Two of five heavy-atom contact differences have weight-ratio limits more than 1.10 for 2K39 and 6V5D at 3.5–5.0 Å.

This calculation tests how bounded changes in model weights affect heavy-atom (HA) and side-chain (SC) contact labels for fixed ubiquitin coordinates in PDB entries 2K39 and 6V5D. At largest-to-smallest weight ratio R=1.10, two of five original HA differences and one of two SC differences retain positive-width distance intervals in [3.5, 5.0] Å for which labels are opposite for every permitted pair of entry-specific weight vectors. Across the six tested R values (1, 1.05, 1.10, 1.25, 1.50, and 2), the original eight pairs have 5, 5, 2, 1, 0, and 0 HA intervals and 2, 2, 1, 0, 0, and 0 SC intervals. For all eligible pairs at R=1.10, the counts are 105 HA and 83 SC. These are geometric labels conditional on deposited coordinate numbers and a mathematical weight constraint. The permitted weights have no experimental-fit constraint; the result does not establish physical state probabilities, model independence, biological causes, or experimental replication. The deposits share experimental information. Coordinate and model-selection uncertainty are not included.

ubiquitin · protein structures · contact labels · model weights · weight ratio · heavy-atom contacts · side-chain contacts · sensitivity analysis · structural bioinformatics