GREMLIN Database
PARC - DNA topoisomerase 4 subunit A
UniProt: Q45066 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 806 (733)
Sequences: 5085 (2524)
Seq/√Len: 93.2

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
73_I84_V5.7661.00
372_K453_E5.5291.00
187_G478_A4.6671.00
198_Q467_T4.4601.00
191_D474_K4.2871.00
195_K202_C4.1221.00
660_T686_I3.9741.00
62_F103_E3.5731.00
195_K210_V3.4681.00
454_S461_K3.3651.00
140_N369_Q3.3461.00
454_S458_N3.2281.00
192_A211_I3.1411.00
390_E411_K3.1061.00
245_A319_Y3.0891.00
451_E461_K3.0691.00
111_I299_L2.9981.00
196_R349_L2.9601.00
196_R202_C2.9401.00
612_K643_E2.9051.00
145_V156_V2.8691.00
369_Q373_D2.8301.00
451_E454_S2.8051.00
661_H693_F2.7661.00
393_A397_S2.7541.00
203_S206_E2.6831.00
661_H692_D2.6781.00
194_I471_K2.6751.00
58_F131_S2.6731.00
187_G480_T2.6201.00
205_D233_E2.6141.00
383_K414_F2.5981.00
68_T124_A2.5961.00
143_E362_N2.5931.00
67_K75_N2.5521.00
162_F167_V2.5091.00
207_L345_L2.5031.00
655_Q667_W2.4871.00
361_T365_V2.4691.00
204_V344_S2.4551.00
639_K681_A2.4481.00
190_I470_L2.4481.00
511_K538_R2.4411.00
472_A476_K2.4041.00
420_E424_S2.4041.00
197_I463_L2.3851.00
187_G191_D2.3631.00
187_G474_K2.3411.00
132_E477_Y2.3341.00
246_E260_T2.3241.00
207_L346_P2.2951.00
195_K199_M2.2741.00
689_K731_R2.2541.00
373_D417_P2.2511.00
255_E311_A2.2411.00
99_N479_D2.2391.00
181_I332_M2.2341.00
652_G670_E2.2211.00
202_C206_E2.2161.00
684_K687_N2.2101.00
666_L730_K2.2061.00
556_N643_E2.1961.00
244_K484_V2.1951.00
139_K367_E2.1661.00
336_H343_M2.1601.00
461_K464_K2.1561.00
103_E125_R2.1461.00
357_K463_L2.1381.00
453_E457_S2.1311.00
448_K452_L2.1301.00
610_F697_G2.1291.00
288_S306_K2.1271.00
666_L726_T2.1221.00
245_A257_I2.1221.00
610_F658_M2.1161.00
676_V680_A2.1121.00
199_M206_E2.1101.00
259_I303_I2.1021.00
444_E448_K2.1001.00
378_V438_L2.0851.00
651_N654_S2.0811.00
128_P476_K2.0601.00
167_V189_V2.0481.00
612_K642_D2.0401.00
146_P153_K2.0311.00
723_F735_M2.0301.00
505_V565_V2.0271.00
374_R441_E2.0221.00
370_K373_D2.0181.00
65_A88_M2.0101.00
205_D229_R2.0081.00
650_T670_E2.0061.00
189_V211_I2.0021.00
612_K693_F1.9691.00
658_M685_G1.9521.00
229_R233_E1.9501.00
361_T456_L1.9491.00
440_E444_E1.9471.00
245_A315_L1.9461.00
364_S452_L1.9351.00
464_K468_N1.9341.00
405_K420_E1.9321.00
360_V466_I1.9261.00
146_P150_D1.9241.00
47_I87_A1.9121.00
394_T407_N1.9021.00
357_K459_D1.8701.00
344_S347_S1.8601.00
436_T440_E1.8591.00
710_T736_L1.8561.00
686_I694_V1.8531.00
240_I325_Q1.8431.00
545_M549_D1.8431.00
502_S546_N1.8381.00
204_V233_E1.8371.00
194_I467_T1.8361.00
36_A351_A1.8331.00
243_G259_I1.8301.00
