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Notes:
Secondary structure is a protein structure that is formed by hydrogen bonding along the backbone. It is not dependant on side chains. It contains the primary structure, but now contains secondary structure, meaning it has more going on than just linear peptide bonds.
Alpha Helices: This helix structure contains hydrogen bonds between the C=O group and N-H group 4 residues ahead.
Beta Sheets: This is a flatter structure that is formed between adjacent beta strands. These strands may be parallel, meaning they run in the same direction, or antiparallel, meaning they run in opposite directions.
Parallel strands must have a long strand in the background in order to line up the two sheets properly.
Peptide flexibility
The peptide bond is planar, meaning that there is no rotation and it must move on the same plane. However, there are other axises that do allow rotation.
These are Phi and Psi bonds.
The Phi bond is between the Amino Nitrogen and the alpha Carbon.
The Psi bond is between the alpha Carbon and the carbonyl Carbon.
The Ramachandran Diagram shows every combination of Phi and Psi bonds possible. As you can see, there are certain angles where different secondary structures form. The pink areas are the most commonly found angle combinations. As you can see, when the two bonds are almost around 135 degrees Psi and -135 degrees Phi, a beta sheet is favored. Conversely, the helix is found around (-)40 degrees Psi and (-)60 degrees Phi. The right handed helix in the bottom left quadrant is more common than the left. This is because they are more energetically favorable!
Lets go over some general characteristics:
The white space is where there are steric clashes and molecule orientation will not occur.
The orientations in blue occur but are less likely.
The orientations in pink occur most frequently.
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