The contact medoid gives 9 and 7 majority contact differences in 2K39 and 6V5D at 8 Å.

Using all deposited models in PDB entries 1D3Z (10 models), 2K39 (116), and 6V5D (176), this exact integer-coordinate analysis compared contact medoids with models that minimize differences from majority C-alpha contact labels. At 8 Å, with a contact defined by distance <8 Å and majority defined as at least half, the medoid/minimum difference counts were 0/0, 9/8, and 7/4, respectively. A separate strict-majority test gave 1/1, 10/8, and 7/4. In the tested 7.9–8.1 Å range, every contact medoid had more differences than the minimum throughout stated continuous intervals for 2K39 and 6V5D; the finding did not hold throughout that range for 1D3Z. Two parsers and scoring programs agreed across all 22,952 C-alpha atoms, 302 primary model scores, 6,834 residue-pair count sets, and 5,898 threshold-state rows. Results describe these archived coordinates and rules; they do not estimate experimental uncertainty, support population inference, establish biological causality, or identify a better physical structure. The work reproduces a prior AutoSci result and does not claim novelty.

ubiquitin · protein structure · PDB · contact map · contact medoid · Hamming distance · majority contact · NMR ensemble · integer arithmetic · reproduction