726_T730_K1.8261.00
346_P350_D1.8201.00
270_N273_K1.8131.00
557_K589_D1.8131.00
616_V685_G1.8121.00
262_I301_V1.8051.00
250_I256_Q1.8011.00
351_A354_G1.7961.00
443_E447_K1.7951.00
400_D403_D1.7891.00
341_M347_S1.7831.00
202_C210_V1.7811.00
375_H442_A1.7801.00
455_I465_V1.7721.00
196_R350_D1.7701.00
82_S86_E1.7671.00
462_L465_V1.7521.00
458_N461_K1.7511.00
249_T255_E1.7511.00
196_R353_I1.7431.00
83_S87_A1.7411.00
555_T592_I1.7351.00
365_V369_Q1.7061.00
383_K387_I1.6931.00
63_R67_K1.6931.00
181_I348_I1.6901.00
204_V346_P1.6841.00
67_K71_N1.6751.00
193_V353_I1.6661.00
350_D354_G1.6491.00
439_K443_E1.6441.00
213_G228_I1.6421.00
162_F473_L1.6311.00
143_E156_V1.6211.00
672_E727_S1.6181.00
206_E209_E1.6131.00
608_L616_V1.6111.00
367_E452_L1.6111.00
336_H351_A1.6081.00
608_L656_I1.6051.00
88_M124_A1.6021.00
402_R406_N1.5981.00
397_S407_N1.5831.00
615_M684_K1.5791.00
401_K428_Y1.5701.00
132_E135_R1.5571.00
434_D437_A1.5391.00
406_N410_A1.5361.00
451_E455_I1.5321.00
658_M694_V1.5301.00
36_A348_I1.5221.00
337_N354_G1.5161.00
391_V408_L1.5091.00
50_A71_N1.5011.00
448_K451_E1.5001.00
450_E454_S1.4931.00
67_K152_S1.4831.00
724_E733_V1.4801.00
655_Q669_G1.4741.00
332_M348_I1.4721.00
240_I327_T1.4611.00
171_T180_D1.4531.00
363_R469_S1.4501.00
89_V116_P1.4481.00
199_M202_C1.4461.00
225_V487_E1.4451.00
503_E547_T1.4411.00
244_K261_E1.4190.99
606_Y675_V1.4180.99
726_T733_V1.4140.99
230_K233_E1.4090.99
226_D230_K1.3970.99
293_E302_V1.3960.99
361_T462_L1.3830.99
91_M97_V1.3820.99
65_A124_A1.3800.99
67_K74_G1.3780.99
546_N549_D1.3780.99
512_D534_K1.3730.99
442_A446_G1.3730.99
323_D326_I1.3710.99
134_L158_L1.3690.99
382_M442_A1.3620.99
610_F694_V1.3570.99
399_S403_D1.3490.99
459_D463_L1.3490.99
272_V301_V1.3480.99
193_V349_L1.3450.99
247_I257_I1.3410.99
708_L735_M1.3370.99
405_K416_E1.3360.99
275_M290_V1.3310.99
718_M723_F1.3270.99
607_L647_V1.3260.99
479_D482_R1.3250.99
50_A73_I1.3090.99
295_D298_G1.3080.99
556_N591_T1.3040.99
67_K119_M1.3030.99
511_K540_L1.3020.99
450_E453_E1.3000.99
287_I303_I1.2980.99
379_E446_G1.2970.99
556_N590_E1.2960.99
75_N152_S1.2930.99
274_K277_E1.2910.99
357_K462_L1.2850.99
608_L673_V1.2810.99
557_K587_D1.2760.99
454_S457_S1.2760.99
254_R288_S1.2730.99
423_V428_Y1.2730.99
447_K451_E1.2710.99
275_M303_I1.2650.99
471_K474_K1.2570.99
379_E442_A1.2550.99
71_N75_N1.2540.99
409_I419_A1.2520.99
232_Y330_F1.2500.99
394_T411_K1.2480.99
180_D329_N1.2470.99
468_N472_A1.2420.99
271_L301_V1.2400.98
98_R479_D1.2400.98
387_I414_F1.2380.98
309_A314_I1.2370.98
232_Y345_L1.2360.98
140_N365_V1.2330.98
347_S350_D1.2320.98
