AMBER Archive (2006)

Subject: Re: AMBER: Backbone & Sidechain atoms: Definition

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 24 2006 - 10:15:44 CDT

On Thu, Aug 24, 2006, Zu Thur Yew wrote:
>
> I read from the Amber mailing list that N, H, C, O, CA, and HA (and
> HA2,3) are considered "backbone"....
>
> I know it sounds silly, but I would just like to confirm that H1,H2,H3
> on the Nterm are considered "sidechain"?

Context is missing here. If some program is interpreting the terms "backbone"
and "sidechain", then you need to say which program; maybe you can run some
simple tests to find out what that program is doing (and/or look at the source
code).

If you are just using the term yourself, you can do whatever you want.
I would classify H1,H2,H3 as backbone, but I've really never given it much
thought.

...dac

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