SCOP domain families with determined protein-DNA interaction classes
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SCOP Domain Family Number of structures Number of domains

Interaction class

Interaction modes
Ax-bend MnG width MnG depth MjG width MjG depth
Nucleosome core histones
(a.22.1.1)
255 23

 H-Bb S-Bb L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mn 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
 H-Bb H-Mj S-Bb S-Mn L-Bb L-Mn 
 H-Bb H-Mj S-Mn L-Bb L-Mn 
 H-Bb L-Bb 
 H-Bb L-Bb L-Mn 
 H-Bb S-Bb 
 H-Bb S-Bb L-Bb 
 H-Bb S-Bb L-Bb L-Mj 
 H-Bb S-Bb L-Bb L-Mn 
 H-Bb S-Bb S-Mn L-Bb 
 H-Bb S-Bb S-Mn L-Bb L-Mn 
 L-Bb 
 L-Bb L-Mn 
 S-Bb L-Bb 
 S-Bb L-Bb L-Mn 
1.0 (0.0–2.6) 6.1 (6.0–6.4) 4.9 (4.7–5.1) 11.0 (10.0–12.0) 4.6 (3.9–5.4)
DnaQ-like 3'-5' exonuclease
(c.55.3.5)
127 9

 L-Bb 

 H-Bb 
 H-Bb L-Bb 
 H-Bb L-Mj 
 H-Mn L-Bb 
 L-Bb 
 L-Bb L-Mj L-Mn 
 L-Mj 
 S-Bb S-Mj S-Mn L-Bb L-Mj 
Classic zinc finger, C2H2
(g.37.1.1)
95 22

Miscellaneous

 H-Bb 
 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mj L-Mj 
 H-Bb H-Mj S-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Mj 
 H-Bb L-Bb 
 L-Bb 
 L-Bb L-Mn 
0.7 (0.1–2.2) 7.5 (6.2–9.0) 4.4 (3.8–5.1) 11.3 (10.0–12.6) 2.0 (-0.6–4.5)
TATA-box binding protein (TBP), C-terminal domain
(d.129.1.1)
86 8

 S-Bb S-Mn L-Bb L-Mn 

 H-Bb S-Bb S-Mn L-Bb L-Mn 
 S-Bb S-Mn L-Bb 
 S-Bb S-Mn L-Bb L-Mn 
 S-Mn L-Bb 
3.6 (2.8–5.4) 11.9 (11.7–12.2) -0.5 (-1.0–-0.2)
Lambda integrase-like, catalytic core
(d.163.1.1)
68 3

 H-Bb H-Mj L-Bb L-Mn 

 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mj L-Bb L-Mn 
 H-Bb H-Mj S-Bb L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
 H-Bb H-Mj S-Bb S-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb S-Mn L-Bb L-Mn 
 H-Bb L-Bb L-Mn 
 H-Bb S-Bb L-Bb L-Mn 
1.6 (1.4–1.9) 6.0 (5.7–6.4) 4.7 (4.6–4.9) 12.2 (11.3–13.1) 5.3 (5.2–5.4)
Homeodomain
(a.4.1.1)
58 19

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mn 
 H-Bb H-Mj L-Mj 
 H-Bb H-Mj L-Mn 
1.1 (0.4–2.5) 5.9 (4.3–7.9) 4.8 (4.0–5.5) 12.5 (11.3–15.2) 4.5 (0.5–6.6)
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain
(b.1.18.1)
56 9

Miscellaneous

 L-Bb 
 S-Bb 
 S-Bb L-Bb 
Rel/Dorsal transcription factors, DNA-binding domain
(b.2.5.3)
54 8

 H-Bb L-Bb L-Mj 

 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj 
 H-Bb H-Mj S-Bb S-Mj L-Mj 
 H-Bb L-Bb L-Mj 
 H-Bb S-Bb L-Bb L-Mj 
 H-Bb S-Bb L-Bb L-Mj L-Mn 
 H-Bb S-Bb S-Mj L-Bb L-Mj 
 L-Bb L-Mj 
 L-Mj 
 S-Bb S-Mj L-Bb 
 S-Bb S-Mj L-Bb L-Mj 
 S-Mj L-Bb L-Mj 
1.2 (0.6–1.8) 5.0 (3.6–5.8) 5.3 (5.1–5.5) 12.1 (11.5–12.7) 4.4 (3.8–5.0)
GalR/LacI-like bacterial regulator
(a.35.1.5)
53 3

