What does it mean by spatial neighbor?

What does it mean by a spatial neighbor (SN) in the case of a protein residue or protein chain?


Why is it different or special as opposed to other neighbors?




Proteins are long chains of amino acids joined together. Atoms or amino acid residues that are a few *bonds* away from each other can be considered "neighbours".


But the long chains of atoms/amino acids usually show complicated folding in 3D space. Indeed, the specific shape of that folding is critical for the protein to function. The implication of the folding in 3D is that residues or atoms that are **far** apart if we count bonds can be very **close** in 3D space. The last amino acid in the chain might be hundreds of bonds away from the residue at the other end of the chain, but might sit right next to it in 3D space. That would be a *spatial neighbour*.


The point is that, in complex 3D structures, we can count "neighbours" by either the number of bonds between them or by how close they are in space when the protein is folded.


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