The excitation energy transfer (EET) between a fluorescent resonance energy transfer (FRET) pair, cyan fluorescent protein chromophore (CFPc)/ green fluorescent protein chromophore (GFPc), is used for measuring molecular proximity in experimental studies. In this article, the role of the bridging protein media has been investigated using the quantum chemical calculations for the EET electronic coupling. We adopted a model peptide connecting GFPc and CFPc, a GFPc-X-CFPc model, and examined the X (amino acids) dependence. The major part of the EET coupling element arises from the direct interaction between GFPc and CFPc via the Förster mechanism. The magnitude of the through-X interactions vary for the type of residues. The contribution of the X was, however, at most 10% of the total value. Together with the contributions from through-peptide and charge-transfer types, X gives minor modifications to the total coupling via the super-exchange mechanism. © 2012 Wiley Periodicals, Inc.