secondary structure

secondary structure

stable local arrangements of polypeptide backbone atoms → areas of contiguous a.a (lowest free energy)

• primarily stabilized by H-bonds

alpha helix

most common

• 3.6 aa/turn

• 5.4 A/turn

• 1.5 A/aa

aa(n) h bonds with aa (n+4)

R-groups interact via ionic or hydrophobic non-covalent interactions

• aa(n) interacts with aa (n + 3/4)

• NO glycine or proline (helix breakers)

• Ala>Arg>Lys>Leu>Met

310 helices

• 3 aa/turn

• 6 A/turn

• 2 A/aa

Stabilized by H-bonds

• weaker than alpha helix due to being farther apart and NOT inline

aa(n) h-bonds with aa(n+3)

• normally intermediate to alpha helix

B-strand

segment of polypeptide with all aa in B-conf.

• 3.5 A/aa (extremely stretched out)

• R groups alternate above and below plane (3-10 aa common)

• formatted in ribbon diagram

• arranged in sheets

B-sheets

multiple B-strands arranged side by side

• H-bonding = primary stabilizing force between backbone atoms

Antiparallel

• H-bonding strong due to being in line

Parallel

• requires more H-bonding to stabilize

• H-bonding weaker because not in line with

R-groups alined:

• glycine and alanine do not interact due to not being big enough

Glycine - rare

Proline - rare but if present will be on edge

B-turn

glycine and proline common at positions 2 and 3

• glycine adopts phi and psi bonds

• proline - introduces a sharp “ridgid” bend

random coil

absence of secondary structures

• no repeating pattern of phi and psi bonds

• no regular pattern of H-bonding

• typically about 5aa in length

loops

backbone reverses direction

• proline common - able to bend chain

terminal arms

very dynamic and long

• near the N’ and C’ terminals