Stability is a property of subtilisin which has proven particularly amenable to enhancement via random mutagenesis and screening, yet the effects of most stabilizing mutations are not understood in structural and energetic detail. This paper seeks to explain the longstanding observation that stabilizing mutations are usually calcium-dependent in their stabilizing effect, irrespective of their proximity to the calcium binding sites. Stabilizing mutations in subtilisin fall into one of three classes. The largest class of mutations stabilize only in the presence of excess calcium. A smaller number of mutations stabilize independently of [calcium], and a few mutations stabilize only in the presence of chelating agents, such as EDTA. This study compares the effects of mutations from each class when introduced into subtilisin BPN' and two calcium-free versions of subtilisin. The calcium-dependent effects of mutations can be explained by considering subtilisin to be in conformational equilibrium between two structurally similar but energetically distinct states: N and N*. The equilibrium from the N* to the N state can be altered either by calcium binding to site A or by mutation. Mutations which stabilize only in the presence of calcium stabilize the N state relative to N*. Mutations which stabilize only in the presence of chelants stabilize the N* state relative to N. As a byproduct of this analysis, we have developed a hyperstable variant of subtilisin whose inactivation at high temperature in the presence of EDTA is 10(5) times slower than wild-type subtilisin.