Pfam and SCOP domain families with determined protein-DNA interaction classes
Interaction classes of Pfam domains
Export table
Pfam Domain Family Number of structures Number of domains

Interaction class

Interaction modes
Histone
(PF00125.26)
2177 93

 H-Bb S-Bb L-Bb 

 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 S-Bb L-Bb 
 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 
  
TAL_effector
(PF03377.15)
791 36

Miscellaneous

 H-Bb 
 H-Bb L-Bb 
 H-Bb L-Bb L-Mj 
 H-Bb L-Mj 
 L-Bb 
 L-Bb L-Mj 
 L-Mj 
  
CENP-T_C
(PF15511.8)
726 13

 H-Bb S-Bb L-Bb 

 H-Bb S-Bb L-Bb 
 H-Bb S-Bb S-Mn L-Bb 
 H-Bb S-Bb S-Mn L-Bb L-Mn 
  
Histone_H2A_C
(PF16211.7)
718 33

 L-Bb 

 L-Bb 
 L-Bb L-Mj 
  
DNA_pol_B_thumb
(PF14791.8)
604 9

 H-Bb H-Mn S-Bb 

 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mj L-Mn 
 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mn 
 H-Bb H-Mn S-Bb 
 H-Bb H-Mn S-Bb L-Bb L-Mn 
  
DNA_pol_lambd_f
(PF10391.11)
573 8

 H-Bb L-Bb 

 H-Bb H-Mn L-Bb 
 H-Bb L-Bb 
  
DNA_pol_B_palm
(PF14792.8)
572 11

 S-Bb L-Bb 

 H-Bb S-Bb S-Mn L-Bb 
 S-Bb L-Bb 
 S-Bb S-Mn L-Bb 
 S-Bb S-Mn L-Bb L-Mn 
  
RNA_pol_Rpb1_5
(PF04998.19)
513 44

 H-Bb 

 H-Bb 
  
IMS
(PF00817.22)
480 10

 H-Bb 

 H-Bb 
 H-Bb H-Mj H-Mn S-Bb S-Mj S-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mn S-Bb L-Bb L-Mj 
 H-Bb H-Mn S-Bb S-Mj S-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mn S-Bb S-Mn L-Bb L-Mn 
 H-Bb S-Bb L-Bb 
 H-Bb S-Bb L-Bb L-Mn 
 H-Bb S-Bb S-Mj S-Mn L-Bb L-Mj 
IMS_C
(PF11799.10)
471 12

 S-Bb 

 H-Bb S-Bb S-Mj L-Bb 
 H-Bb S-Bb S-Mj L-Bb L-Mj 
 H-Bb S-Bb S-Mj S-Mn L-Bb L-Mj 
 S-Bb 
 S-Bb S-Mj L-Bb 
RNA_pol_Rpb1_1
(PF04997.14)
457 39

 L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb L-Bb 
 L-Bb 
  
RVT_1
(PF00078.29)
341 15

 H-Bb H-Mn S-Bb S-Mn L-Bb L-Mn 

 H-Bb H-Mn S-Bb S-Mj S-Mn L-Bb L-Mn 
 H-Bb H-Mn S-Bb S-Mn L-Bb L-Mn 
  
zf-H2C2_2
(PF13465.8)
305 59

Miscellaneous

 H-Bb 
 H-Bb H-Mj 
 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj H-Mn S-Bb 
 H-Bb H-Mj H-Mn S-Bb L-Bb 
 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mj 
 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-Mj 
 H-Bb H-Mj S-Bb S-Mj L-Bb 
 H-Bb L-Bb 
 H-Bb S-Bb 
 H-Bb S-Bb L-Bb 
 H-Mj S-Bb L-Bb L-Mj 
 S-Bb 
  
RVT_connect
(PF06815.15)
282 4

 H-Bb S-Bb L-Bb 

 H-Bb S-Bb L-Bb 
 H-Bb S-Bb L-Bb L-Mj 
RVT_thumb
(PF06817.16)
282 4

 H-Bb L-Bb 

 H-Bb H-Mn L-Bb 
 H-Bb H-Mn L-Bb L-Mn 
 H-Bb L-Bb 
 H-Bb L-Bb L-Mn 
IMS_HHH
(PF11798.10)
277 5

