The comparative analysis of spatial structure of β- and ϒ-melanotropins, which stimulate physiological and morphological changes of skin and hair coloration, have been conducted. By the molecular mechanics, molecular dynamics, quantum chemical methods and modern computer programs the conformational-electronic peculiarities characterized the spatial structure of these peptides are revealed. On the basis received results and data of the structure-functional investigations the biologically active conformation of melanotropins was assessed. It was found the stability of spatial structure of melanotropins is defined by mutual arrangement of pharmacophore elements: the aromatic rings the side chains of the tyrosine, phenylalanine and triptofan residues and charged ganidine group of Arg and characterized by a specific distribution of electron density, that plays an important role in the interaction with the receptor. The conformational-electron similarity of the "common fragment" suggests that the helical structure of the His-Phe-Arg-Trp tetrapeptide fragment of melanotropins provides the specificity of melanotropin-receptor.