GREMLIN Database
PTRA - Protease 3
UniProt: P05458 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10786
Length: 962 (861)
Sequences: 3732 (3051)
Seq/√Len: 104.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
386_K390_D5.7771.00
364_N367_Q5.2891.00
378_L382_K4.7551.00
216_Q220_D4.5731.00
82_A217_A4.2831.00
848_P852_A4.2481.00
580_L585_N4.1041.00
580_L583_L4.0661.00
45_Q242_P3.9821.00
790_Q794_E3.9811.00
375_Y378_L3.8771.00
100_K143_D3.7791.00
99_K151_E3.7021.00
377_N381_E3.6281.00
847_K850_E3.4931.00
245_A249_A3.4091.00
824_Q827_F3.3051.00
90_L154_L3.2711.00
240_P243_E3.2461.00
504_N508_P3.2341.00
494_A498_L3.1711.00
631_E635_E3.0861.00
589_V592_I3.0441.00
904_K907_D3.0391.00
217_A220_D2.9901.00
562_S565_N2.9711.00
579_A582_Q2.8891.00
564_R686_E2.8791.00
903_Q907_D2.8401.00
235_I248_A2.8381.00
370_A374_S2.8321.00
215_Q219_K2.8091.00
220_D224_K2.7791.00
587_A590_G2.7741.00
761_V833_K2.7431.00
587_A592_I2.7081.00
642_N680_P2.6761.00
582_Q585_N2.6321.00
423_P426_H2.6001.00
87_A221_F2.5571.00
355_A372_I2.5281.00
606_A616_L2.4961.00
397_D401_R2.4911.00
447_A451_P2.4881.00
440_K444_E2.4871.00
333_V336_I2.4811.00
840_E910_H2.4561.00
565_N693_A2.4311.00
848_P902_P2.4171.00
76_S199_S2.3921.00
901_T904_K2.3791.00
468_T472_V2.3751.00
472_V476_Y2.3731.00
72_V231_M2.3421.00
778_L900_L2.3291.00
902_P906_A2.2901.00
827_F830_E2.2851.00
579_A583_L2.2641.00
380_R447_A2.2461.00
54_V232_K2.2451.00
505_P508_P2.2441.00
503_L506_Y2.2091.00
101_Y143_D2.1991.00
868_T872_E2.1991.00
121_S128_A2.1931.00
863_L894_V2.1631.00
891_D895_A2.1621.00
220_D223_E2.1551.00
869_L872_E2.1351.00
903_Q906_A2.1061.00
100_K147_D2.1041.00
424_V427_T2.0911.00
495_D508_P2.0751.00
747_F750_A2.0661.00
830_E834_A2.0611.00
139_P247_M2.0401.00
88_H91_E2.0261.00
57_L241_L2.0241.00
892_K895_A2.0081.00
495_D499_S2.0051.00
424_V428_L2.0031.00
533_R701_E2.0021.00
482_S485_T1.9991.00
859_I898_K1.9981.00
837_P841_A1.9851.00
229_N257_N1.9841.00
48_R54_V1.9751.00
907_D911_Q1.9441.00
45_Q241_L1.9191.00
622_E626_S1.9091.00
475_P479_D1.9051.00
834_A837_P1.8951.00
88_H92_H1.8761.00
498_L504_N1.8731.00
89_Y159_A1.8671.00
508_P511_F1.8671.00
377_N380_R1.8661.00
205_T208_D1.8631.00
110_Y140_G1.8581.00
550_V704_V1.8561.00
498_L507_I1.8511.00
583_L586_Q1.8481.00
495_D498_L1.8441.00
779_L909_F1.8441.00
423_P428_L1.8421.00
580_L584_S1.8371.00
159_A215_Q1.8311.00
675_R678_I1.8211.00
174_R198_F1.8201.00
246_K249_A1.7971.00
775_Y900_L1.7961.00
94_S152_P1.7911.00
45_Q245_A1.7841.00
276_G280_H1.7761.00
426_H429_D1.7451.00
565_N686_E1.7421.00
750_A753_S1.7401.00
71_V128_A1.7361.00
868_T871_E1.7301.00
851_F902_P1.7241.00
286_P359_D1.7181.00
921_I924_Q1.7181.00
