The integral matrix protein M2 of the influenza A virus (H3N2) has been proposed to form a proton-selective channel, and is a target of the antiviral drug amantadine hydrochloride (Am). A significant increase in the number of drug-resistant strains containing the predominant M2-S31N mutant have emerged. We have previously developed a stoichiometric analysis of oligomeric states of membrane proteins by utilizing a coiled-coil method and fluorescence resonance energy transfer phenomenon and demonstrated that full-length M2-WT proteins in living cells formed a dimer at neutral pH, which was converted to a tetramer at acidic pH. In the present study, we revealed that the M2-S31N mutant stably formed dimers independent of pH, which was stabilized by multiple interactions between the protomers. We also found that neither the channel activity nor the oligomeric state of S31N were affected by Am. Molecular dynamics (MD) simulations revealed that Asn31 and Ile35 are involved in proton conduction via steady interactions with cholesterol. These results indicate that Am resistance could be attributed to a change in the arrangement of helices interfering with drug binding.