Secondary Structure

Alpha Helix

Cylinder following the same rise as a screw

3.6 residues per rotation, or 100 degrees per residue. 1.5 length rise along the cylinder.

is 0.1 nm

H bonds between C'O and NH of residues n and n+4.

Proline bends the alpha helix due to steric collisions and lacks H bond as the N is looped onto the C alpha.

Dipole moment is a charge added up by all the H bonds. The N terminus of the alpha helix is positive, so negatively charged molecules like phosphate ions bind to the N end of helices.

Beta Sheets

Comprised of beta strands. These are drawn as arrows in tertiary structure.

Strands can be parallel or anti parallel.

Again, H bonds between NH and CO

R alternates above and below the sheet.

Draw the bonds at approx hexagonal angles.

For parallel, draw them as > > , with N aligned

For anti-parallel, draw them as > <, with Cα in the middle.

An anti-parallel beta sheet can be made from 2 beta strands joined by a reverse turn or short hairpin loop.

A reverse turn is 2 residues. Draw C'=O H bond to N, then add 2 more residues without any H bonds.

Loops

Active sites

Different between homologous proteins

polar, charged, happy in aqueous environment.

Angles Phi and Psi and Omega

There is a plane around C', N, and Cα.

The Cα atom is at the corner of each plane.

Phi Φ (circle with vertical line through it), is bond rotation between the N and C alpha atom. Defined as 4 atoms C', N, Cα, C'

Psi Ψ (pitchfork), is bond rotation between Cα and C' atom. Defined as 4 atoms N, Cα, C', N.

Ramachandran plot. Show regions for beta sheet, alpha helices and left alpha helix.