User:Karsten Theis/turns

Here is a turn (reload original ) that you can explore with the buttons below. To get a low energy conformation, you want a good hydrogen bond, i.e. carbonyl oxygen, amide hydrogen and nitrogen colinear , and want to avoid any clashes, e.g. carbonyl oxygen too close to beta carbon of the side chains.

Phi 2

Psi 2

Try to use the buttons to make a type 1 turn with the features shown below. Are there any clashes? How is the different from an alpha helix (where all carbonyl groups are pointing in the same direction)?

And now try to get a type I prime conformation, as shown below. Hint: the pepflip button might serve as a bit of a shortcut. Why is that? Are there any clashes? If you had to choose, would you place a glycine at position 2 or position 3?