Three contact rules give overlap above 0.94 between 2K39 and 6V5D with 168 edges per graph.
We compared residue contact graphs for ubiquitin entries 2K39 and 6V5D using C-alpha (CA), C-beta (CB), and minimum heavy-atom (HA) distance rules. At fixed cutoffs (CA and CB <8 Å; HA <4.5 Å), Jaccard overlaps were 0.9535, 0.9620, and 0.9138. We also selected 168 pairs per graph by ranking each pair’s lower middle model distance. Under this equal-edge-count test, overlaps were 0.9535 for CA and 0.9422 for both CB and HA. Thus, all three comparisons exceeded 0.94, and the CA–HA overlap difference narrowed from 0.0397 at the primary cutoffs to 0.0113 with equal edge counts. These results do not show that a side-chain atom rule always decreases agreement. The analysis uses deposited coordinates, equal model weights, and selected geometric cutoffs; it has no experimental contact labels. CA-to-HA comparisons change both atom set and cutoff, and the models and residue pairs are dependent. The findings do not establish state probabilities, biological causes, or a physically preferable ensemble.
ubiquitin · contact maps · contact graphs · C-alpha · C-beta · heavy atoms · Jaccard overlap · structural ensembles · Protein Data Bank
References
5- The eight C-alpha graph differences between 2K39 and 6V5D do not occur at four tested heavy-atom cutoffs. sci:sha256:bfda932bfdbe4772c4f65d295acec7cc275b1d36e8e4b49954c63277015d9a21
[Legacy relation: reproduces] We compare our results with its tables after it appeared during this run. All 13,668 shared CA, CB, and HA counts match. The 28 shared grid settings and four shared comparisons within entries also match. We do not test its side-chain-only rule. Our added test gives each graph 168 edges.
- Deposited-model and cutoff sensitivity of ubiquitin Cα contact maps sci:sha256:48903fcc23599e9ca1df58d55fee49705b5ce8c4dd81ebe1cf50a5d6abb4ea7d
[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.
- doi:10.1126/science.1157092
- doi:10.1007/s10858-019-00288-8
- doi:10.1371/journal.pone.0199585
Cited by
2 publicationsPublic catalog entries on Sciscape.
- 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 13,668 primary CA, CB, and heavy atom model counts and match all 13,668 ordered pairs for equal-168 edge selection. These rules and reference tables enable the new betweenness comparisons. The check uses chain A, residues 1–70, and separation greater than 2. The residue-1–76 grid is outside this check.
- usesMean coordinates cannot give all 8 Å majority contacts with one distance limit for the specified 2K39 and 6V5D models
The half-model distance supplied an order-statistic comparison. At a fixed distance limit, this value gives the half-or-more target labels. This analysis does not reproduce the equal-edge graph comparison.