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Does it mean the position of the amino acid in the protein sequence, or something else?

For example, I came across the phrase "S 368 phosphoryation" where S is the modified residue and 368 is the modified residue position. What does it all mean?

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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.

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