 H-Bb L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb L-Bb 
DNA_pol_B_exo1
(PF03104.21)
273 26

Miscellaneous

 H-Bb 
 H-Bb H-Mn S-Bb L-Bb L-Mj 
 H-Bb L-Bb 
 H-Mn L-Bb 
 L-Bb 
 L-Bb L-Mj 
  
DNA_pol_A
(PF00476.22)
257 15

 H-Bb H-Mn S-Bb L-Mn 

 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mj L-Mn 
 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mn 
 H-Bb H-Mn S-Bb L-Bb L-Mn 
 H-Bb H-Mn S-Bb L-Mn 
  
RNase_H
(PF00075.26)
249 7

 L-Bb 

 H-Bb H-Mn L-Bb L-Mn 
 H-Bb L-Bb 
 H-Bb L-Bb L-Mn 
 L-Bb 
  
DNA_pol_B
(PF00136.23)
230 17

 H-Bb L-Bb L-Mn 

 H-Bb H-Mj H-Mn S-Bb S-Mn L-Bb L-Mn 
 H-Bb H-Mn S-Bb L-Bb L-Mn 
 H-Bb H-Mn S-Bb S-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mn S-Bb S-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mn S-Bb S-Mn L-Bb L-Mn 
 H-Bb L-Bb L-Mj L-Mn 
 H-Bb S-Bb L-Bb L-Mn 
  
Homeodomain
(PF00046.31)
196 48

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj H-Mn 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 
  
Toprim
(PF01751.24)
194 16

 H-Bb S-Bb L-Bb 

 H-Bb H-Mn S-Bb L-Bb L-Mn 
 H-Bb S-Bb L-Bb 
 H-Bb S-Bb L-Bb L-Mn 
  
zf-C4
(PF00105.20)
190 27

 H-Bb H-Mj S-Bb L-Bb 

 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mj 
 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-Bb S-Mj L-Bb L-Mj L-Mn 
  
TBP
(PF00352.23)
190 10

 S-Bb S-Mn L-Bb L-Mn 

 H-Bb S-Bb S-Mj S-Mn L-Bb L-Mj L-Mn 
 S-Bb S-Mj S-Mn L-Bb L-Mj L-Mn 
 S-Bb S-Mj S-Mn L-Bb L-Mn 
 S-Bb S-Mn L-Bb L-Mj L-Mn 
 S-Bb S-Mn L-Bb L-Mn 
  
LAGLIDADG_1
(PF00961.21)
189 25

 H-Bb S-Bb S-Mj L-Bb L-Mj 

 H-Bb S-Bb S-Mj L-Bb L-Mj 
  
DNA_topoisoIV
(PF00521.22)
189 14

 H-Bb L-Bb 

 H-Bb H-Mj H-Mn S-Bb S-Mj S-Mn L-Bb 
 H-Bb H-Mj H-Mn S-Bb S-Mj S-Mn L-Bb L-Mn 
 H-Bb H-Mj S-Bb S-Mj S-Mn L-Bb 
 H-Bb H-Mj S-Bb S-Mj S-Mn L-Bb L-Mn 
 H-Bb L-Bb L-Mj L-Mn 
  
P53
(PF00870.20)
152 4

 H-Mj S-Bb L-Bb L-Mj 

 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 L-Mn 
 H-Mj S-Bb L-Bb L-Mj 
Exo_endo_phos
(PF03372.25)
152 11

 S-Bb L-Bb L-Mj L-Mn 

 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj L-Mn 
 H-Bb S-Bb L-Bb L-Mj L-Mn 
 S-Bb L-Bb L-Mj L-Mn 
  
DNA_gyraseB_C
(PF00986.23)
147 16

 H-Bb 

 H-Bb 
 H-Bb L-Bb 
  
TetR_N
(PF00440.25)
140 28

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
  
HTH_3
(PF01381.24)
140 18

 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 
  
Fapy_DNA_glyco
(PF01149.26)
105 9

 L-Bb L-Mj L-Mn 

 H-Bb S-Bb S-Mn L-Bb L-Mj L-Mn 
 L-Bb L-Mj L-Mn 
 S-Bb L-Bb L-Mj L-Mn 
HhH-GPD
(PF00730.27)
105 9

