GCN4 protein from yeast; only a part of the full protein is shown here, that which corresponds to the leucine zipper motif, bound to a fragment of DNA.
Each chain is displayed using a different colour: the 2 DNA strands and 2 chains in the protein.
The structure common with other proteins, and hence called the motif, consists of the two peptide segments in alpha helix, which themselves coil slightly around each other (so forming a coiled coil). At one end, these helices interact with each other, and at the other end they interact with specific sequences of bases in the major groove of DNA.
to appreciate the mutual coiling of the two helicoid protein chains.
The interaction between the two helices is mainly kept thanks to the interaction between leucine sidechains, located every 7 residues in the sequence (that is, nearly 2 turns of the alpha helix).
On the other hand, in the region contacting DNA there is an abundance of positively charged amino acids, like arginine.
Spacefilling model
Enlarged view of one of the contacts between leucines from both chains (sidechains in a darker tint, other amino acids in CPK colour: CON).