Table 1. Interaction classes of SCOP families with average values of DNA shape parameters.
| Interaction class | Families (SCOP ID) | Ax–bend | MnW | MnD | MjW | MjD |
|---|---|---|---|---|---|---|
| Miscellaneous | Middle domain of MutM-like DNA repair proteins (a.156.1.2) | 0.2 | – | – | – | – |
| NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain (b.1.18.1) | – | – | – | – | – | |
| Classic zinc finger, C2H2 (g.37.1.1) | 0.7 | 7.5 | 4.4 | 11.3 | 2.0 | |
| C-terminal, Zn-finger domain of MutM-like DNA repair proteins (g.39.1.8) | 0.3 | – | – | – | – | |
| H – Bb | AraC type transcriptional activator (a.4.1.8) | 0.7 | – | – | – | – |
| Replication initiation protein (a.4.5.10) | 0.7 | 7.5 | 4.6 | 12.5 | 5.6 | |
| Transcription factor IIB (TFIIB), core domain (a.74.1.2) | 0.3 | 9.2 | 3.3 | – | – | |
| Leucine zipper domain (h.1.3.1) I | 1.0 | 11.9 | 1.5 | – | – | |
| L – Bb | DnaQ-like 3′-5′ exonuclease (c.55.3.5) | – | – | – | – | – |
| S – Bb L – Bb | N-terminal domain of MutM-like DNA repair proteins (b.113.1.1) | 0.5 | – | – | – | – |
| H – Bb S – Bb L – Bb | Nucleosome core histones (a.22.1.1) | 1.0 | 6.1 | 4.9 | 11.0 | 4.6 |
| H – Bb H – Mj | HLH, helix-loop-helix DNA-binding domain (a.38.1.1) | 1.0 | 7.9 | 4.1 | 11.2 | 1.9 |
| Leucine zipper domain (h.1.3.1) II | 0.7 | 7.2 | 4.5 | 13.1 | 2.1 | |
| H – Bb H – Mj L – Bb | POU-specific domain (a.35.1.1) | 0.8 | 9.8 | 0.6 | 11.4 | 1.2 |
| Phage repressors (a.35.1.2)a | 1.8 | 7.1 | 4.6 | 12.5 | 4.2 | |
| Homeodomaina (a.4.1.1) | 1.1 | 5.9 | 4.8 | 12.5 | 4.5 | |
| Myb/SANT domain (a.4.1.3) | 0.5 | 6.4 | 4.5 | – | – | |
| ets domain (a.4.5.21) | 0.9 | 8.2 | 3.8 | 13.6 | 6.3 | |
| Interferon regulatory factor (a.4.5.23) | 1.6 | 5.8 | 5.2 | 11.0 | 5.1 | |
| Nuclear receptor (g.39.1.2) | 0.9 | 6.5 | 4.8 | 12.3 | 4.0 | |
| H – Bb H – Mj S – Bb | Viral DNA-binding domain (d.58.8.1) | 2.8 | 7.1 | 4.6 | 8.4 | 5.2 |
| H – Bb L – Bb L – Mj | Rel/Dorsal transcription factors, DNA-binding domain (b.2.5.3)a | 1.2 | 5.0 | 5.3 | 12.1 | 4.4 |
| H – Bb H – Mj L – Bb L – Mj | Zn2/Cys6 DNA-binding domain (g.38.1.1) | 1.5 | 7.4 | 4.1 | 11.3 | 0.6 |
| Zinc finger design (k.12.1.1) | 1.1 | 6.3 | 4.6 | 13.2 | 5.8 | |
| H – Bb S – Bb S – Mj L – Bb L – Mj | Group I mobile intron endonuclease (d.95.2.1) | 1.8 | 6.2 | 4.9 | 13.9 | 4.2 |
| H – Bb H – Mn L – Bb | HMG-boxa (a.21.1.1) | 5.1 | 10.9 | 1.2 | 10.6 | 4.8 |
| H – Bb S – Bb L – Bb L – Mn | Prokaryotic DNA-bending protein (a.55.1.1) | 2.4 | 11.0 | 1.1 | 11.3 | -1.2 |
| H – Bb H – Mj L – Bb L – Mn | Recombinase DNA-binding domain (a.4.1.2) | 1.7 | 5.5 | 5.5 | 11.2 | 3.6 |
| Paired domain (a.4.1.5) | 1.2 | 7.8 | 4.7 | 9.7 | 5.7 | |
| SRF-like (d.88.1.1) | 2.7 | 6.7 | 5.1 | 10.9 | 4.1 | |
| Lambda integrase-like, catalytic core (d.163.1.1) | 1.6 | 6.0 | 4.7 | 12.2 | 5.3 | |
| S – Bb S – Mn L – Bb L – Mn | TATA-box binding protein (TBP), C-terminal domain (d.129.1.1) | 3.6 | 11.9 | -0.5 | – | – |
| H – Bb H – Mj H – Mn L – Bb L – Mj | GalR/LacI-like bacterial regulator (a.35.1.5) | 3.4 | 8.4 | 4.3 | 12.7 | 3.4 |
| H – Bb L – Bb | Restriction endonuclease FokI, N-terminal (recognition) domaina (a.4.5.12) | 1.1 | – | – | 12.6 | -0.4 |
afamilies for which new structures will be likely to improve the classification by enlarging the list of contact types.
In the column ‘Interaction class’ H is for helix, S is for sheet, L is for loop or unstructured segment of protein, Bb is for the DNA backbone, Mj is for the DNA major groove, Mn is for the DNA minor groove. Right five columns contain the average values of: Ax-bend, that is the mean angle between axes of the DNA helix in subsequent base pairs in contact zone of a domain, the width of the DNA minor groove (MnW), the depth of the DNA minor groove (MnD), the width of the DNA major groove (MjW), and the depth of the DNA major groove (MjD). Ax-bend is in degrees, the widths and depths are in Angstroms. The dash (‘–’) means that this parameter cannot be computed for structures of the family.