238_K327_T1.2320.98
660_T692_D1.2280.98
467_T471_K1.2240.98
293_E300_R1.2190.98
248_E300_R1.2160.98
554_F647_V1.2080.98
204_V207_L1.2050.98
734_V737_R1.2030.98
61_N125_R1.1990.98
471_K475_K1.1960.98
468_N471_K1.1910.98
272_V290_V1.1910.98
204_V208_M1.1880.98
291_R304_E1.1860.98
736_L742_N1.1800.98
655_Q725_K1.1780.98
618_K675_V1.1720.98
190_I474_K1.1680.98
382_M439_K1.1680.98
403_D407_N1.1640.98
637_N680_A1.1640.98
196_R346_P1.1610.98
444_E447_K1.1610.98
390_E393_A1.1610.98
256_Q304_E1.1600.98
409_I416_E1.1550.98
609_F644_L1.1530.98
333_V342_L1.1500.98
29_Q335_I1.1500.98
195_K206_E1.1470.97
49_Y52_H1.1460.97
455_I461_K1.1460.97
377_I421_A1.1420.97
11_P14_E1.1410.97
228_I239_I1.1330.97
243_G324_L1.1330.97
354_G357_K1.1320.97
352_Y356_Q1.1270.97
360_V469_S1.1250.97
20_F30_D1.1250.97
447_K450_E1.1180.97
738_E742_N1.1180.97
368_L449_I1.1160.97
606_Y618_K1.1150.97
552_L560_Y1.1140.97
221_I244_K1.1130.97
73_I148_F1.1130.97
376_H415_T1.1110.97
247_I315_L1.1100.97
241_I326_I1.1050.97
562_Y627_Q1.1040.97
13_E17_G1.0940.97
365_V372_K1.0930.97
241_I483_S1.0920.97
213_G485_I1.0910.97
245_A259_I1.0890.97
63_R151_T1.0870.97
54_D71_N1.0850.96
221_I241_I1.0810.96
603_P622_T1.0760.96
654_S701_Q1.0710.96
705_S717_R1.0700.96
381_L438_L1.0700.96
657_F665_G1.0690.96
718_M722_E1.0680.96
18_D22_R1.0670.96
615_M681_A1.0660.96
48_L134_L1.0610.96
375_H449_I1.0570.96
334_A348_I1.0550.96
502_S547_T1.0550.96
138_D367_E1.0540.96
528_G573_W1.0530.96
220_G243_G1.0530.96
559_S587_D1.0510.96
360_V462_L1.0510.96
400_D406_N1.0510.96
620_E675_V1.0490.96
58_F128_P1.0470.96
305_L309_A1.0470.96
610_F685_G1.0460.96
231_A330_F1.0440.96
435_I439_K1.0400.96
239_I330_F1.0390.95
382_M438_L1.0390.95
687_N731_R1.0380.95
571_I575_D1.0370.95
378_V445_L1.0370.95
133_L160_A1.0370.95
545_M565_V1.0340.95
608_L650_T1.0300.95
404_A431_T1.0270.95
572_R575_D1.0240.95
662_L692_D1.0220.95
388_L396_R1.0220.95
336_H341_M1.0210.95
460_K468_N1.0200.95
497_E564_P1.0200.95
102_I124_A1.0160.95
225_V228_I1.0160.95
248_E258_V1.0120.95
613_N641_E1.0120.95
472_A475_K1.0070.95
50_A84_V1.0070.95
161_M356_Q1.0060.95
162_F190_I1.0050.95
701_Q704_D1.0030.95
183_P217_P1.0030.95
648_H697_G0.9960.94
73_I82_S0.9910.94
191_D194_I0.9880.94
72_V84_V0.9870.94
620_E623_H0.9860.94
57_T60_K0.9840.94
190_I193_V0.9840.94
182_P332_M0.9830.94
140_N362_N0.9820.94
374_R378_V0.9810.94
364_S455_I0.9790.94
129_I164_N0.9770.94
407_N410_A0.9740.94
227_G230_K0.9740.94
36_A343_M0.9730.94
219_G244_K0.9720.94
44_Q96_K0.9710.94
387_I390_E0.9710.94
259_I324_L0.9700.94
398_S407_N0.9680.93
194_I474_K0.9670.93
547_T565_V0.9660.93
