The structure of phycobiliproteins and their spatial organization in the phycobilisome provide the environment for high efficiency in light harvesting and conduction towards photosystem II. This article focuses on the analysis of R-phycoerythrin, a light harvesting hexameric phycobiliprotein that is part of the phycobilisomes. The interaction surfaces and the environment of the chromophores of R-phycoerythrin were studied in order to explain its structural stability and spectroscopic sensitivity, properties revealed by perturbation experiments. Three interaction surfaces are described (alpha beta), (alpha beta)3 and (alpha beta)6. The analysis shows the importance of alpha subunits in the interaction between trimers, the homodimeric nature of the monomer (alpha beta) and also the presence of anchor points in every interaction surface studied: alpha18Phe and beta18Tyr for (alpha beta), beta76Asn for (alpha beta)3 and alpha25Asn for (alpha beta)6. Side chains of arginine, lysine or glutamine residues are located in the proximity of the chromophores providing the correct stabilization of their carboxylates. Aspartic acids residues are associated through H-bonds to the N atom of the two central rings of the tetrapyrrolic chromophores. Changes in the spectroscopic properties are observed in perturbation experiments, confirming the spatial requirement for an efficient resonance energy transfer among chromophores and through the phycobilisome.