Protein Classification and Structure Prediction Amino acid ...

Properties of the alpha helix
• φ ≈ ψ ≈ −60°
• Hydrogen bonds
between C=O of
residue n, , and
NH of residue
n+4
• 3.6 residues/turn
• 1.5 Å/residue rise
• 100°/residue turn
Properties of a-helices
• 4 – 40+ residues in length
• Often “dual-natured”
• Half hydrophobic and half hydrophilic
• Mostly when surface-exposed
exposed
• For many α-helices
• Helix formers: Ala, Glu, Leu,
Met
• Helix breakers: Pro, Gly, Tyr,
Ser
Krane & Raymer
Krane & Raymer
The beta strand (& sheet)
φ ≈ − 135°
ψ ≈ +135°
Properties of beta sheets
• Formed of stretches of 5-105
residues in extended
conformation
• Pleated – each C α a bit above or
below the previous
• Parallel/aniparallel
aniparallel,
contiguous/non-contiguous
Krane & Raymer
Parallel and anti-parallel
b-sheets
Anti-parallel is slightly energetically favored
Anti-parallel
Parallel
Turns and Loops
• Secondary structure elements are connected by regions
of turns and loops
• Turns – short regions
of non-α, , non-β
conformation
• Loops – larger stretches with no secondary structure.
Often disordered.
• “Random coil”
• Sequences vary much more than secondary structure regions
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