772_S911_Q1.7141.00
81_E197_K1.7071.00
303_F436_R1.6951.00
70_L233_A1.6811.00
581_D585_N1.6721.00
834_A838_T1.6631.00
786_W850_E1.6521.00
746_I749_K1.6481.00
511_F515_K1.6461.00
381_E447_A1.6391.00
170_L200_G1.6331.00
455_R461_P1.6321.00
672_R678_I1.6251.00
470_Y473_D1.6251.00
219_K223_E1.6251.00
276_G281_Y1.6201.00
332_L336_I1.6151.00
587_A591_G1.6131.00
775_Y908_F1.6121.00
47_I55_V1.6021.00
276_G282_V1.5961.00
685_K689_A1.5861.00
835_F838_T1.5861.00
98_S152_P1.5851.00
498_L502_E1.5801.00
771_T904_K1.5791.00
232_K419_M1.5721.00
294_F373_F1.5701.00
579_A584_S1.5681.00
397_D404_S1.5511.00
892_K896_Q1.5451.00
494_A497_A1.5451.00
68_S73_P1.5381.00
57_L239_K1.5351.00
779_L905_L1.5331.00
711_A714_T1.5291.00
233_A252_F1.5261.00
608_G616_L1.5211.00
243_E246_K1.5201.00
590_G598_A1.5051.00
487_A490_Q1.5041.00
852_A856_Q1.5021.00
483_A487_A1.4921.00
121_S126_R1.4901.00
322_T326_W1.4761.00
503_L508_P1.4741.00
487_A491_K1.4731.00
614_P618_Q1.4721.00
580_L586_Q1.4711.00
192_A267_V1.4681.00
895_A899_L1.4641.00
535_V701_E1.4631.00
94_S98_S1.4611.00
568_M686_E1.4581.00
634_L684_L1.4581.00
301_A304_R1.4571.00
499_S508_P1.4471.00
125_Y195_G1.4411.00
709_T712_Q1.4401.00
683_T686_E1.4371.00
424_V429_D1.4361.00
511_F514_I1.4361.00
271_T274_Q1.4281.00
236_Y412_V1.4241.00
139_P251_T1.4141.00
579_A585_N1.4111.00
314_L384_I1.4111.00
572_N576_A1.4071.00
612_R615_Q1.4061.00
353_I372_I1.4011.00
151_E255_V1.4001.00
672_R675_R1.4001.00
203_L207_S1.3931.00
536_Y708_M1.3931.00
684_L688_L1.3901.00
827_F831_R1.3881.00
426_H431_V1.3831.00
138_L244_L1.3801.00
615_Q618_Q1.3781.00
183_Q187_E1.3761.00
554_L700_P1.3691.00
481_I489_W1.3681.00
93_M218_L1.3671.00
782_I905_L1.3671.00
581_D584_S1.3611.00
367_Q370_A1.3590.99
239_K244_L1.3590.99
293_E352_A1.3580.99
888_D892_K1.3570.99
762_F813_G1.3570.99
749_K752_N1.3570.99
705_I873_A1.3520.99
91_E169_E1.3510.99
119_N122_T1.3480.99
745_V748_E1.3470.99
504_N507_I1.3450.99
69_A416_A1.3430.99
188_T456_I1.3430.99
771_T896_Q1.3400.99
297_D448_M1.3390.99
322_T325_D1.3370.99
774_A896_Q1.3320.99
379_L384_I1.3320.99
532_L721_Q1.3310.99
333_V355_A1.3280.99
862_M897_I1.3230.99
159_A218_L1.3230.99
184_V187_E1.3220.99
52_G257_N1.3200.99
366_D370_A1.3180.99
312_T351_L1.3090.99
131_L141_A1.3070.99
837_P840_E1.3060.99
712_Q715_T1.3050.99
92_H122_T1.3040.99
374_S378_L1.3040.99
332_L364_N1.2970.99
88_H122_T1.2970.99
494_A508_P1.2960.99
274_Q280_H1.2940.99
223_E258_K1.2940.99
488_D491_K1.2940.99
718_R722_K1.2900.99
752_N755_D1.2890.99
423_P427_T1.2880.99
246_K250_D1.2870.99
654_F802_F1.2840.99
621_L723_Q1.2840.99
441_A444_E1.2780.99
154_L215_Q1.2770.99
325_D329_K1.2730.99
876_L880_F1.2730.99
83_Y205_T1.2690.99
85_G201_G1.2670.99
