Troponin C (TnC) is an EF-hand Ca(2+) binding protein that regulates skeletal muscle contraction. The mechanisms that control the Ca(2+) binding properties of TnC and other EF-hand proteins are not completely understood. We individually substituted 27 Phe, Ile, Leu, Val, and Met residues with polar Gln to examine the role of hydrophobic residues in Ca(2+) binding and exchange with the N-domain of a fluorescent TnC(F29W). The global N-terminal Ca(2+) affinities of the TnC(F29W) mutants varied approximately 2340-fold, while Ca(2+) association and dissociation rates varied less than 70-fold and more than 45-fold, respectively. Greater than 2-fold increases in Ca(2+) affinities were obtained primarily by slowing of Ca(2+) dissociation rates, while greater than 2-fold decreases in Ca(2+) affinities were obtained by slowing of Ca(2+) association rates and speeding of Ca(2+) dissociation rates. No correlation was found between the Ca(2+) binding properties of the TnC(F29W) mutants and the solvent accessibility of the hydrophobic amino acids in the apo state, Ca(2+) bound state, or the difference between the two states. However, the effects of these hydrophobic mutations on Ca(2+) binding were contextual possibly because of side chain interactions within the apo and Ca(2+) bound states of the N-domain. These results demonstrate that a single hydrophobic residue, which does not directly ligate Ca(2+), can play a crucial role in controlling Ca(2+) binding and exchange within a coupled and functional EF-hand system.