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.

Phenylalanine


Name3 Letter1 Letter
Phenylalanine PHE F

Phenylalanine phe3d


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 im water Free amino acid Mass = 165 g/M
Probability of being found in a:
α-Helix β-Sheet β-Turn
70% 70% 30%
Special Attributes

Aromatic amino acid side chain. Side chain is not polar but can be "induced" to have a small polar moment.

In the demonstration below, the PHE is in a β-sheet and is well sequested from water inside the protein strucuture


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/