Proline

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.

Proline

Name

3 Letter

1 Letter

Proline

PRO

Drawn as if part of protein to emphasize the sidechain properties.
NOTE: all three bonds to the mainchain "N" are to Carbon. There is no N-H bond. Therefore this amino acid cannot form H-bonds to others in the chain.

The "Sidechain Polarity" button draws an an envelope around the sidechain that is colored by charge according to the scale above.

pK_R= The sidechain is NOT ionizable in water

Free amino acid mass = 115 g/M

Probability of being found in a:

α-Helix

β-Sheet

β-Turn

30%

90%

Special Attributes

This is the only amino acid in which the side chain is makes a ring with the main atoms. This constrains the phi/psi angle set immensly.

Proline is rarely seen in a helix and ONLY at the N-term end of one at that. The reason is NOT that proline cannot bend into the proper angles, in deed it can. But restricts the phi angle of the previous amino acid into angles not consistent with an α-helix and because the amine group of the main chain cannot form the required H-bond that is a necessary part of the α-helix;

In the demonstration below, the proline is in a random coil section of the peptide

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/