390_D393_A1.2660.99
852_A855_Q1.2660.99
494_A499_S1.2650.99
685_K688_L1.2610.99
635_E638_K1.2600.99
715_T718_R1.2550.99
789_N794_E1.2540.99
322_T327_L1.2520.99
858_V897_I1.2500.99
247_M250_D1.2470.99
91_E122_T1.2450.99
525_L533_R1.2440.99
277_I281_Y1.2430.99
288_K359_D1.2330.99
68_S75_G1.2320.99
561_D565_N1.2320.99
869_L873_A1.2260.99
745_V749_K1.2230.99
147_D151_E1.2200.99
439_A443_K1.2190.99
494_A507_I1.2190.99
91_E119_N1.2090.99
528_D533_R1.2090.99
202_N205_T1.2060.99
173_A200_G1.2050.99
484_Q488_D1.2000.99
828_L835_F1.1980.99
122_T162_E1.1960.99
859_I894_V1.1940.99
498_L508_P1.1910.99
485_T488_D1.1900.99
96_M793_T1.1890.99
711_A715_T1.1860.99
88_H119_N1.1800.99
371_A375_Y1.1800.99
500_L503_L1.1780.99
67_L412_V1.1760.99
769_E772_S1.1750.99
552_L702_F1.1730.98
119_N792_R1.1720.98
582_Q586_Q1.1700.98
745_V750_A1.1700.98
243_E247_M1.1690.98
746_I750_A1.1690.98
634_L638_K1.1680.98
688_L692_D1.1670.98
829_W833_K1.1670.98
276_G279_I1.1650.98
831_R834_A1.1640.98
277_I282_V1.1630.98
686_E689_A1.1610.98
590_G594_F1.1590.98
277_I280_H1.1580.98
507_I510_D1.1550.98
142_V247_M1.1520.98
73_P76_S1.1460.98
778_L905_L1.1430.98
98_S154_L1.1410.98
327_L333_V1.1400.98
53_M233_A1.1400.98
468_T475_P1.1370.98
369_V456_I1.1350.98
92_H119_N1.1320.98
438_D441_A1.1320.98
88_H169_E1.1310.98
432_N435_D1.1280.98
422_V426_H1.1260.98
642_N646_D1.1230.98
120_A169_E1.1220.98
319_S322_T1.1200.98
652_K655_E1.1190.98
122_T792_R1.1190.98
156_K160_E1.1190.98
92_H120_A1.1190.98
182_A186_A1.1180.98
91_E120_A1.1170.98
748_E752_N1.1150.98
744_S747_F1.1110.98
70_L231_M1.1100.98
154_L219_K1.1070.98
428_L431_V1.1050.98
597_N603_M1.1050.98
119_N201_G1.1050.98
311_I442_V1.1040.98
493_A497_A1.1030.98
590_G593_S1.1030.98
156_K215_Q1.1030.98
99_K255_V1.0970.98
122_T169_E1.0960.98
771_T775_Y1.0940.98
325_D582_Q1.0940.98
653_A656_Q1.0940.98
108_A118_H1.0920.98
292_V369_V1.0920.98
502_E505_P1.0900.98
88_H120_A1.0900.98
89_Y218_L1.0880.98
828_L832_Y1.0870.98
562_S693_A1.0860.98
631_E684_L1.0840.97
455_R462_K1.0830.97
484_Q487_A1.0830.97
227_S230_L1.0780.97
907_D910_H1.0770.97
427_T430_A1.0770.97
498_L505_P1.0770.97
74_V221_F1.0760.97
397_D406_T1.0740.97
880_F883_G1.0740.97
780_G803_A1.0730.97
792_R799_Y1.0710.97
373_F377_N1.0710.97
119_N799_Y1.0690.97
359_D363_A1.0670.97
499_S503_L1.0670.97
568_M687_V1.0660.97
579_A586_Q1.0640.97
528_D531_N1.0630.97
91_E799_Y1.0630.97
279_I282_V1.0630.97
84_Q202_N1.0630.97
146_A150_A1.0620.97
838_T844_R1.0610.97
88_H799_Y1.0600.97
802_F815_G1.0600.97
435_D439_A1.0600.97
120_A162_E1.0570.97
355_A368_V1.0560.97
661_A762_F1.0550.97
56_L415_L1.0550.97
483_A486_F1.0540.97
788_Y793_T1.0540.97
920_A924_Q1.0540.97
