In the web-lecture #5, the picture labeled "Alpha-helix 3.6 aa's per
turn", the "chain links" are shown as NHCRHCOs (the R and one of the H's are
implied),with the nitrogen being on the same plane as the _second_ nearest
carboxyl carbon. However, in the diagram immediately preceding this depiction,
we see that the pivot carbon is actually the carbon that is attached to the R,
suggesting that a nitrogen would be on the same plane with it's _nearest_ carboxyl
carbon, but not it's second nearest. Have I overlooked something or am I
viewing it wrong?
I can understand your confusion. The blue "plates" in the lecture
diagram to which you refer are not meant to represent atoms in a plane but just
amino acid residues, so that they would be easy to count in the search foir the NH
H-bond donor.