HIV gp41 is the transmembrane glycoprotein responsible for fusion of viral and cellular membranes, enabling viral entry. The structure of gp41 was studied using two synthetic peptides derived from the ectodomain of gp41: a 38-residue peptide from the "heptad repeat" region (hr.wt), and a 34-residue peptide from a region closer to the C-terminus (bt wt). These peptides were found to form a trimer of heterodimers with approximately 80% alpha-helicity. To study their alignment, distances between spin-labels attached to Cys residues on Cys-substituted peptides were measured using a recently-developed electron paramagnetic resonance method [Rabenstein, M.D., & Shin, Y.-K. (1995) Proc Natl. Acad. Sci. U.S.A. 92, 8239-8243]. The heterotrimeric peptides were found to be antiparallel, consistent with a study on proteolytically cleaved peptide fragments of gp41 [Lu, M., Blacklow, S.C., & Kim, P.S. (1995) Nat. Struct. Biol. 2, 1075-1082]. Furthermore, the C-terminal 19 residues of hr.wt are not apposed to bt.wt, and 15 residues of bt.wt extend beyond the end of br.wt. Consistent with this alignment are tertiary interactions between specific sites of these peptides probed by spin-label mobility. Additionally, a second pair of peptides was studied. From the model, these are expected to align with complete overlap. Alone, neither was helical, but when mixed, they were 83% helical. Based on the alignment of the peptides, a model of the prefusogenic form of gp41 was constructed which is significantly different from the structure of influenza hemagglutinin.