Interaction class
Class:  H-Bb H-Mj L-Bb 
Description: Conserved protein-DNA contacts are provided by helix(es) (H) with DNA backbone atoms (Bb), helix(es) (H) with the major groove of DNA (Mj), loop(s) (L) with DNA backbone atoms (Bb).
Pfam families with interaction class  H-Bb H-Mj L-Bb 
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Pfam Domain Family Number of structures Number of domains Interaction modes
zf-C4
(PF00105.17)
147 22  H-Bb H-Mj S-Bb S-Mj L-Bb 
 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj 
 H-Bb H-Mj S-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-Mj 
TetR_N
(PF00440.22)
72 13  H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj H-Mn L-Bb L-Mj 
Ets
(PF00178.21)
59 12  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-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
GerE
(PF00196.18)
22 3  H-Bb H-Mj L-Bb 
MarR_2
(PF12802.6)
18 3  H-Bb H-Mj 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 
IRF
(PF00605.16)
14 4  H-Bb H-Mj L-Bb 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
HTH_18
(PF12833.6)
7 3  H-Bb H-Mj L-Bb 
HTH_Crp_2
(PF13545.5)
7 4  H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
E2F_TDP
(PF02319.19)
4 4  H-Bb H-Mj L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mj 
All Pfam and SCOP domain families with determined protein-DNA interaction classes
SCOP families with interaction class  H-Bb H-Mj L-Bb 
Note: this data is based only on structures available at the moment of the last SCOP release (2009)
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SCOP Domain Family Number of structures Number of domains Interaction modes Ax-bend MnG width MnG depth MjG width MjG depth
Homeodomain
(a.4.1.1)
58 19  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)
Nuclear receptor
(g.39.1.2)
46 12  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)
Phage repressors
(a.35.1.2)
24 5  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)
ets domain
(a.4.5.21)
20 7  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
Interferon regulatory factor
(a.4.5.23)
18 3  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)
Myb/SANT domain
(a.4.1.3)
14 6  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
POU-specific domain
(a.35.1.1)
12 3  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
Replication initiation protein
(a.4.5.10)
8 4  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
All Pfam and SCOP domain families with determined protein-DNA interaction classes
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