Systematic N-methylated derivatives of the melanocortin receptor ligand, SHU9119, lead to multiple binding and functional selectivity toward melanocortin receptors. However, the relationship between N-methylation-induced conformational changes in the peptide backbone and side chains and melanocortin receptor selectivity is still unknown. We conducted comprehensive conformational studies in solution of two selective antagonists of the third isoform of the melanocortin receptor (hMC3R), namely, Ac-Nle-c[Asp-NMe-His⁶-d-Nal(2′)⁷-NMe-Arg⁸-Trp⁹-Lys]-NH₂ (15) and Ac-Nle-c[Asp-His⁶-d-Nal(2′)⁷-NMe-Arg⁸-NMe-Trp⁹-NMe-Lys]-NH₂ (17). It is known that the pharmacophore (His⁶-DNal⁷-Arg⁸-Trp⁹) of the SHU-9119 peptides occupies a β II-turn-like region with the turn centered about DNal⁷-Arg⁸. The analogues with hMC3R selectivity showed distinct differences in the spatial arrangement of the Trp⁹ side chains. In addition to our NMR studies, we also carried out molecular-level interaction studies of these two peptides at the homology model of hMC3R. Earlier chimeric human melanocortin 3 receptor studies revealed insights regarding the binding and functional sites of hMC3R selectivity. Upon docking of peptides 15 and 17 to the binding pocket of hMC3R, it was revealed that Arg⁸ and Trp⁹ side chains are involved in a majority of the interactions with the receptor. While Arg⁸ forms polar contacts with D154 and D158 of hMC3R, Trp⁹ utilizes π–π stacking interactions with F295 and F298, located on the transmembrane domain of hMC3R. It is hypothesized that as the frequency of Trp⁹-hMC3R interactions decrease, antagonistic activity increases. The absence of any interactions of the N-methyl groups with hMC3R suggests that their primary function is to modulate backbone conformations of the ligands.