738_E741_K0.9630.93
613_N642_D0.9610.93
208_M233_E0.9600.93
167_V186_L0.9560.93
533_M539_M0.9560.93
305_L314_I0.9520.93
646_D697_G0.9520.93
199_M203_S0.9490.93
274_K323_D0.9480.93
366_Y370_K0.9480.93
615_M639_K0.9480.93
191_D471_K0.9480.93
221_I486_E0.9450.93
624_Y635_A0.9420.92
619_T624_Y0.9410.92
619_T623_H0.9390.92
609_F635_A0.9380.92
56_N68_T0.9370.92
739_L743_P0.9370.92
687_N729_A0.9370.92
451_E468_N0.9360.92
225_V229_R0.9350.92
443_E446_G0.9340.92
416_E420_E0.9330.92
637_N679_R0.9310.92
375_H446_G0.9270.92
101_L133_L0.9260.92
740_K743_P0.9260.92
451_E458_N0.9260.92
54_D67_K0.9230.92
657_F706_I0.9190.92
461_K465_V0.9140.91
554_F560_Y0.9090.91
349_L353_I0.9060.91
367_E448_K0.9040.91
54_D68_T0.9030.91
708_L723_F0.9020.91
202_C353_I0.9010.91
460_K464_K0.9000.91
509_V595_A0.8970.91
736_L741_K0.8970.91
266_V271_L0.8970.91
369_Q372_K0.8960.91
193_V470_L0.8960.91
421_A425_L0.8940.90
385_L435_I0.8930.90
165_L334_A0.8920.90
99_N129_I0.8920.90
211_I345_L0.8890.90
660_T694_V0.8860.90
664_Y731_R0.8820.90
609_F647_V0.8810.90
451_E465_V0.8810.90
676_V681_A0.8800.90
63_R75_N0.8800.90
394_T419_A0.8800.90
464_K475_K0.8790.90
195_K209_E0.8780.90
199_M210_V0.8760.89
71_N148_F0.8720.89
59_D131_S0.8720.89
295_D299_L0.8710.89
379_E415_T0.8700.89
224_G227_G0.8690.89
507_V565_V0.8640.89
112_D268_K0.8600.89
553_L595_A0.8590.89
591_T643_E0.8550.88
129_I162_F0.8540.88
636_L644_L0.8530.88
383_K413_E0.8520.88
425_L429_R0.8510.88
505_V547_T0.8490.88
135_R356_Q0.8480.88
226_D229_R0.8460.88
557_K590_E0.8460.88
50_A76_Y0.8440.88
197_I467_T0.8400.87
457_S461_K0.8380.87
242_R325_Q0.8380.87
455_I462_L0.8350.87
440_E443_E0.8350.87
198_Q471_K0.8340.87
25_K29_Q0.8340.87
50_A54_D0.8330.87
473_L477_Y0.8270.87
658_M686_I0.8260.87
258_V302_V0.8260.87
688_L692_D0.8230.86
272_V276_D0.8190.86
395_I427_L0.8180.86
99_N478_A0.8170.86
605_A649_V0.8160.86
186_L473_L0.8160.86
391_V412_Y0.8160.86
610_F616_V0.8130.86
368_L453_E0.8120.86
604_S622_T0.8100.85
15_V19_R0.8060.85
37_R157_V0.8050.85
668_F673_V0.8050.85
437_A440_E0.8050.85
257_I315_L0.8040.85
126_L130_A0.8040.85
101_L164_N0.8030.85
161_M473_L0.8030.85
245_A311_A0.8020.85
509_V543_F0.8000.85
140_N373_D0.7990.85
211_I344_S0.7980.85
391_V414_F0.7940.84
187_G475_K0.7940.84
549_D599_K0.7930.84
204_V210_V0.7920.84
196_R200_P0.7920.84
290_V303_I0.7920.84
624_Y676_V0.7900.84
394_T412_Y0.7900.84
148_F151_T0.7900.84
57_T131_S0.7900.84
446_G450_E0.7890.84
194_I198_Q0.7890.84
608_L685_G0.7880.84
30_D170_S0.7880.84
586_I592_I0.7860.84
390_E412_Y0.7860.84
611_T636_L0.7850.84
315_L319_Y0.7840.84
644_L647_V0.7830.83