323_L372_I1.0530.97
179_M186_A1.0520.97
100_K151_E1.0510.97
145_L148_A1.0500.97
249_A253_G1.0490.97
688_L691_R1.0470.97
831_R835_F1.0460.97
778_L897_I1.0450.97
185_S293_E1.0450.97
672_R682_I1.0450.97
167_N203_L1.0440.97
462_K465_H1.0430.97
879_D883_G1.0400.97
581_D586_Q1.0400.97
689_A693_A1.0390.97
748_E751_G1.0390.97
747_F751_G1.0390.97
397_D403_P1.0380.97
70_L73_P1.0380.97
841_A845_A1.0360.97
756_S759_A1.0330.97
791_L798_G1.0320.97
94_S222_H1.0270.97
90_L218_L1.0260.96
92_H799_Y1.0260.96
120_A792_R1.0250.96
92_H169_E1.0220.96
538_P710_E1.0220.96
756_S765_T1.0220.96
501_P505_P1.0220.96
275_K280_H1.0210.96
121_S130_Y1.0200.96
497_A507_I1.0190.96
493_A496_I1.0190.96
84_Q217_A1.0170.96
326_W375_Y1.0170.96
139_P250_D1.0160.96
167_N207_S1.0150.96
588_S612_R1.0150.96
614_P719_D1.0140.96
235_I239_K1.0130.96
444_E447_A1.0090.96
851_F905_L1.0080.96
191_P196_S1.0070.96
156_K216_Q1.0030.96
495_D504_N1.0020.96
738_V742_K1.0020.96
275_K279_I1.0010.96
88_H162_E0.9990.96
825_P828_L0.9980.96
98_S148_A0.9980.96
510_D513_L0.9970.96
422_V428_L0.9960.96
139_P244_L0.9960.96
825_P835_F0.9960.96
119_N162_E0.9960.96
514_I712_Q0.9960.96
368_V372_I0.9950.96
360_K363_A0.9950.96
565_N568_M0.9940.96
124_P199_S0.9920.96
247_M251_T0.9910.96
158_Y161_R0.9910.96
896_Q899_L0.9900.96
64_V867_Q0.9900.96
638_K679_L0.9900.96
588_S591_G0.9870.96
173_A179_M0.9860.96
868_T873_A0.9860.96
468_T471_F0.9840.96
176_R179_M0.9830.96
461_P464_P0.9800.95
826_S830_E0.9790.95
162_E169_E0.9790.95
423_P431_V0.9790.95
855_Q897_I0.9770.95
83_Y197_K0.9740.95
503_L507_I0.9710.95
96_M158_Y0.9710.95
303_F440_K0.9710.95
840_E913_V0.9700.95
495_D506_Y0.9700.95
170_L173_A0.9670.95
318_R322_T0.9670.95
140_G144_R0.9670.95
333_V340_S0.9620.95
638_K642_N0.9620.95
824_Q840_E0.9610.95
312_T338_A0.9610.95
275_K281_Y0.9610.95
499_S504_N0.9570.95
836_F840_E0.9570.95
677_K681_S0.9560.95
893_I897_I0.9560.95
895_A898_K0.9550.95
307_T441_A0.9550.95
749_K753_S0.9540.95
708_M713_A0.9500.95
398_I402_Y0.9490.95
617_F716_L0.9450.94
91_E792_R0.9440.94
274_Q277_I0.9380.94
422_V425_E0.9380.94
146_A251_T0.9370.94
508_P514_I0.9360.94
167_N171_T0.9340.94
818_L828_L0.9340.94
653_A665_S0.9340.94
568_M572_N0.9330.94
673_D676_R0.9330.94
72_V149_I0.9320.94
424_V431_V0.9300.94
190_N350_V0.9290.94
66_S135_N0.9260.94
463_E466_N0.9260.94
99_K254_R0.9260.94
820_S828_L0.9260.94
625_F725_G0.9250.94
169_E792_R0.9250.94
501_P507_I0.9250.94
152_P222_H0.9230.94
425_E431_V0.9230.94
59_S241_L0.9220.94
714_T718_R0.9210.94
92_H162_E0.9180.94
104_A161_R0.9170.94
494_A504_N0.9170.94
830_E833_K0.9170.94
591_G594_F0.9160.93
590_G596_T0.9160.93
426_H430_A0.9140.93
498_L503_L0.9130.93
73_P232_K0.9130.93
143_D147_D0.9130.93
