Earlier studies have shown that the helical content of α-helical peptide decreases upon its interaction with carbon nanotube (CNT). Further, the length of the α-helix varies from few residues in the small globular protein to several number of residues in structural and membrane proteins. In structural and membrane proteins, helices are widely present as the supercoil i.e., helical bundles. Thus, in this study, the length-dependent interaction pattern of α-helical peptides with CNT and the stability of isolated α-helical fragment versus supercoiled helical bundle upon interaction with CNT have been investigated using classical molecular dynamics (MD) simulation. Results reveal that the disruption in the helical motif on interaction with CNT is directly proportional to the length of the helix. Also it is found that the shorter helix does not undergo noticeable changes in the helicity upon adsorption with CNT. On the other hand, helicity of longer peptides is considerably affected by its interaction with CNT. In contrast to the known fact that the stability of the helix increases with its length, the disruption in the helical peptide increases with its length upon its interaction with CNT. Comparison of results shows that structural changes in the isolated helical fragment are higher than that in supercoiled helix. In fact, helical chain in supercoiled bundle does not undergo significant changes in the helicity upon interaction with CNT. Both the length of the helical peptide and the inherent stability of the helical unit in the supercoiled helix influence the interaction pattern with the CNT. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 357–369, 2013.