The exact sites, structures, and molecular mechanisms of interaction between junction organizing zona occludence protein 1 (ZO-1) and the tight junction protein occludin or the adherens junction protein alpha-catenin are unknown. Binding studies by surface plasmon resonance spectroscopy and peptide mapping combined with comparative modeling utilizing crystal structures led for the first time to a molecular model revealing the binding of both occludin and alpha-catenin to the same binding site in ZO-1. Our data support a concept that ZO-1 successively associates with alpha-catenin at the adherens junction and occludin at the tight junction. Strong spatial evidence indicates that the occludin C-terminal coiled-coil domain dimerizes and interacts finally as a four-helix bundle with the identified structural motifs in ZO-1. The helix bundle of occludin406-521 and alpha-catenin509-906 interacts with the hinge region (ZO-1591-632 and ZO-1591-622, respectively) and with (ZO-1726-754 and ZO-1756-781) in the GuK domain of ZO-1 containing coiled-coil and alpha-helical structures, respectively. The selectivity of both protein-protein interactions is defined by complementary shapes and charges between the participating epitopes. In conclusion, a common molecular mechanism of forming an intermolecular helical bundle between the hinge region/GuK domain of ZO-1 and alpha-catenin and occludin is identified as a general molecular principle organizing the association of ZO-1 at adherens and tight junctions.