 H-Bb L-Bb L-Mj L-Mn 

 H-Bb H-Mj H-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mn L-Bb L-Mj L-Mn 
 H-Bb L-Bb L-Mj L-Mn 
H2TH
(PF06831.16)
105 15

 H-Bb 

 H-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb L-Bb 
 H-Bb L-Bb L-Mn 
  
Phage_integrase
(PF00589.24)
92 7

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj H-Mn L-Bb L-Mj 
 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mj 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 S-Mn L-Bb L-Mj L-Mn 
  
HMG_box
(PF00505.21)
88 21

 H-Bb H-Mj H-Mn L-Bb L-Mn 

 H-Bb H-Mj H-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mj H-Mn L-Bb L-Mn 
  
Ets
(PF00178.24)
84 17

 H-Bb H-Mj 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-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
  
zf-FPG_IleRS
(PF06827.16)
81 7

Miscellaneous

 L-Bb 
 S-Bb L-Bb L-Mj 
 S-Bb L-Mj 
 S-Bb S-Mj L-Bb L-Mj 
  
HLH
(PF00010.28)
80 22

 H-Bb H-Mj 

 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj L-Mj 
  
TFIIB
(PF00382.21)
79 9

 H-Bb 

 H-Bb 
 H-Bb H-Mj H-Mn L-Bb L-Mn 
 H-Bb H-Mj L-Bb L-Mj 
 H-Bb L-Bb 
  
DNA_methylase
(PF00145.19)
78 7

 H-Bb L-Bb L-Mj 

 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
 H-Bb L-Bb L-Mj L-Mn 
 H-Bb S-Bb S-Mj L-Bb L-Mj L-Mn 
  
LacI
(PF00356.23)
74 5

 H-Bb H-Mj L-Bb L-Mj 

 H-Bb H-Mj L-Bb L-Mj 
  
HTH_Crp_2
(PF13545.8)
72 8

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
  
RHD_DNA_bind
(PF00554.24)
71 11

 H-Bb L-Bb L-Mj 

 H-Bb H-Mj L-Bb L-Mj 
 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj 
 H-Bb S-Bb S-Mj L-Bb L-Mj L-Mn 
  
RHD_dimer
(PF16179.7)
70 9

 L-Bb 

 L-Bb 
 S-Bb L-Bb 
 S-Bb L-Bb L-Mj 
  
Myb_DNA-binding
(PF00249.33)
68 22

 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-Mn 
 H-Bb L-Bb 
  
MerR_1
(PF13411.8)
62 10

 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 
  
Bac_DNA_binding
(PF00216.23)
60 11

 S-Bb 

 H-Bb S-Bb S-Mn L-Bb 
 S-Bb S-Mj 
 S-Bb S-Mn L-Bb 
  
MarR
(PF01047.24)
58 11

 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-Mj 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 
  
z-alpha
(PF02295.19)
58 11

 H-Bb H-Mj 

 H-Bb H-Mj 
 H-Bb H-Mj H-Mn S-Bb 
 H-Bb H-Mj H-Mn S-Bb L-Bb 
 H-Bb H-Mj S-Bb 
 H-Bb H-Mj S-Bb L-Bb 
  
SRF-TF
(PF00319.20)
54 4

 H-Bb H-Mj 

 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
  
UDG
(PF03167.21)
54 10

 H-Mn L-Bb 

 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj H-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mn L-Bb L-Mj L-Mn 
 H-Mn L-Bb L-Mj L-Mn 
  
XPG_N
(PF00752.19)
53 13

 H-Bb 

 H-Bb H-Mj H-Mn 
 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj H-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mj H-Mn S-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Mj L-Bb L-Mj L-Mn 
 H-Bb L-Bb L-Mj L-Mn 
  
XPG_I
(PF00867.20)
52 7

 L-Bb 

 H-Bb L-Bb 
 H-Bb S-Bb L-Bb 
 L-Bb 
 S-Bb L-Bb 
  
MutS_III
(PF05192.20)
50 5

 L-Bb 

 H-Bb S-Bb L-Bb 
 L-Bb 
 S-Bb L-Bb 
 S-Bb L-Bb L-Mj 
MutS_I
(PF01624.22)
50 8

 L-Bb 

 H-Bb H-Mn S-Bb S-Mj S-Mn L-Bb L-Mn 
 H-Bb S-Bb S-Mj S-Mn L-Bb 
 H-Bb S-Bb S-Mj S-Mn L-Bb L-Mn 
 H-Bb S-Bb S-Mn L-Bb L-Mj L-Mn 
 L-Bb 
  
