In this study, we investigate the excited states and absorption spectra of a natural light-harvesting system by means of subsystem density functional theory. In systems of this type, both specific interactions of the pigments with surrounding protein side chains as well as excitation energy transfer (EET) couplings resulting from the aggregation behavior of the chromophores modify the photophysical properties of the individual pigment molecules. It is shown that the recently proposed approximate scheme (J. Chem. Phys. 2007, 126, 134116) for coupled excitations within a subsystem approach to time-dependent DFT is capable of describing both effects in a consistent manner, and is efficient enough to study even the large assemblies of chromophores occurring in the light-harvesting complex 2 (LH2) of the purple bacterium Rhodopseudomonas acidophila. A way to extract phenomenological coupling constants as used in model calculations on EET rates is outlined. The resulting EET coupling constants and spectral properties are in reasonable agreement with the available reference data. Possible problems related to the effective exchange-correlation kernel are discussed.