Atom Label Key

Naming Convention for α-amino acids


Atom Label

Description


CMain chain Carbon of amide/acid
CAMain chain α carbon
NMain chain nitrogen of amide/amine
OMain chain Oxygen of amide/acid
HMain chain hydrogen of amide
HAMain chain hydrogen of on the α carbon
CBβ Carbon, first carbon of the sidechain
HB?Hydrogen on the β Carbon. '?' is a number 1,2 or 3
OGOxygen on the β Carbon.
CG?γ Carbon. - the '?' if present is a number 1 or 2

The results are shown. The H from the -OH group on C6 is now on the amino acid side chain. The phosphate group has been transferred to the alcohol carbon of glucose and ADP is the other product.

Valine


Name3 Letter1 Letter
Valine VAL V

valine val3d


Drawn as if part of protein to emphasize the sidechain properties The "Sidechain Polarity" button draws an an envelope around the sidechain that is colored by charge according to the scale above.

pKR= The sidechain is NOT ionizable in water Free amino acid mass = 117 g/M
Probability of being found in a:
α-Helix β-Sheet β-Turn
70% 90% 80%
Special Attributes

Bulky hydrophobic sidechain. A strong sheet forming amino acid.

in the demonstration below, the valine is in a β-sheet and is well buried in the protein structure sequstered away from water.


In the demonstration below you may "left click and drag" to rotate the molecule "SHIFT left click and drag (up or down)" to make smaller or bigger
Click on the white squares in succession to turn or/off identifying features. Some text describing the issues is in the lower right text box



Atom Label Description

Click an atom to diplay it's identity here


Messages about the currently highlighted features

Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/