Misplaced hydrogen in line+H view?

Case number:845833-993817
Topic:Game: Display
Opened by:truestone
Opened on:Saturday, October 27, 2012 - 19:38
Last modified:Sunday, October 28, 2012 - 22:05

If you set the view to any Line+H, Line+PolarH, Stick, Stick+PolarH, white things pop up that look suspicously like hydrogen atoms. Blue dots tooltipped as "donor" look like nitrogen atoms and red dots labeled "acceptor" look like oxygen atoms. All nice and dandy up to now. But on the first segment (of a polypetide), the blue ball has 3 white sticks, where according to my understanding the nitrogen atom would have two hydrogens; and on the last segment, the second red ball has no white stick, while to my understanding it is an OH. Is the visualization just a bit sloppy here? I know it doesn't matter for anything in the game.

(Sat, 10/27/2012 - 19:38  |  2 comments)

brow42's picture
User offline. Last seen 51 weeks 4 days ago. Offline
Joined: 09/19/2011
Groups: None

This is real. At physiological pH, the nitrogen end of a amino acid is NH3+ and the carbon end is COO-. Whether that H sits on the N or C group depends on the pH. When two amino acids bond, the C and N bond and an H2O goes free.

You can also see the H on the end of the cysteine disappear in atom view when it forms a disulfide bridge.


Joined: 03/18/2012
Groups: Gargleblasters
Topic: General » Game: Display
Status: Open » Closed

Thanks. I'll watch out for the expelled hydrogen when disulfide bridges leave the rest of foldit in peace (http://fold.it/portal/node/993709)


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