Results of molecular dynamics simulations of different stoichiometric complexes constituted by poly(alpha,L-glutamate) and oppositely charged amphiphilic surfactants (n-hexylammonium, n-dodecylammonium, n-hexyltrimethylammonium and n-dodecyltrimethylammonium) are presented. Simulations were performed in dilute chloroform solution using explicit solvent molecules. It is shown that the conformation of the polypeptide chain is strongly influenced by the constitution of the surfactant polar headgroup. Thus, the polypeptide adopts a canonical alpha-helix conformation in complexes containing n-alkyltrimethylammonium surfactants, while a nonregular but also elongated conformation was found in complexes formed by alkylammonium surfactants. The latter structure is due to the interaction of alkylammonium cations with the amide group of the polypeptide chain. On the other hand, we show the intrinsic tendency of the molecular cations to form multiple interactions with the polypeptide chain, independently of their constitution.