 H-Bb H-Mj H-Mn L-Bb L-Mj 

 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj H-Mn L-Bb L-Mj 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb L-Bb L-Mj 
 H-Mn L-Bb 
 L-Bb 
3.4 (3.0–3.7) 8.4 (8.1–8.7) 4.3 (3.8–4.7) 12.7 (12.2–13.3) 3.4 (2.5–4.2)
Leucine zipper domain II
(h.1.3.1)
50 9

 H-Bb H-Mj 

 H-Bb 
 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
0.7 (0.3–1.1) 7.2 (5.9–8.0) 4.5 (4.0–5.1) 13.1 2.1
Nuclear receptor
(g.39.1.2)
46 12

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj 
 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
 H-Bb H-Mj S-Bb S-Mj L-Bb 
 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mn 
0.9 (0.2–2.0) 6.5 (4.2–7.6) 4.8 (4.5–5.2) 12.3 (12.0–12.8) 4.0 (2.0–5.8)
Group I mobile intron endonuclease
(d.95.2.1)
40 7

 H-Bb S-Bb S-Mj L-Bb L-Mj 

 H-Bb S-Bb S-Mj L-Bb L-Mj 
 H-Bb S-Bb S-Mj L-Bb L-Mj L-Mn 
 H-Bb S-Mj L-Bb L-Mj 
1.8 (0.5–2.9) 6.2 (5.0–7.1) 4.9 (4.2–5.6) 13.9 (12.9–15.1) 4.2 (2.3–5.8)
N-terminal domain of MutM-like DNA repair proteins
(b.113.1.1)
27 4

 S-Bb L-Bb 

 H-Bb S-Bb L-Bb L-Mj L-Mn 
 L-Bb 
 S-Bb L-Bb 
 S-Bb L-Bb L-Mj L-Mn 
 S-Bb L-Bb L-Mn 
0.5 (0.4–0.6)
C-terminal, Zn-finger domain of MutM-like DNA repair proteins
(g.39.1.8)
27 4

Miscellaneous

 L-Bb 
 L-Bb L-Mj 
 S-Bb 
 S-Bb L-Bb 
 S-Mj L-Bb 
0.3 (0.3–0.4)
Phage repressors
(a.35.1.2)
24 5

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 L-Bb L-Mn 
1.8 (1.0–2.6) 7.1 (5.9–8.2) 4.6 (4.3–4.9) 12.5 (11.8–13.6) 4.2 (2.4–5.5)
HLH, helix-loop-helix DNA-binding domain
(a.38.1.1)
23 8

 H-Bb H-Mj 

 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
1.0 (0.2–2.6) 7.9 (7.2–8.3) 4.1 (3.1–4.6) 11.2 1.9
SRF-like
(d.88.1.1)
22 4

 H-Bb H-Mj L-Bb L-Mn 

 H-Bb 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mn 
 H-Bb H-Mj L-Mn 
 H-Bb L-Bb 
 H-Bb L-Mn 
 L-Bb 
2.7 (1.6–3.6) 6.7 (5.3–8.4) 5.1 (4.3–5.7) 10.9 (10.3–12.2) 4.1 (3.0–5.2)
Recombinase DNA-binding domain
(a.4.1.2)
21 5

 H-Bb H-Mj L-Bb L-Mn 

 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mj L-Bb L-Mn 
 H-Mj L-Bb 
1.7 (1.0–2.4) 5.5 (3.6–6.2) 5.5 (5.3–5.8) 11.2 (10.4–12.4) 3.6 (1.8–5.8)
Middle domain of MutM-like DNA repair proteins
(a.156.1.2)
21 4

Miscellaneous

 H-Bb 
 L-Bb 
 L-Mn 
0.2
ets domain
(a.4.5.21)
20 7

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
 L-Bb 
0.9 (0.5–1.5) 8.2 (7.3–10.5) 3.8 (3.0–4.4) 13.6 6.3
Zn2/Cys6 DNA-binding domain
(g.38.1.1)
20 5

