= Solution
\b[1 = AB, 2 = AC, 3 = BC.] A and B are within the N-terminal portion of the chain and correspond to the darker, lower-error block. C lies in the later portion; the off-diagonal comparisons to it are paler and less confidently positioned.
The matrix reports <predicted aligned error>, not physical separation: a large matrix value does not mean that the two residues are far apart. It indicates uncertainty in their relative placement after alignment on one residue.<PAE: A measure of global confidence in AlphaFold2 predictions by EMBL-EBI>[Definition of PAE and interpretation of dark versus pale inter-domain blocks]{ref}
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