My textbook in biochemistry ("Biochemistry" - Berg,Tymoczom Gatto, Stryer) tells me that:
"Almost all peptide bonds in proteins are trans" (p. 40)
At the same time, it states the following regarding the structure of the $\alpha$-helix:
"A tightly coiled backbone forms the inner part of the rod and the side chains point outwards" (p.42)
How do I reconcile these two statements?
If the peptide sequence in an $\alpha$-helix is predominantly trans, that would imply that every other amino acid residue would point inwards, towards the center of the helix.
Does this imply that peptide sequences involved in $\alpha$-helixes are predominantly cis, or that the amino acid residues pointing towards the center of the helix must be very short, like for instance glycine?