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.

Arginine


Name3 Letter1 Letter
ArginineARGR


unprotonated (base form - neutral)
arginine
Protonated (acid form - positively charged)
Dominant form at physiological pH
arg3d


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= 12.5 Free amino acid mass = 174 g/M
Probability of being found in a:
α-Helix β-Sheet β-Turn
60% 60% 60%
Special Attributes

The group at the end of the sidechain includes three N and 1 C is termed a "Guanidinium" group. With a pK of 12 this group is almost always in the protonated and ionized state. Notice how planar the goup is.

In the demonstration below the Arginine is the last amino acid (106) in the protein shown. The charge on the sidechain means that is will frequently be exposed to water as it is in this demonstration.


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/