Intermolecular structures are important factors for understanding the conformational properties of amyloid fibrils. In this study, vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy and circular dichroism (CD) theory were used for characterizing the intermolecular structures of beta(2)-microglobulin (beta(2)m) core fragments in the amyloid fibrils. The VUVCD spectra of beta(2)m(20-41), beta(2)m(21-31), and beta(2)m(21-29) fragments in the amyloid fibrils exhibited characteristic features, but they were affected not only by the backbone conformations but also by the aromatic side-chain conformations. To estimate the contributions of aromatic side-chains to the spectra, the theoretical spectra were calculated from the simulated structures of beta(2)m(21-29) amyloid fibrils with various types of beta-sheet stacking (parallel or antiparallel) using CD theory. We found that the experimental spectrum of beta(2)m(21-29) fibrils is largely affected by aromatic-backbone couplings, which are induced by the interaction between transitions within the aromatic and backbone chromophores, and these couplings are sensitive to the type of stacking among the beta-sheets of the fibrils. Further theoretical analyses of simulated structures incorporating mutated aromatic residues suggested that the beta(2)m(21-29) fibrils are composed of amyloid accumulations in which the parallel beta-sheets stack in an antiparallel manner and that the characteristic Phe-Tyr interactions among the beta-sheet stacks affect the aromatic-backbone coupling. These findings indicate that the coupling components, which depend on the characteristic intermolecular structures, induce the spectral differences among three fragments in the amyloid fibrils. These advanced spectral analyses using CD theory provide a useful method for characterizing the intermolecular structures of protein and peptide fragment complexes.