Peptides selected from phage-displayed libraries have been found to exhibit high-affinity binding to carbon nanotubes including single-walled carbon nanotubes (SWNTs), multi-walled carbon nanotubes, and single-walled carbon nanohorns. One unique feature of these peptides is that their amino acid sequences are rich in tryptophan and histidine residues. The aim of this study was to investigate the importance of the tryptophan residue in a newly identified SWNT-binding peptide, UW-1, which contains the motif, XTHXXPWTX, where X is any amino acid. Tryptophan was altered in the following ways: mutation to alanine or substitution with three unnatural tryptophan analogues, i.e., 5-fluorotryptophan, 5-hydroxytryptophan, and 7-azatryptophan. Analysis of experimental and computational data suggests that the highest occupied molecular orbital of the tryptophan residue in the peptide interacts with the lowest unoccupied molecular orbital from the SWNT. This information should be important in permitting modulation of peptide affinities to these nanomaterials.