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.

Glycine


Name3 Letter1 Letter
Glycine GLY G

glycine gly3d


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= NOT ionizable in water under physiological conditions Free amino acid mass = 75 g/M
Probabiltiy of being found in a:
α-Helix β-Sheet β-Turn
40% 40% 80%
Special Attributes

Lack of a β-Carbon: the only common amino acid that is NOT chiral, gives this amino acid considerably more flexibilty that all others, therefore a much larger area of the phi/psi plot is available. (more on this later)

It is frequently found in β-turns where its flexibilty is required. Infrequently found in a α-helix since its flexibilty gives it more degrees of freedom.

in the demonstration below, the highlighted glycine is part of a β-sheet just prior to where a β-turn begins. It is buried inside the protein away from water in this case


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/