This is what the CASP organizers have told us about this protein:

CASP targets T0797 and T0798 are two parts of the PKGII leucine zipper /Rab11b complex comprising two zipper subunits and two Rab11b subunits...
The main modeling task here is to get structure of the leucine zipper in correct conformation with the Rab11b GTPase that remodels upon binding.

http://predictioncenter.org/casp11/target.cgi?id=51

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Here is the sequence logo predicted by the SAM server:

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

I think you are saying the native contains two helices (which make a leucine zipper) and two blobs, and we have been given one helix and one blob to stick together. The leucines on our helix are supposed to stick to the leucines on the other helix, so they should not be hidden by the blob.

I like blobs almost as much speghetti