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

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

Where might you guess is the active site??

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

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