Abstract
Publisher Summary This chapter summarizes some theoretical methods that are used to obtain information on the interactions and conformational preferences of amino acid residues in a polypeptide. Some significant theoretical results concerning such preferences are cited, together with the examples of related experimental findings that are derived from statistical analyses of known protein and peptide structures. The conformational behavior of the amino acid side chains is also discussed in the chapter. The interactions between side chains and their conformational preferences, as well as their preferential location inside or on the surface of the protein molecule, are related to the polarity of the side chains. The polarity determines the nature of their interactions with a solvent. The examples of the effects of side-chain interactions on the conformational stability of polypeptides are also provided in the chapter. Theoretical methods used for the computations of side-chain interactions are intramolecular interactions and solvent interactions. The preferences of side chains for the interior or exterior of the protein are derived from the statistical analysis of their distribution in the proteins of known structure.
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