Hierarchy of regions of amino acid sequence with respect to their role in the protein spatial structure

The method of the representation of amino acid sequence by graph of the int eractions energy between parts of spatial structure has been elaborated. Ou r method provides the possibility to establish the compatibility between ea ch point of a polypeptide chain and the Van der Waals interactions energy o f regions of a native globule adjacent to this amino acid residue. We have undertaken an exhaustive analysis of a set of proteins. Boundaries of domai n and module structures have been found. Nonequivalence of different parts of sequences in respect to their contribution to stabilization of the spati al structure of the protein macromolecules has been revealed. On the basis of the number of energetic levels which are necessary to identify all indep endent parts of the globule, the contribution from each part of the sequenc e to stabilization of the spatial structure of the globule is defined. Thus , it has been found that the sequence of amino acid residues coincides with the sequence of the numerical values which can be used in turn in formal p rocedures, such as an alignment, a search of consensus, the recognition of composition peculiarities, etc. An example of the comparison of proteins wi th various sequence identities is considered to demonstrate the scheme of a n alignment procedure.