modules perform: 1) prediction of the plot of residue-coordination numbers (number of contacts) on the basis of amino-acid sequence; 2) calculation of the matrix of intraglobular contacts on the basis of coordination-numbers plot and amino-acid sequence; and 3) reconstruction of the three-dimensional structure starting with the contact matrix. This approach provides insight into important regularities governing globule formation, for example, problems of interior/exterior residue distribution and apparent residue-residue affinities. The current state of development is illustrated by calculation of the three-dimensional structure of sea snake neurotoxin.