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).
Here are some possible things to discuss: the orientation of the carbonyl groups, hydrogen bonding patterns, potential clashes of side chains with the main chain secondary structure conformation, regions of the Ramachandran plot, distance of certain pairs of atoms, cis and trans peptides (what?).
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