Electrospray ionization mass spectrometry was used to measure the binding of copper and nickel ions to the newly synthesized model peptides H(2)N-AAAAHAAAAHAAAAHAAAA-COOH (P19-H5) and H(2)N-AAAHAAAHAAAHAAAAAAA-COOH (P19-H4). The affinity of histidine-containing peptides toward heavy metal ions proved to be related to the position of each histidine residue in the peptide sequence. In contrast to P19-H5, P19-H4 peptide bound no nickel or copper ions in the gas phase, whereas its spectra showed an intense fragmentation. The role of spacing residues (Ala repeats) in selecting the various conformations was also investigated. Finally, the circular dichroism and Fourier transform infrared spectra indicated that these isomer peptides have quite different conformations. A close relationship between the conformation of alanine-based peptides and their affinity toward metal ions may result in different patterns of metal ion-peptide systems.