1. C to C Phi φ
N to N Psi ψ
Takes 4 atoms to define rotation
about a bond!
Trans vs. Cis peptide bonds
Trans, carbonyl oxygen is on opposite side of peptide bond from amide hydrogen
Fischer & Sumner Proteins have regular structure
Hydrophobic effect
Helices (, 310, π) n to n+4, n to n+3, n to n+5
 has 3.6 residues/turn, 1.5Å rise/residue
-sheets parallel, antiparallel, mixed 3.5Å (C - C)
Turns Must connect secondary structure somehow –
usually not regular structure so backbone exposed

2. Sequence preference for helices, sheets, turns(loops)
Helices usually are amphipathic, so are sheets! Where do the sidechains point?
Motifs H-L-H, -H-, -hairpin, Greek key
Ramachandran diagrams – 3 major regions (B, A, L)
Staggaered conformation of sidechains (rotomers)
Supersecondary structure
Domains, mosaic proteins
Tertiary, Quaternary structure
 structures,  structures, / structures,  +  structures

3. Where might you guess is the active site??

4. A crystallographic view of interactions between Dbs and Cdc42:
PH domain-assisted guanine nucleotide exchange
Kent L. Rossman,1 David K. Worthylake,2 Jason T. Snyder,
1 David P. Siderovski,2,3 Sharon L. Campbell,1,3 and John Sondek1,2,3,4

15. Nature Reviews Molecular Cell Biology 6, 167-180 (2005);