The chromophore/protein interactions in the photocycle intermediates of photoactive yel- low protein (PYP) were probed by site-directed mutagenesis. The absorption spectra of L- intermediates produced from E46Q, T50V, and R52Q mutants were calculated using the absorption spectra of dark states and difference absorption spectra between L-intermediates and dark states, and compared with that of PYP$\_$L/. The absorption spectrum of R52Q$\_$L/ agreed with that of PYP$\_$L/, but those of E46Q$\_$L/ and T50V$\_$L/ were red-shifted. The effect of these mutations on the absorption spectrum for L-intermediate was comparable to that for the dark state, suggesting that the interaction around the phe-nolic oxygen of the chromophore is conserved in PYP$\_$L/ unlike the crystal structure. On the other hand, we have reported that the absorption spectra of Y 42F$\_$M/, T50V $\_$M/, and R52Q$\_$M/ agreed with that of PYP$\_$M/, but that of E46Q$\_$M/ was red-shifted, suggesting that the hydrogen bond of the chromophore with Glu46 is conserved but that with Tyr42 is broken in PYP$\_$M/. These results suggest that the chromophore inter-acts with Glu46 throughout the photocycle, but never directly interacts with Arg52. This model con- flicts with some of the structural model of PYP intermediates proposed based on the high-resolution X -ray crystallography.