We have previously shown that a 34-residue synthetic peptide representing the calcium-binding site I11 of troponin C formed a symmetric two-site dimer consisting of two helix-loop-helix motifs arranged in a head-to-tail fashion (Shaw, G.S., Hodges, R.S., & Sykes, B.D., 1990, Science249, 280-283). In this study the hydrophobicities of the a-helices were altered by replacing L-98 and F-102 in the N-terminal region and/or 1-121 and L-122 in the C-terminal region with alanine residues. Our results showed that substitution of hydrophobic residues either in the N-or C-terminal region have little effect on a-helix formation but resulted in a 100-and 300-fold decrease in Ca2+ affinity, respectively. Simultaneous substitution of both hydrophobes in the N-and C-terminal region resulted in a 1,000-fold decrease in Ca2+ affinity. Data from guanidine hydrochloride denaturation studies suggested that intermolecular interactions occur and that the less hydrophobic analogs had a lower overall conformational stability. These data support the contention that the hydrophobic residues are important in the formation of the two-site domain in troponin C, and this hydrophobic association stabilizes Ca2+ affinity.