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You are correct, the 368 stands for the position of the amino acid in the protein's sequence - this particular serine is the 368th residue in the protein counting from the amino-terminal end.


This is mostly because of the nature of the amino acids. You need to have a Hydroxy-group in the sidechain of the amino acid which is the point where the phosphogroup is attached. Since this process needs to be reversible, this can only happen here. See the image below (from here) about the chemical structure: In eukaryotes not only these three are ...


Phosphorylation requires a nucleophile and hydroxyl oxygen acts like one. Serine, theronine and tyrosine get phosphorylated on the free $OH$ group in their side chains. Nitrogen, in some cases also can act as a nucleophile. In case of histidine, the imidazole nitrogen is phosphorylated during bacterial chemotaxis signaling. As far as I know eukaryotes do ...


Those residues are phosphorylated because they have a free hydroxyl group available to be bonded to a phosphate. Many other resides can be modified, like acetylation of lysines, but only those residues are chemically compatible with reversible phosphorylation.

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