The loss of surface area accessible to solvent associated with coenzyme binding in Clostridium flavodoxin, in dogfish lactate dehydrogenase and in lobster glyceraldehyde-3-phosphate dehydrogenase was calculated. The coenzymes are nearly buried in the complexes and lose on the order of 600 .ANG.2, while the proteins lose a similar amount of accessible surface area. Some of the loss can be attributed to conformation changes in the protein, at least in the case of lactate dehydrogenase, were it was shown that the apoenzyme has a larger accessible surface area than the holoenzyme. Using known correlations with the hydrophobic contribution to the free energy, it was demonstrated that hydrophobicity is the major source of stabilization free energy in FMN binding to flavodoxin and in NAD binding to the 2 dehydrogenases: it contributes 25-30 kcal/mol to the free energy of dissociation, more than required in order to compensate for the loss of 6 degrees of translational/rotational freedom by the coenzyme.