The peptide sequence KLVFFAE that spans the region 16-22 in the amyloid peptide Aβ1-40 has the ability to form fibrils or nanotubes in aqueous medium, depending on the conditions of dissolution. Interaction between the phenylalanine residues is presumed to play an important role in the self-assembly of Aβ16-22. We have investigated the importance of these aromatic residues by substituting them with p-chloro-, p-fluoro- and p-methylphenylalanine. Nanostructures different from the parent peptide were obtained with the substituted analogs, both in methanol as well as aqueous conditions (pH 2 and pH 7). Concentration-dependent effects observed in methanol, suggest that intermediate states occur during fibrillation. A balance between the crucial parameters such as charge, hydrophobicity and steric constraints implicated in self assembly, appear to modulate the nanostructure formation.