Cis amides in cyclic peptides

[isohelio]

Hi,

I'm using pyPept to build simple peptide macrocycles. I'm finding the BILN notation extremely useful for this and the pyPept interface is very straightforward to use.

Unfortunately, there seems to be a problem with the geometry of peptide bonds in cyclic peptides. If I build a simple linear deca-alanine then the geometry is all sensible, entirely trans peptide bond (N-H points away from C=O).

run_pyPept --biln A-A-A-A-A-A-A-A-A-A

If I cyclise that structure then essentially all of the peptide bonds become cis (N-H points in same direction as C=O).

run_pyPept --biln 'A(1,1)-A-A-A-A-A-A-A-A-A(1,2)'

I think non-proline peptide bonds are nearly always trans even in relatively small cyclic peptides.
e.g. as seen in PDB structure 7zkr.

Is this a known problem, or a misunderstanding on my part?

Many thanks,
Mikie

[isohelio]

Attaching pdb file output for the two structures.

pept.zip