The use of site-directed mutagenesis to determine, for residues of a complex, usually an uncrystallized protein, their proximity to other residues of the protein, their mileiu (extracellular, cytoplasmic, transmembrane) or the participation of the residues' side chains in specific interactions. Every residue of a protein is systematically replaced by a cysteine residue. Being of a moderate size so that physical disruption is unlikely to cause changes in function, and being easily converted into a useful reporter group by chemical modification, cysteine is a generally useful residue for modification.