Tryptophan

Atom Label Key

Naming Convention for α-amino acids

The Organic acid carbon is labled the acid.
Each carbon afterwards is labeled in order by the greek alphabet
α, β, γ, δ, ε, etc.
Every atom is labeled by element type and then its position ie. the alpha carbon is CA; the beta carbon is CB

Atom Label	Description

C	Main chain Carbon of amide/acid
CA	Main chain α carbon
N	Main chain nitrogen of amide/amine
O	Main chain Oxygen of amide/acid
H	Main chain hydrogen of amide
HA	Main chain hydrogen of on the α carbon
CB	β Carbon, first carbon of the sidechain
HB?	Hydrogen on the β Carbon. '?' is a number 1,2 or 3
OG	Oxygen 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.

Tryptophan

Name

3 Letter

1 Letter

Tryptophan

TRP

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.

pK_R in H₂O= The sidechain is NOT ionizable in water

Free amino acid Mass = 204 g/M

Probability of being found in a:

α-Helix

β-Sheet

β-Turn

70%

60%

Special Attributes

very large bulky ring structure sidechain that is pretty hydrophobic and aromatic

Almost all proteins absorb light in the ultraviolet region (not vivble to humans) at 280 nm due the presence of aromatic amino acids tyrosine and tryptophan.

Due to the large aromatic ring structure this side chain has a large light absorption property at 280nm. On a molar basis about 4 times higher than that of tyr. But since there is (on average) less TRP than TYR accounts for less of the total absorption for proteins.

Aromatic side chain. The Nitrogen in the ring gives it some polarity, In deed, the nitorgen can act as a hydrogen bond donor under some circumstances.

In the demonstration below, the TRP is in a section of random coil. Most of it is buried in the protein structure sequestered away from water, however the nitrogen if the ring is peeking out into the 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/