The main problem discussed in this paper concerns the importance of the
presence of a hydrophobic core in β-sandwich supersecondary structures.
The aim of this research is to propose an alternative structural
classification of the relationship between sequence and spatial
structure. The set of analyzed proteins contains very diverse examples
(taking into consideration source organisms, chain length, domain
composition, ligand and metal complexation, quaternary structure),
allowing for generalization of conclusions. The biological function of
the proteins in question is also fundamentally different. The only
common feature of these proteins is the presence of a β-sandwich or
β-sandwich-like domain. The data base is taken from alternative
classification of secondary and supersecordary of sandwich-like domains.
The results show that the secondary and supersecondary despite of high
topological similarity represent different forms of hydrophobic core
structure. In consequence the stability of sandwich-like domains is
differentiated. The local stability/instability has a significant
repercussion on biological activity. It is expressed by identified local
discordance between idealized and observed hydrophobicity distribution.
The closer is the structure of hydrophobic core to the idealized one the
higher stability is assumed for the domain under consideration.