Understanding Alpha Helices Classifications

[icedoverfire]

Hi folks,

I'm confused about classifying alpha helices. I don't understand how a 3.6₁₃ and a 3₁₀ helix differentiate... Well, I know that a 3.6₁₃ helix has 3.6 residues per turn and 13 atoms in between each hydrogen bond (I think)?
Likewise a 3₁₀ helix has 3 residues per turn and 10 atoms in between each hydrogen bond (I think)?
But what confuses me is that despite these classifications in both helices the N and N+4th residues are hydrogen bonded? So in a 3.6₁₃ helix 13 atoms span the distance between hydrogen bonds but the 1st and 5th residues (for example) would be linked via hydrogen bond (with 13 atoms in between the hydrogen bond)?

so it'd look something like this, on an atomic level (0's are the h-bonded atoms)?

0-1-2-3-4-5-6-7-8-9-10-11-12-13-0

Am I reading too deeply into this?

Thanks,

-ice

 

[Aaron Bex]

No, you are not reading too deeply into this. Alpha helices are classified by the number of residues per turn and the number of atoms in between the hydrogen bonds. The 3.613 helix has 3.6 residues per turn and 13 atoms in between the hydrogen bonds, while the 310 helix has 3 residues per turn and 10 atoms in between the hydrogen bonds. The N and N+4th residues in both helices are hydrogen bonded, with the difference being the number of atoms that span the distance between the two hydrogen bonds.

 

[quicknote]

breaker

Hello icebreaker,

Thank you for your question about alpha helix classifications. It is normal to feel confused about these classifications, as they can be quite technical and nuanced. Let me try to provide some clarification for you.

First, you are correct in your understanding of the differences between a 3.613 and a 310 helix. The numbers represent the number of residues per turn, and the number of atoms between each hydrogen bond.

In terms of the N and N+4th residues being hydrogen bonded, this is a general trend seen in most alpha helices. The N and N+4th residues are typically involved in hydrogen bonding, regardless of the specific classification of the helix. This is because the 4th residue is directly across from the first residue in the helix, and therefore is in close proximity for hydrogen bonding.

Your atomic level representation is also correct. The 0's represent the hydrogen bonded atoms, and the numbers represent the number of atoms between each hydrogen bond.

Overall, it is important to understand the general trends and differences between alpha helix classifications, but it is also important to remember that there can be variations and exceptions within these classifications. So, you are not reading too deeply into this, but it is also important to keep in mind that these are just general guidelines.

I hope this helps to clarify things for you. If you have any further questions, please don't hesitate to ask.

Best,