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I've been trying to find conclusive information regarding where within an amino acid (AA) it attaches to the protein backbone (PBB). I know that, coming off of the PBB, the AA side chain is connected at the $C_{\alpha}$ position.

But, what about coming off the AA and onto the PBB? Is there a standardized position that AAs use for attachment to the PBB?

For example, consider this AA chart that was just taken off Wikipedia:

Amino Acids Chart

In my attempts of finding an answer, I've come across dozens of these kinds of charts in educational textbooks, internet articles, and misc. text, however, none of them explicitly show attachment to the protein backbone (as @GerardoFurtado points out in a comment, the charts only depict free amino acids, and not residues).

That being said, how can I interpret this to identify which atom within the amino acid it's attached to the protein backbone? Is this configuration consistent 100% of the time?

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closed as unclear what you're asking by Bryan Krause, David, canadianer, kmm, Alan Boyd Aug 31 '17 at 8:00

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

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    $\begingroup$ "How can I interpret this to identify which atom within the amino acid it's attached to the protein backbone?" No atom: those are free amino acids, not amino acid residues. In other words, those AA in the table are monomers. $\endgroup$ – user24284 Aug 25 '17 at 14:36
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    $\begingroup$ Do you know how AA are polymerized? Those amino groups at the right will react with carboxylic acid groups forming an amide. Is really that what you're asking? $\endgroup$ – user24284 Aug 25 '17 at 14:45
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    $\begingroup$ I really don't know what you are asking here. In any amino acid residue, the backbone is the carbon from the carboxylic group, the alpha carbon and the nitrogen, just that. A free amino acid that reacts with a growing backbone will simply form an amide, as you claim to already understand, and its 3 atoms (carboxylic C, alpha C and N) will be now part of the backbone. What's the question here? $\endgroup$ – user24284 Aug 25 '17 at 14:55
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    $\begingroup$ @Charles - Would it not be sensible to look at some protein structures in a viewer (Rasmol/Jmol/Chime/etc) to get a feel for how they are put together? It's a little surprising that you are implementing an algorithm like this (that you describe on bioinformatics SE) but don't know this basic stuff... $\endgroup$ – gilleain Aug 25 '17 at 16:55
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    $\begingroup$ @Charles - True, but it might give you an idea of the actual chemistry involved. One assumption might be that proteins can be represented by a graph without cycles (IE a tree) - that would be wrong. Another might be that there are no breaks in the chain - that would be wrong. Another might be that the residue number always increases - that would be wrong. etc. I think that if you don't even know what primary structure is, you might have a hard time implementing a graph reconstruction from NMR distance constraints... $\endgroup$ – gilleain Aug 25 '17 at 21:48
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It's not entirely clear to me what you're asking, but the crux of your question seems to be Is this configuration consistent 100% of the time?

Yes, the main chain of a protein (polypeptide) is formed by peptide bonds between the carboxyl and α-amine of an amino acid (main chain shown in bold red):

enter image description here

That's kind of the definition. The only potential exception I can think of is isopeptide bonds, in which amino acids are joined by peptide bonds between their side chains, or between a side chain and main chain. For example, the ε-amine of lysine can form an isopeptide bond with the main chain carboxyl (main chains in blue and red, isopeptide bond in green):

enter image description here

Here's a review of a isopeptides: Intramolecular isopeptide bonds: protein crosslinks built for stress?

Technically the second picture shows an unbroken chain of amino acids joined by peptide bonds. However, I wouldn't call this peptide part of the backbone, and no one else would either. It is two separate chains joined together, and this is especially clear in the case of an isopeptide bond between a lysine and a glutamine carboxyamide:

enter image description here

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The protein backbone is formed by amine and carboxylic acid attached to the Cα and the Cα itself. Amino acids undergo step wise condensation forming amide linkage. A picture from Wikipedia nicely illustrates this condensation reaction

enter image description here

As shown in your picture the amino acids differ because of their side chains, denoted in the reaction as R.

The very first amino acid residue will have a free amine and the very last a free carboxy terminus. These groups are often modified by things such acetylation but in general when we There are exceptions to this rule for things such as glutathione and non ribsomal peptides but all 'normal' peptides have their protein backbones made up this way.

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    $\begingroup$ Maybe you could be slightly more specific – the backbone is formed by the Cα, the C atom of the carboxylate group, and the N atom of the amino group. $\endgroup$ – Alan Boyd Aug 25 '17 at 14:51

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