To understand the nature of the linkage between chromophore and apoprotein in the photoreceptor of Stentor coeruleus, a conformational analysis has been carried out on the dipeptide amides linked to the chromophore hypericin using an empirical potential function. The conformational energies for the dipeptide amides of Glu (OHyp)-X-NHMe, where X = Leu, Phe, Asp, and Tyr, have been calculated to investigate the influence of peptide residues in stabilizing conformers. It was found that the increase of acidity of hypericin upon photoexcitation may be facilitated by the formation of intramolecular hydrogen bonds between hydroxyl groups of hypericin and carbonyl groups of peptide backbone, and that the stabilities of dipeptide amides do not significantly depend on peptide residues directly linked to chromophore.