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 3
Psi 2 3
Excercise 1
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)?
Excercise 2
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?
Phi 2 3
Psi 2 3
Exercise 3
Compare and contrast the two turns we discussed, and compare them to alpha helix and beta sheet. Clicking the buttons will preserve the orientation of the 2->3 peptide plane while adjusting the torsion angles. You can press the last button to flip the entire molecules as a rigid body (different from the pepflip button above, which changes torsion angles).
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