Helix and Sheet Problem Set

1) Draw a helical wheel for G helix of whale myoglobin. To do this you must open the myoglobin PDB file (see link on the a-helix web page) with a text editor. Scroll down and find the fields giving the residue numbers of the helices. Figure out the G helix sequence from looking through the rest of the file. Draw the helical wheel. Identify the hydrophobic and hydrophilic faces of the helix.

2) For an alpha helix, what are the pitch (rise per turn), the number of residues per turn, and the rise per residue?

3) Two alpha helices can pair to form a coiled-coil (a helix of helices). See alpha-keratin (book, page 132) or the GCN4 structure on the a-helix page for an example. For the resulting super helix, what would you expect for the helical pitch (rise/turn)? To determine this you need to consider the parameters in #2.

4) Design a 36 residue peptide that seems likely to form a beta-sheet with a hydrophobic face and a hydrophilic face.