Involved in numerous key biological functions, protein helix-helix interactions follow a well defined intermolecular recognition pattern. The characteristic structure of the α-helical coiled-coil allows for the specific randomization of clearly defined interaction partners within heteromeric systems. In this work, a rationally designed heterodimeric coiled-coil, VPK/VPE, was used to investigate potential factors influencing the sequence selectivity in interhelical interactions. In a phage-display screen, a single enriched sequence was isolated from a peptide library, in which three hydrophobic core positions had been fully randomized. The original sequence, VPE, and the sequence selected by phage display, VPE-L16Y23, both form heterodimeric coiled-coils with VPK; but the former exhibits higher thermal stability than the latter. In order to investigate these two systems, molecular dynamics simulations were carried out and possible assembly processes of the parent sequence and the selected variant were studied in silico.