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In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids MKL... Where would I get the coordinates of M and K and L separately? Is there any method by which the coordinates of the amino acids can be calculated? I don't want the coordinates of the atoms, I want the absolute coordinate of each of the amino acid in a protein sequence as a whole...

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    $\begingroup$ It depends what you want them for. You could take an average of all the atomistic co-ordinates of each residue, you could take the co-ordinates of only the carbon in C-R. It's unclear what you're asking for. Are you asking for a sensible method, an available tool, or are you more broadly wondering what constitutes the center of an amino acid conceptually? $\endgroup$ – James May 24 '16 at 7:38
  • $\begingroup$ Each atom is annotated in the PDB-file in terms of which aminoacid it belongs to - is this what you are interested in? It might be useful if you would clarify your question, as I think that we are trying to guess at the moment what you actually want to know. $\endgroup$ – Gerhard May 24 '16 at 22:02
  • $\begingroup$ @Gerhard now is the question clear? $\endgroup$ – girl101 May 25 '16 at 3:42
  • $\begingroup$ Are you saying that you want the 3D-structure of an individual amino acid? I assume so, as you have accepted the corresponding answer. $\endgroup$ – Gerhard May 25 '16 at 8:45
  • $\begingroup$ How is this question unclear? To me it's pretty clear that she wants the "pivot point" or "origin" of each individual amino acid on the chain (most likely along with its orientation in space), as if the amino-acid was a single molecule as a whole, not subdivided into particular atoms. $\endgroup$ – SasQ Aug 25 '18 at 10:03
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If what you are after are the structural co-ordinates of particular amino acids crystalized individually (i.e. considered as small molecules independently of any role in proteins), then you should find them along with other small molecules in the Cambridge Structural Database.

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  • $\begingroup$ Another way of approaching this problem is to focus on the middle carbon atom between the H2N- from one side and -COO from the other side that make peptide bonds with adjacent amino-acids. This middle carbon has the rest of the amino-acid molecule attached to it, and it's definitely on the chain, so you can use that atom's center as the "pivot point" for the entire amino-acid; perhaps even calculate its orientation in space relative to the chain by looking at the bonds connecting this atom with its neighbors. That would be my answer if the question wasn't blocked ;q $\endgroup$ – SasQ Aug 25 '18 at 10:09
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It may not make a lot of sense to consider one amino acid as an indicator of the position of the entire amino acid as different amino acids vary a lot in size. For non-sensitive applications such as plotting the protein backbone you may use the alpha Carbon. If side chains are important you can use what is known as the last heavy atom (What is the last heavy atom of an amino acid?).

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