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Determining an Asn/Gln Flip

Java Mage stereo animation between the best (green) and the second-best (pink) amide orientations for a doubly-Hbonded sidechain pair (Gln 34 - Asn 128 in 1ARU). Rotate by dragging slowly, and click the "animate" button, or press the "a" key to switch between the two conformations and their all-atom contacts. All H-bonds are equivalent for the two states, but the incorrect flip state has a physically impossible overlap of 0.75 Å between the NH2 and the C-alpha hydrogen. Try turning on "close contact" and "wide contact" to see the rest of the contact dots. For tools to diagnose amide flips this way, follow this link to Asn/Gln/His flips in the Validation Section.

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