 H-Bb H-Mj L-Bb L-Mj 

 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj L-Bb L-Mj L-Mn 
 H-Bb L-Bb L-Mj 
 H-Mj L-Bb L-Mj 
 H-Mj L-Bb L-Mj L-Mn 
 L-Bb L-Mj L-Mn 
1.5 (0.8–2.5) 7.4 (4.7–10.9) 4.1 (1.1–5.8) 11.3 (11.1–11.5) 0.6 (-1.2–2.5)
Leucine zipper domain I
(h.1.3.1)
20 5

 H-Bb 

 H-Bb 
 H-Bb L-Bb 
 L-Bb 
 S-Bb S-Mn 
1.0 11.9 1.5
Interferon regulatory factor
(a.4.5.23)
18 3

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
1.6 (0.3–2.8) 5.8 (3.6–7.6) 5.2 (5.0–5.4) 11.0 (10.5–11.4) 5.1 (4.9–5.3)
Prokaryotic DNA-bending protein
(a.55.1.1)
18 3

 H-Bb S-Bb L-Bb L-Mn 

 H-Bb S-Bb L-Bb L-Mn 
 H-Bb S-Bb S-Mn L-Bb L-Mn 
 S-Bb L-Bb L-Mn 
 S-Bb S-Mn 
 S-Bb S-Mn L-Bb 
 S-Bb S-Mn L-Bb L-Mn 
2.4 (0.6–5.6) 11.0 (10.8–11.1) 1.1 (0.3–1.9) 11.3 -1.2
Transcription factor IIB (TFIIB), core domain
(a.74.1.2)
16 4

 H-Bb 

 H-Bb 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb L-Bb 
 H-Bb L-Bb L-Mj 
0.3 9.2 3.3
Myb/SANT domain
(a.4.1.3)
14 6

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb L-Bb 
0.5 (0.1–0.6) 6.4 4.5
HMG-box
(a.21.1.1)
14 8

 H-Bb H-Mn L-Bb 

 H-Bb H-Mn L-Bb 
 H-Bb H-Mn L-Bb L-Mn 
 H-Bb L-Bb L-Mn 
 H-Mn L-Bb L-Mn 
5.1 (3.5–8.1) 10.9 (10.1–11.2) 1.2 (-0.1–2.0) 10.6 (9.6–11.4) 4.8 (0.4–7.5)
POU-specific domain
(a.35.1.1)
12 3

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
0.8 (0.7–0.9) 9.8 0.6 11.4 1.2
Paired domain
(a.4.1.5)
10 6

 H-Bb H-Mj L-Bb L-Mn 

 H-Bb H-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mj L-Bb L-Mn 
 H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
1.2 (0.2–1.8) 7.8 (7.6–8.0) 4.7 (4.6–4.9) 9.7 (9.3–9.9) 5.7 (5.0–6.2)
AraC type transcriptional activator
(a.4.1.8)
10 4

 H-Bb 

 H-Bb 
 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
 H-Bb L-Bb 
0.7 (0.3–1.4)
Viral DNA-binding domain
(d.58.8.1)
9 4

 H-Bb H-Mj S-Bb L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb H-Mj S-Bb 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
2.8 (2.1–3.9) 7.1 (6.3–8.8) 4.6 (4.0–5.0) 8.4 5.2
Zinc finger design
(k.12.1.1)
9 3

 H-Bb H-Mj L-Bb L-Mj 

 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mj 
 H-Bb H-Mj S-Mj L-Bb L-Mj 
1.1 (1.0–1.3) 6.3 (4.9–7.1) 4.6 (4.5–4.8) 13.2 (12.5–13.8) 5.8 (5.5–6.3)
Replication initiation protein
(a.4.5.10)
8 4

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
0.7 (0.4–1.1) 7.5 4.6 12.5 5.6
Restriction endonuclease FokI, N-terminal (recognition) domain
(a.4.5.12)
3 3

 H-Bb L-Bb 

 H-Bb H-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb L-Bb L-Mj 
 H-Bb L-Bb 
1.1 (0.8–1.4) 12.6 -0.4
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