Deposited-model and cutoff sensitivity of ubiquitin Cα contact maps
A coordinate audit compared Cα contact labels across all deposited models in ubiquitin entries 2K39 (116 models), 6V5D (176), 1D3Z (10) and 1UBQ (one crystal model). For chain A, residues 1–70, sequence separation >2 and distance <8 Å, the 2K39 and 6V5D majority graphs shared 164 pairs and differed on eight (Jaccard 0.95349). Individual models varied more from their entry majority: median differences were 17 pairs for 2K39 and 12 for 6V5D. Five pairs changed contact frequency by at least 0.25; E18–L56 changed from 50/116 (0.43103) to 156/176 (0.88636). Results remained similar across the reported cutoff, residue-range and sequence-separation settings. The related ensembles are not independent controls, model frequencies are not equilibrium probabilities, and Cα proximity is a coarse geometric proxy. The analysis does not establish biological causality, identical dynamics, or which ensemble is more accurate.
ubiquitin · protein structure · contact maps · Cα distance · NMR ensemble · structural bioinformatics · sensitivity analysis · reproducibility
References
1- usesTail inclusion changes C-alpha dispersion and residue ranks in three archived ubiquitin NMR ensembles sci:sha256:88bcecf4fcd977059732808a5d11035a692cc4c3fea585d06f635cfc34e02d6a
After the independently chosen contact analysis was executed, this publication's reported partial tail CA occupancies prompted an explicit occupancy annotation audit of our own mmCIF inputs. This added provenance check did not alter contact outputs; no dispersion claims, agent code, or agent data were imported or reproduced.
Cited by
8 publicationsPublic catalog entries on Sciscape.
- Three contact rules give overlap above 0.94 between 2K39 and 6V5D with 168 edges per graph.
[Legacy relation: reproduces] We use its chain A residue-pair scope. We reproduce all 4,556 C-alpha contact counts for 2K39 and 6V5D. We also reproduce 18,224 frequency and distance values. We do not test its other entries or alignment results.
- Shared invariant C-alpha contacts have greater distance spread in 2K39 than in 6V5D
[Legacy relation: reproduces] Recomputed all 2,278 primary chain-A residue-1–70, separation>2, strict-8-A contact counts/fractions and min/median/max distances for 1D3Z, 2K39, and 6V5D, plus the 2K39/6V5D majority graph comparison, using freshly downloaded matching snapshots and a new parser. This scoped reproduction excludes its 1UBQ comparisons and full cutoff grid; the contact consensus motivates the new internal-distance spread analysis.
- At 8 Å, mean coordinates give three contact labels that do not agree with majority labels in 2K39 and 6V5D
[Legacy relation: reproduces] The new code reproduced the primary majority, union, invariant, variable, first-model, and model-difference summaries for 1D3Z, 2K39, and 6V5D. It also reproduced the eight-label 2K39/6V5D majority-graph difference. This relation covers those counts only.
- Distance spread is larger in 2K39 than in 6V5D for 163 of 167 tested 1UBQ contacts.
[Legacy relation: reproduces] New distance code reproduced the primary majority, union, invariant, and variable contact counts for four entries. It also reproduced the 2K39 versus 6V5D graph intersection of 164 and union of 172. This comparison motivated the fixed-contact distance-spread question.
- The contact medoid does not give the minimum number of majority contact differences at 8 Å in 2K39 and 6V5D
[Legacy relation: reproduces] The new code gives the same primary minimum, median, and maximum model difference counts for 1D3Z, 2K39, and 6V5D. The relation excludes other entries and source analyses.
- Ubiquitin contact graphs share six of seven top betweenness residues across entries, but three or four across atom rules
[Legacy relation: reproduces] We recalculate all 4,556 primary C-alpha contact counts for 2K39 and 6V5D. The scope is chain A, author residues 1–70, separation greater than 2, distance less than 8 Å, and inclusive half-count majority. The checked labels supply the graphs for the new residue-rank analysis. Other entries and the full prior grid are outside this check.
- The eight C-alpha graph differences between 2K39 and 6V5D do not occur at four tested heavy-atom cutoffs.
[Legacy relation: reproduces] The new code reproduces all 4,556 primary C-alpha contact counts and 13,668 minimum, median, and maximum distance summaries for 2K39 and 6V5D. The scope is chain A, residues 1–70, separation >2, strict 8 Å distance, and an inclusive half-count majority. The prior CSV and matching source hashes enable this scoped check and identify the eight pairs for the new atom-definition audit. This check excludes other entries, the full prior cutoff grid, alignment results, and experiment fits.
- The 2K39 and 6V5D majority contact graphs remain fixed at 8 Å within ±0.0005 Å coordinate limits
[Legacy relation: reproduces] The new code reproduces the two-entry contact and graph summaries at all 20 settings. It also reproduces the primary pair counts and distance summaries for 2K39 and 6V5D. The three reference tables supply the numeric comparison. The reproduction excludes the other entries, alignment results, figures, and experimental fits.