The membrane-bound closed channel structure of helices 4 and 5 (Lys-406-Asp-446) of the colicin E1 channel domain was investigated by using a site-directed fluorescence labeling technique. A bimane probe was covalently attached to a cysteine residue in a series of single-cysteine mutant proteins to scan each helix in a residue-by-residue fashion. A variety of fluorescence properties of the bimane fluorophore were measured for both the soluble and membrane-bound states of the channel peptide, including the fluorescence emission maximum, fluorescence anisotropy, and membrane bilayer penetration depth. The fluorescence properties were collated for construction of a membrane-bound topology model of helices 4 and 5 of the channel domain. Finally, the data reveal that both helices 4 and 5 are two separate amphipathic alpha-helices that are situated parallel to the membrane surface. Dual fluorescence quencher analysis shows that helix 4 adopts a tilted topology in which its C-terminus is more buried than its N-terminus within the bilayer. In contrast, helix 5 is relatively solvent-exposed and located parallel to the interfacial region of the membrane surface. However, the loop region of both helices 4 and 5 was shown to be relatively buried within the bilayer. In addition, a least-squares fit of the data to a harmonic wave function indicated that both periodicity and frequency are typical for an amphipathic alpha-helix (3.75 +/- 0.1 residues per turn for helix 4 and 3.70 +/- 0.1 residues per turn for helix 5). Squared residual plots of the harmonic wave function also reveal that the N-terminus of helix 4 is elongated by two residues from Lys-406 to Phe-404, while the C-terminus of helix 5 is elongated by three residues from Tyr-434 to Ile-437 upon membrane association.