I would like some clarification on whether it matters where the NH and double bond are placed in these two structures of tryptophan (W) that I drew. I marked the right side as correct and the left side as the incorrect one, but suddenly I am thinking that where you place the double bond and NH don't matter as long its placed in either orientation of the structure it should be tryptophan right?

Simply put, I took my chemistry classes a few years ago and don't remember if this changes the structure if I changed the position of the NH and double bonds, that is all, and would some clarification on it.

enter image description here


I noticed a mistake and re-drew the structure, but am still not clear about the so called "trivial" rotation mentioned. Does the new picture reflect whether or orientation not mattering? I am still confused if I drew it correct. enter image description here

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    $\begingroup$ Care to explain why that is the case?? Don't really understand why this question is so poorly received I am genuinely trying to learn about amino acids. $\endgroup$ Commented Feb 3, 2020 at 21:14
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    $\begingroup$ But its not a homework question, how do you want me to prove this? I'm not taking any classes and am studying for the MCAT exam, I wanted to memorize the amino acids, but am confused if switching or rotating the orientation of the NH and double bond would make it a different molecule other than tryptophan $\endgroup$ Commented Feb 3, 2020 at 21:31
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    $\begingroup$ I have looked at the structure beside what I drew at least 100 times over and I cannot spot the difference between what I drew (incorrectly) and the correct structure. If I were asking a homework question, how come I did not reference a problem or something, I'm not trying to pick this molecule out of a list or anything like that, it is for my own personal understanding, not a homework related question, not sure how you would like me to prove this. $\endgroup$ Commented Feb 3, 2020 at 21:34
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    $\begingroup$ Hi Tylersome, Thanks for attempting to put on the right pathway. And no I did not see "homework", and have since read that in your new posts. I guess a follow-up question I have is how would I be able to discern what is a "trivial" question is for one person and not for another? Questions I ask whether they are trivial or not, are intended for my own personal understanding, not for homework purposes as I have already graduated from university and am currently trying my best to refresh my knowledge. However, I would still like somebody feedback on the second image I uploaded of the structures $\endgroup$ Commented Feb 4, 2020 at 0:15
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    $\begingroup$ I dont think this is a trivial question, it is rather a core biochemistry question regarding the positioning of amino acids side chain in proteins. The various positions are called rotamers, and it is important to understand this in structural-biology and enzyme catalysis $\endgroup$ Commented Sep 7, 2020 at 8:03

1 Answer 1


Good question, this regards rotamers!

Basically, the side chain of amino acids can rotate as shown in the figure below for glutamate (Glu; E). The various option for side-chain rotation is called rotamers! Some amino-acids side chains have the potential of many rotamers (such as glutamate) while some can only adopt a few (such as tryptophan) due to steric restraints. You can read about it here on FolditWiki or in the article 'Rotamers: To be or not to be?: An Analysis of Amino Acid Side-chain Conformations in Globular Proteins'.

The set of amino acid side-chain conformations in globular proteins cannot be considered as normally distributed around some rotamer points. Outliers occur systematically. The rotamericity of an amino acid depends essentially on the different environments the amino acid meets in real protein structures. Factors such as the backbone torsion angles of the residue itself, the secondary structure and tertiary contacts influence the rotamericity. (...)

enter image description here

When solving a protein structure, scientists spend a lot of time on placing the amino-acid side chains into their correct rotamer position. Which rotamer a particular side chain should adapt, depend on the surrounding environments. Some amino acids side-chain are also very flexible and will move around the various rotamer position that they can adopt. In the example of glutamate (figure above), it would most likely adapt a rotamer position pointing either out towards solvents (if the the side chain is on the surface of the protein), or perhaps towards a positively charged amino acids side chain such as Arginine (R) or Lysine (K) to form salt-bridges or H-bonds.

In the case of Tryptophan (W), it is often involved in pi-stacking and would therefore be found in a rotamer position that stacks with other aromatic amino acids side chains. It is also a very bulky amino acid, and might therefore only have space in one particular conformation. Note that tryptophan (W) only has two rotamers, which are similar to the two that you drew in the updated figure, and again shown below. Note that both of these are correct, and that my hand-drawn bond angles are a bit off. These two rotamer options for tryptophan are even found in enzymes catalytic site, where the 'flipping' from one confirmation to the other is the key-mechanisms the allows substrates into or out of the active site!

enter image description here

These structural arrangements are a lot easier to understand in three-dimensions, if you are still struggling then it could be a good idea to use a visualisation program (e.g. PyMol or Coot) and take a look at tryptophane's and other amino acids side chains by downloading some protein structure from the PDB database.

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