364_S456_L0.7830.83
49_Y53_T0.7820.83
343_M351_A0.7820.83
167_V190_I0.7820.83
628_R631_K0.7820.83
399_S432_N0.7820.83
401_K420_E0.7810.83
191_D478_A0.7790.83
580_F592_I0.7780.83
191_D210_V0.7770.83
54_D148_F0.7750.83
193_V352_Y0.7740.83
233_E346_P0.7740.83
212_K225_V0.7740.83
608_L697_G0.7730.83
507_V568_L0.7730.83
504_D546_N0.7730.83
385_L438_L0.7730.83
68_T73_I0.7720.83
331_N342_L0.7710.83
99_N480_T0.7690.82
54_D75_N0.7690.82
607_L621_L0.7690.82
664_Y689_K0.7660.82
69_V119_M0.7660.82
659_A735_M0.7650.82
189_V192_A0.7650.82
545_M597_P0.7640.82
621_L649_V0.7640.82
393_A396_R0.7630.82
210_V346_P0.7630.82
386_S435_I0.7630.82
375_H379_E0.7630.82
161_M472_A0.7620.82
61_N151_T0.7620.82
135_R161_M0.7610.82
384_A388_L0.7600.82
628_R633_L0.7590.82
191_D212_K0.7580.81
63_R152_S0.7580.81
364_S465_V0.7560.81
502_S548_T0.7560.81
62_F105_H0.7560.81
249_T252_G0.7550.81
727_S730_K0.7550.81
238_K329_N0.7540.81
136_D141_T0.7530.81
221_I484_V0.7530.81
710_T713_G0.7520.81
165_L348_I0.7520.81
661_H695_V0.7520.81
606_Y652_G0.7520.81
277_E281_D0.7520.81
387_I394_T0.7520.81
273_K277_E0.7510.81
190_I473_L0.7490.81
555_T590_E0.7480.81
610_F646_D0.7480.81
550_V562_Y0.7470.81
362_N365_V0.7470.81
33_L334_A0.7450.80
191_D475_K0.7450.80
129_I186_L0.7450.80
69_V81_D0.7450.80
268_K292_D0.7440.80
105_H578_Q0.7430.80
426_Q429_R0.7420.80
224_G228_I0.7410.80
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44_Q84_V0.5540.58
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714_A742_N0.5530.58
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236_K331_N0.5470.57
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400_D404_A0.5460.57
707_V713_G0.5450.57
49_Y137_I0.5450.57
193_V196_R0.5450.57
715_V723_F0.5450.57
247_I255_E0.5440.57
454_S460_K0.5440.57
394_T397_S0.5440.57
201_S468_N0.5440.57
419_A690_E0.5430.57
313_G500_V0.5420.57
667_W700_L0.5420.57
44_Q86_E0.5420.57
265_E423_V0.5420.57
609_F636_L0.5410.57
165_L181_I0.5410.57
206_E471_K0.5410.57
167_V187_G0.5410.57
662_L691_D0.5400.56
553_L563_C0.5390.56
197_I353_I0.5390.56
425_L432_N0.5390.56
275_M318_L0.5390.56
12_L16_I0.5390.56
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231_A345_L0.5390.56
579_H736_L0.5380.56
512_D536_T0.5380.56
431_T436_T0.5380.56
222_I330_F0.5370.56
233_E344_S0.5370.56
105_H296_R0.5360.56
613_N691_D0.5360.56
114_D268_K0.5360.56
208_M212_K0.5360.56
271_L275_M0.5350.56
723_F726_T0.5350.56
54_D57_T0.5340.56
262_I269_A0.5330.56
63_R119_M0.5330.56
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557_K643_E0.5300.55
508_T523_F0.5290.55
223_Q488_K0.5290.55
400_D428_Y0.5290.55
