[gmx-users] Backbone and MainChain

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> Hi 
>  From Gromacs Manual:
> 
>     * Backbone: all protein backbone atoms (C-alpha, N, C)
>     * MainChain: backbone atoms, plus the carbonyl oxygens
> 
> 
> The following is part of .gro file.
> I listed the atom number, are those all correct ?
> 
> C-alpha: 161,170,179

These are not C-alpha atoms (those are "CA").

> N:158,163, 172
> C:  ???   what does this "C" represent ? 

Perhaps you should have a look at the structure of your protein (with atoms 
labeled), as well as the nature of an amide bond itself.

-Justin

> carbonyl oxygens: 162,171,180
> 
> Thank you
> Lin
> 
> 
> 
>    16GLY      N  158   4.365  -0.145   3.067 -0.6971 -0.0210  0.0556
>    16GLY      H  159   4.280  -0.127   3.017  0.4468  0.2941 -1.8808
>    16GLY     CA  160   4.377  -0.037   3.166 -0.3605  0.4870 -0.5237
>    16GLY      C  161   4.250  -0.037   3.252  0.0432 -0.0265  0.0901
>    16GLY      O  162   4.180  -0.137   3.266  0.2570 -0.1341  0.3963
>    17LEU      N  163   4.216   0.087   3.287  0.7572  0.0242  0.6305
>    17LEU      H  164   4.276   0.160   3.254  0.7410 -0.8313 -1.4811
>    17LEU     CA  165   4.102   0.123   3.372 -0.0401 -0.2644 -0.2910
>    17LEU     CB  166   4.156   0.220   3.477  0.1016 -0.1889 -0.4337
>    17LEU     CG  167   4.275   0.181   3.566 -0.0012 -0.5604 -0.4598
>    17LEU    CD1  168   4.338   0.303   3.632  1.2085 -0.9864 -0.7919
>    17LEU    CD2  169   4.233   0.084   3.676  0.8349 -0.3795  0.0241
>    17LEU      C  170   3.980   0.184   3.303 -0.0634  0.2558  0.2056
>    17LEU      O  171   3.993   0.297   3.258 -0.2180  0.0717 -0.3035
>    18ASP      N  172   3.867   0.113   3.302  0.0759  0.0338 -0.0172
>    18ASP      H  173   3.855   0.036   3.364 -0.9960  1.0931  1.1466
>    18ASP     CA  174   3.744   0.153   3.233 -0.1100 -0.0437  0.2680
>    18ASP     CB  175   3.638   0.047   3.201 -0.1316  0.1250 -0.2304
>    18ASP     CG  176   3.612  -0.052   3.315 -0.1959  0.1668 -0.2089
>    18ASP    OD1  177   3.588  -0.170   3.282  0.1094  0.1194 -0.2643
>    18ASP    OD2  178   3.643  -0.033   3.435 -0.2608 -0.1375 -0.1441
>    18ASP      C  179   3.665   0.270   3.294  0.1485  0.2274  0.0883
>    18ASP      O  180   3.660   0.382   3.245 -0.2873  0.2105  0.0864
>    
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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