MBD
(PF01429.21)
49 9

 H-Bb S-Bb S-Mj L-Bb L-Mj 

 H-Bb S-Bb S-Mj L-Bb L-Mj 
  
Trans_reg_C
(PF00486.30)
49 7

 H-Bb H-Mj S-Bb L-Bb 

 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
  
MutS_IV
(PF05190.20)
46 4

 L-Bb 

 H-Bb S-Bb L-Bb 
 L-Bb 
 S-Bb L-Bb 
 S-Bb L-Bb L-Mj 
SAD_SRA
(PF02182.19)
45 6

 H-Bb S-Bb L-Bb L-Mj L-Mn 

 H-Bb S-Bb L-Bb L-Mj L-Mn 
Forkhead
(PF00250.20)
43 15

 H-Bb H-Mj S-Bb 

 H-Bb H-Mj S-Bb 
 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 
  
Cdd1
(PF11731.10)
42 4

 H-Bb L-Bb 

 H-Bb L-Bb 
zf-C2H2
(PF00096.28)
39 15

 H-Bb 

 H-Bb 
 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-Mj 
 H-Bb L-Bb 
  
bZIP_2
(PF07716.17)
38 4

 H-Bb H-Mj 

 H-Bb H-Mj 
  
GerE
(PF00196.21)
36 6

 H-Bb H-Mj L-Bb 

 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj L-Bb 
 H-Bb H-Mj L-Bb L-Mj 
  
MH1
(PF03165.18)
35 10

 H-Bb S-Bb S-Mj L-Bb L-Mj 

 H-Bb S-Bb S-Mj L-Bb L-Mj 
  
Zn_clus
(PF00172.20)
34 8

 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 H-Mj S-Bb S-Mn L-Bb L-Mj L-Mn 
  
Myb_DNA-bind_6
(PF13921.8)
34 12

 H-Bb H-Mj 

 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
  
bZIP_1
(PF00170.23)
34 12

 H-Bb H-Mj 

 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
  
HMG_box_2
(PF09011.12)
34 5

 H-Bb H-Mj H-Mn 

 H-Bb H-Mj H-Mn 
 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj H-Mn L-Bb L-Mn 
  
GntR
(PF00392.23)
31 5

 H-Bb H-Mj S-Bb L-Bb L-Mj 

 H-Bb H-Mj S-Bb L-Bb L-Mj 
 H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
  
Runt
(PF00853.21)
30 4

 S-Bb S-Mj L-Bb L-Mj L-Mn 

 S-Bb S-Mj L-Bb L-Mj L-Mn 
  
HIN
(PF02760.17)
29 7

 L-Bb 

 H-Bb H-Mj S-Bb L-Bb 
 H-Bb S-Bb L-Bb 
 H-Bb S-Bb L-Bb L-Mj 
 L-Bb 
 S-Bb L-Bb 
  
DNA_ligase_A_M
(PF01068.23)
28 8

 S-Bb L-Bb 

 H-Bb H-Mn S-Bb L-Bb 
 H-Bb H-Mn S-Bb L-Bb L-Mn 
 H-Bb S-Bb L-Bb 
 H-Bb S-Bb L-Bb L-Mn 
 H-Bb S-Bb S-Mj L-Bb L-Mn 
 S-Bb L-Bb L-Mn 
  
TOPRIM_C
(PF16898.7)
28 3

 H-Bb 

 H-Bb 
 H-Bb H-Mn 
 H-Bb H-Mn L-Bb L-Mj 
Pou
(PF00157.19)
28 7

 H-Bb H-Mj L-Bb L-Mj 

 H-Bb H-Mj L-Bb L-Mj 
  
GATA
(PF00320.29)
28 7

 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj 

 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj 
  
zf-CXXC
(PF02008.22)
26 13

 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 L-Mn 
 L-Bb L-Mj 
 L-Bb L-Mj L-Mn 
  
