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.

Asparagine


Name3 Letter1 Letter
Asparagine ASN N

asparagine ans3d


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 in H2O= The amide group at the end of ASN is not ionizable under physiological conditions Free amino acid mass = 132 g/M
Probability of being found in a:
α-Helix β-Sheet β-Turn
40% 60% 90%
Special Attributes

Asparagine ends in an amide group that is very similar to the peptide bond. It too is very polar and planar. Very good a forming H-bonds. Since it ends in an amide (not an amine) this group is NOT ionizable (does NOT pick up or lose a proton)

As the terminal amide in aparagine is polar (just like the peptide bond - which is also an amide bond), it is frequently exposed to water as it is in the demonstration below. In this case, the asparagine is found in a β-turn.


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/