Objective: It has been demonstrated that there are structural and functional similarities between interferon-α (INF-α) and endorphins. We have reported that there are distinct domains in the IFN-α molecule that mediate immune and analgesic effects, respectively, and that the opioid-like analgesic effect of IFN-α is mediated by the µ opioid receptor, thus inferring that the analgesic domain of IFN-α consists of Tyr122 and the residues around Tyr122 in the tertiary structure. The aim of this work was to further explore the molecular basis for the analgesic domain of IFN-α. Methods: By using site-directed mutagenesis, the structure of IFN-α was changed and a mutant of IFN-α was obtained. Then, the antiviral activity and opioid-like analgesic activity of IFN-α were measured. Results: When the Pro39 residue of IFN-α, which is located close to the Tyr122 residue in the tertiary structure, was mutated to Gly, the analgesic activity of this mutant was lost completely, but the antiviral activity of IFN-α was maintained compared with wild-type IFN-α. Conclusions: Combining the sequence of the endomorphin, it is suggested that the Pro39 residue is one of the constituents of the analgesic domain of IFN-α and contributes to IFN-α binding to the µ opioid receptor.