MethyltransfD12
(PF02086.17)
26 4

 H-Bb L-Bb L-Mj 

 H-Bb H-Mj H-Mn L-Bb L-Mj 
 H-Bb L-Bb L-Mj 
 H-Bb S-Bb L-Bb L-Mj L-Mn 
DNA_photolyase
(PF00875.20)
23 5

 L-Bb 

 H-Bb L-Bb 
 L-Bb 
  
T-box
(PF00907.24)
22 8

 H-Bb H-Mn S-Bb S-Mj L-Bb L-Mj 

 H-Bb H-Mn S-Bb S-Mj L-Bb L-Mj 
  
LAG1-DNAbind
(PF09271.13)
22 4

 L-Bb L-Mj 

 L-Bb L-Mj 
  
IRF
(PF00605.19)
21 5

 H-Bb H-Mj S-Bb L-Bb L-Mn 

 H-Bb H-Mj S-Bb L-Bb L-Mj L-Mn 
 H-Bb H-Mj S-Bb L-Bb L-Mn 
  
CBFD_NFYB_HMF
(PF00808.25)
21 11

 H-Bb 

 H-Bb 
 H-Bb H-Mj S-Bb L-Bb 
 H-Bb H-Mj S-Bb S-Mn L-Bb 
 H-Bb L-Bb 
  
Topoisom_I
(PF01028.22)
20 6

 H-Bb L-Bb L-Mj 

 H-Bb H-Mj H-Mn L-Bb L-Mj 
 H-Bb H-Mn L-Bb L-Mj 
 H-Bb S-Bb L-Bb L-Mj L-Mn 
  
T_Ag_DNA_bind
(PF02217.18)
19 4

 H-Bb S-Bb S-Mj L-Bb L-Mj 

 H-Bb S-Bb S-Mj L-Bb L-Mj 
  
B3
(PF02362.23)
19 5

 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj 

 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj 
 H-Bb H-Mj S-Bb S-Mj L-Bb L-Mj L-Mn 
  
MazE_antitoxin
(PF04014.20)
18 5

 H-Bb S-Bb S-Mj L-Bb L-Mj 

 H-Bb S-Bb S-Mj L-Bb L-Mj 
  
HSF_DNA-bind
(PF00447.19)
18 4

 H-Bb H-Mj S-Bb L-Bb 

 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-Mj L-Mn 
  
Topo_C_assoc
(PF14370.8)
16 5

 H-Bb L-Bb 

 H-Bb H-Mj L-Bb 
 H-Bb L-Bb 
Homeobox_KN
(PF05920.13)
14 3

 H-Bb H-Mj 

 H-Bb H-Mj 
 H-Bb H-Mj L-Bb 
bZIP_Maf
(PF03131.19)
14 4

 H-Bb H-Mj 

 H-Bb H-Mj 
RQC
(PF09382.12)
12 4

 S-Bb L-Bb 

 H-Bb S-Bb L-Bb 
 H-Bb S-Bb L-Bb L-Mj 
 H-Bb S-Bb L-Bb L-Mj L-Mn 
 S-Bb L-Bb L-Mj L-Mn 
AGT
(PF11440.10)
11 5

 H-Bb H-Mn 

 H-Bb H-Mj H-Mn L-Bb 
 H-Bb H-Mj H-Mn L-Bb L-Mj L-Mn 
 H-Bb H-Mn 
  
DNA_ligase_OB_2
(PF14743.8)
10 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 
CBFB_NFYA
(PF02045.17)
9 6

 H-Bb H-Mn L-Bb L-Mj L-Mn 

 H-Bb H-Mn L-Bb L-Mj L-Mn 
  
PAX
(PF00292.20)
6 4

 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 
Tet_JBP
(PF12851.9)
6 4

 L-Bb 

 H-Bb H-Mj H-Mn S-Bb L-Bb L-Mn 
 H-Mj H-Mn S-Bb L-Bb 
 L-Bb 
  
Zn-ribbon_8
(PF09723.12)
3 3

 H-Bb H-Mj S-Bb L-Bb L-Mj 

 H-Bb H-Mj S-Bb L-Bb L-Mj 
HHH_2
(PF12826.9)
3 3

 H-Bb L-Bb 

 H-Bb L-Bb 
Interaction classes of SCOP domains
Note: this data is based only on structures available at the moment of the last SCOP release (2009)
Export table
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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