This chapter describes the effects of local environments on the pattern of amino-acid substitution in homologous protein structures. In a study described in the chapter, ten classes that varied in the number of amides and carbonyls that were in contact with the side chains were considered. Cluster analysis was used to display the relationships among them. The chapter presents similarities among the ten subclasses of side-chain to main-chain interactions. The classes where no main-chain amide interactions were observed form one cluster. Classes 11, 12, 10, and 13 were not closely associated but formed a large cluster with the classes not having any main-chain amide contacts. The probability distributions of amino-acid substitutions in environments that contain one amide function are distinct from the closely associated cluster of classes that reflect interactions with two or more main-chain amides. © 1994 ACADEMIC PRESS, INC.