User:Stephen Mills/Peptide tutorial 1: Difference between revisions
From Proteopedia
Jump to navigationJump to search
| Line 293: | Line 293: | ||
Peptide bonds almost always assume the trans conformation: that in which successive alpha carbon atoms are on opposite sides of the peptide (C-N) bond joining them. Click <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtransamide/1'>here</scene> to | Peptide bonds almost always assume the trans conformation: that in which successive alpha carbon atoms are on opposite sides of the peptide (C-N) bond joining them. Click <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtransamide/1'>here</scene> to show this trans bond. The exception are peptide bonds involving proline (when P is on the C-terminal side of the bond) - these can be trans or cis. | ||
==Backbone Atoms== | |||
<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' /> | |||
If the R groups (side chains) of the amino acids are no longer displayed, then you will be looking at the backbone of the dipeptide. <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrbackbone/1'>Click here to turn off the side chains.</scene> | |||
This dipeptide has a completely extended conformation. | |||
Rotate the molecule and you should notice how planar the peptide bond is. | |||
