Five of eight tested ubiquitin pairs have heavy-atom majority label differences between test limits for 2K39 and 6V5D

A prior study found no heavy-atom majority contact-label differences for eight specified ubiquitin residue pairs at distance limits of 3.5, 4.0, 4.5, and 5.0 Å in PDB entries 2K39 and 6V5D. This work reproduces that finite test and calculates the intervals where labels differ between the sampled limits. It uses chain A, author residues 1–70, pairs with sequence separation greater than two, and equal weights for all 116 models of 2K39 and 176 models of 6V5D. Five of the original eight pairs have heavy-atom differences within [3.5,5.0] Å, and two have side-chain differences; none occurs at the four tested limits. Across all eligible pairs, the four limits miss 82 of 135 positive-width heavy-atom intervals and 70 of 101 side-chain intervals under the main majority rule. These are distinct-pair counts; the full contact graphs can still differ at each tested limit. The two entries are dependent because 6V5D uses an alternative model of the original 2K39 data. A conditional coordinate-precision bound retains positive interval width for 81 missed heavy-atom pairs and 69 missed side-chain pairs. This bound is not an estimate of physical measurement error. The result applies to these two entries, the stated residue scope, and the tested contact rules. It does not identify a better ensemble or physical contact rule, establish a biological cause, or report a confidence interval.

ubiquitin · protein ensembles · contact maps · distance limits · majority labels · NMR · PDB · coordinate precision · reproducibility