Biochemistry I Secondary Structural Elements
 
  Peptide Bond
 Ala-Ala Trans
 Ala-Ala cis
 
 Ala-Pro Trans   
 Ala-Pro cis  
Protein G:
 Protein G
 remove sidechains
   Protein G [cartoon]

Secondary Structure:
  a-helix (R)
 
  helix (L)
 3-10-helix

 b-stand.
 || b-sheet.
 anti || b-sheet.

 
 
 
Notes:
  1. In trans peptide bond the amide proton is opposite from the carbony oxygen. In a cis peptide bond they are on the same side. The close contacts between the a carbons and other side-chain atoms cause the cis bond to be higher in energy.
  2. The peptide bond before a proline is unfavourable as either cis or trans due to crowding. The energy of the trans bond is increased such that it is now only slightly more favourable than the cis configuration.
  3. a-Helix
    • Usually right-handed
    • 3.6 residues/turn
    • 5.4 A rise/turn
    • i, i+4 residues form H-bonds
    • H-bonds || to helical axis
    • Side chains point outward.
  4. 3-10 helix
      i, i+3 residues form H-bonds
    • Hbonds not || not || to helical axis
    • Thinner than a-Helix
  5. b-Strand
    • Highly extended (F,Y=180)
    • 2 residues/'turn'
    • 6.6 A rise/turn
    • hydrogen bonds: N/A
  6. b-Sheets
    • Two types, || and anti-||
    • inter-chain hydrogen bonds
    • zig-zag pattern
    • Side chains alternate up-and-down
Last modified December 14, 2007.