Effects of pH on protein association are not well understood. To understand them better, we combine kinetic experiments, calculations of electrostatic properties, and a new theoretical treatment of pH effects. The familiar proton-linkage model, when used to analyze the dependence of the association constant K on pH, reveals little about the individual proteins. We modified this model to allow determination not only of the numbers of the H+ ions involved in the association but also of the pK(a) values, in both the separate and the associated proteins, of the side chains that are responsible for the dependence of K on pH. Some of these side chains have very similar pK(a) values, and we treat them as a group having a composite pK(a) value. Use of these composite pK(a) values greatly reduces the number of parameters and allows meaningful interpretation of the experimental results. We experimentally determined. the variation of K in the interval 5.4 less than or equal to pH less than or equal to 9.0 for four diprotein complexes, those that the wild-type cytochrome c forms with the wild-type plastocyanin and its mutants Asp42Asn, Glu59Gln, and Glu60Gln. The excellent fittings of the experimental results to the modified model verified this model and revealed some unexpected and important properties of these prototypical redox metalloproteins. Protein association causes a decrease in the pKa values of the acidic side chains and an increase in the pK(a) values of the basic side chains. Upon association, three carboxylic side chains in wild-type plastocyanin each release a H+ ion. These side chains in free plastocyanin have an anomalously high composite pK(a) value, similar to6.3. Upon association, five or six side chains in cytochrome c, likely those of lysine, each take up a H+ ion. Some of these side chains have anomalously low pK(a) values, less than 7.0. The unusual pK(a) values of the residues in the recognition patches of plastocyanin and cytochrome c may be significant for the biological, functions of these proteins. Although each mutation in plastocyanin markedly, and differently, changed the dependence of K on pH, the model consistently gave excellent fittings. They showed decreased numbers of H+ ions released or taken up upon protein association and altered composite pK(a) values of the relevant side chains. Comparisons of the fitted composite pK(a) values with the theoretically calculated pK(a) values for plastocyanin indicated that Glu59 and Asp61 in the wild-type plastocyanin each release a H+ ion upon association with cytochrome c. Information of this kind cannot readily be obtained by spectroscopic methods. Our modification of the proton-linkage model is a general one, applicable also to ligands. other than H+ ion and to processes other than association.