Effects of the residues on the excitation energies of protonated Schiff base of retinal (PSBR) in bacteriorhodopsin have been investigated by means of time-dependent density functional theory. The residues around PSBR are replaced by the point charges on atoms. The structures of PSBR and residues are referred from X-ray data. The atomic charges on the each residue were calculated the B3LYP/6-311G(d,p) level. The excitation energy of PSBR perturbed by the point charges on atoms of each residue was calculated at the B3LYP/6-31G(d,p) level. A total of 23 residues and five water molecules around PSBR were considered in the calculations. The large spectral shifts were caused by the Asp212 and Asp85. The origin of the spectral shifts was discussed on the basis of theoretical results.