276_D280_I0.5290.55
44_Q83_S0.5280.55
554_F644_L0.5280.55
110_S114_D0.5280.55
523_F544_E0.5270.55
138_D141_T0.5270.55
76_Y338_R0.5270.55
140_N153_K0.5270.55
383_K412_Y0.5270.55
272_V292_D0.5270.55
327_T330_F0.5270.55
20_F105_H0.5270.55
514_Y577_G0.5260.55
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516_K577_G0.5230.54
665_G735_M0.5230.54
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393_A407_N0.5220.54
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654_S699_I0.5210.54
167_V473_L0.5210.54
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96_K273_K0.5190.54
213_G660_T0.5180.53
190_I462_L0.5180.53
162_F356_Q0.5180.53
129_I477_Y0.5180.53
236_K329_N0.5180.53
399_S431_T0.5180.53
50_A56_N0.5170.53
366_Y369_Q0.5170.53
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194_I470_L0.5170.53
20_F331_N0.5170.53
537_D577_G0.5170.53
709_F713_G0.5160.53
124_A127_S0.5160.53
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334_A343_M0.5150.53
218_T264_F0.5150.53
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324_L729_A0.5140.53
646_D658_M0.5130.53
177_Y333_V0.5130.53
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132_E138_D0.5110.52
68_T84_V0.5110.52
250_I304_E0.5100.52
389_D395_I0.5100.52
105_H131_S0.5090.52
257_I314_I0.5090.52
188_E208_M0.5090.52
394_T426_Q0.5080.52
84_V284_V0.5080.52
357_K466_I0.5080.52
56_N124_A0.5080.52
388_L445_L0.5080.52
27_I32_A0.5070.52
382_M443_E0.5070.52
293_E304_E0.5070.52
22_R25_K0.5070.52
421_A432_N0.5070.52
50_A119_M0.5060.52
305_L311_A0.5060.52
132_E473_L0.5060.52
112_D294_T0.5050.52
698_E706_I0.5050.52
144_F641_E0.5050.52
501_A547_T0.5050.52
266_V323_D0.5050.52
655_Q702_Q0.5030.51
611_T644_L0.5030.51
600_E618_K0.5030.51
15_V26_Y0.5030.51
606_Y670_E0.5030.51
356_Q469_S0.5030.51
54_D152_S0.5030.51
517_R547_T0.5030.51
249_T253_G0.5020.51
406_N409_I0.5020.51
401_K429_R0.5020.51
96_K265_E0.5020.51
360_V463_L0.5010.51
708_L718_M0.5010.51
237_G242_R0.5010.51
435_I438_L0.5010.51
412_Y447_K0.5010.51
432_N436_T0.5010.51
189_V689_K0.5010.51
568_L583_L0.5000.51
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
1zvuA 2 0.83 100 0.187 Contact Map
2inrA 2 0.5484 100 0.319 Contact Map
4i3hA 2 0.6017 100 0.319 Contact Map
2novA 2 0.562 100 0.321 Contact Map
2xcsB 2 0.5968 100 0.323 Contact Map
2xkjE 2 0.5943 100 0.331 Contact Map
3ilwA 2 0.5695 100 0.336 Contact Map
4ckkA 2 0.5608 100 0.348 Contact Map
4gfhA 2 0.562 100 0.449 Contact Map
3l4jA 1 0.5608 100 0.468 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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