AMBER Archive (2009)

Subject: RE: [AMBER] Histidine, which form?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jun 15 2009 - 10:06:49 CDT

Hi

The mapping in AMBER is:

     CB
     |
     CG
   / \
 CD2 ND1
  | |
 NE1---CE1
    
You can also get this information by running xleap, and entering edit HID. The choose Display->Names and you will see all the atom names.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of s_bill36_at_yahoo.co.uk
> Sent: Monday, June 15, 2009 7:54 AM
> To: amber_at_ambermd.org
> Subject: [AMBER] Histidine, which form?
>
> Dear AMBER
> For Histidine, there are three forms of it, HIE, HID, and HIP.
> Delta poistion is position number 1 and Epsilon Position is position
> number 3.
> The problem is that:
> There two different systems of numbering the atoms in the
> imidazole ring of histidine had both been used for a considerable time
> (biochemists
> generally numbering as 1 the nitrogen atom adjacent to the side chain,
> and organic chemists
> designating it as 3).
>
> So, could you tell me which nitrogen atom is the delta one, please?
> Also, could you give me an example of HIP when histidine is protonated
> on both positions, please?
>
> Thanks in Advance
>
>
>
>
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