592_I598_A0.9130.93
652_K656_Q0.9130.93
172_M200_G0.9120.93
101_Y147_D0.9120.93
385_D388_Y0.9120.93
462_K466_N0.9120.93
614_P716_L0.9070.93
68_S141_A0.9070.93
682_I686_E0.9060.93
216_Q223_E0.9050.93
180_R183_Q0.9040.93
57_L244_L0.9030.93
94_S148_A0.9030.93
93_M115_G0.9030.93
88_H792_R0.9000.93
704_V713_A0.9000.93
848_P903_Q0.8980.93
775_Y905_L0.8970.93
673_D678_I0.8950.93
92_H792_R0.8940.93
326_W330_Q0.8930.93
757_A825_P0.8930.93
322_T388_Y0.8920.93
336_I340_S0.8910.93
93_M96_M0.8900.92
568_M690_Y0.8900.92
133_V141_A0.8890.92
471_F475_P0.8890.92
629_A688_L0.8880.92
502_E507_I0.8880.92
738_V744_S0.8870.92
455_R459_I0.8860.92
744_S748_E0.8860.92
150_A255_V0.8840.92
290_L355_A0.8830.92
501_P508_P0.8820.92
401_R404_S0.8810.92
113_M116_G0.8790.92
782_I854_I0.8790.92
816_F832_Y0.8780.92
151_E254_R0.8780.92
83_Y217_A0.8770.92
511_F516_S0.8770.92
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787_F835_F0.5480.62
145_L170_L0.5470.62
120_A127_T0.5470.62
164_N203_L0.5470.62
497_A501_P0.5460.62
50_D256_P0.5460.62
671_S678_I0.5460.62
347_N350_V0.5460.62
738_V741_K0.5460.62
139_P143_D0.5460.62
761_V764_P0.5450.61
770_Y774_A0.5440.61
96_M148_A0.5440.61
886_R892_K0.5440.61
412_V418_T0.5430.61
98_S173_A0.5430.61
92_H201_G0.5430.61
790_Q831_R0.5430.61
537_A872_E0.5430.61
107_L110_Y0.5420.61
576_A623_G0.5420.61
721_Q725_G0.5420.61
529_E718_R0.5410.61
536_Y713_A0.5410.61
899_L903_Q0.5400.61
474_A478_V0.5390.61
494_A501_P0.5390.61
560_M699_R0.5380.61
48_R51_N0.5380.61
751_G755_D0.5370.60
326_W378_L0.5370.60
176_R180_R0.5370.60
791_L831_R0.5370.60
100_K250_D0.5370.60
310_L321_G0.5360.60
672_R680_P0.5360.60
322_T330_Q0.5350.60
139_P239_K0.5350.60
229_N258_K0.5340.60
316_G320_P0.5340.60
454_A461_P0.5340.60
541_Y872_E0.5330.60
314_L322_T0.5330.60
742_K748_E0.5330.60
188_T455_R0.5320.60
576_A629_A0.5310.60
206_L791_L0.5310.60
359_D364_N0.5310.60
683_T704_V0.5310.60
315_I321_G0.5290.59
85_G119_N0.5290.59
504_N510_D0.5290.59
89_Y95_L0.5290.59
844_R851_F0.5280.59
165_A793_T0.5280.59
51_N57_L0.5270.59
519_K522_H0.5270.59
520_Y524_E0.5260.59
81_E204_E0.5260.59
109_E379_L0.5260.59
759_A832_Y0.5250.59
530_S718_R0.5250.59
111_L116_G0.5250.59
467_K471_F0.5250.59
65_K166_V0.5240.59
653_A658_I0.5230.58
840_E909_F0.5230.58
48_R52_G0.5230.58
159_A162_E0.5230.58
714_T717_A0.5230.58
763_V766_G0.5220.58
97_G122_T0.5210.58
437_Y442_V0.5210.58
450_T454_A0.5210.58
504_N608_G0.5210.58
485_T490_Q0.5200.58
315_I318_R0.5200.58
602_L699_R0.5200.58
355_A359_D0.5190.58
634_L682_I0.5190.58
552_L559_A0.5190.58
310_L320_P0.5190.58
512_S515_K0.5180.58
123_A413_E0.5180.58
339_N351_L0.5180.58
201_G799_Y0.5180.58
757_A765_T0.5170.58
566_Q571_L0.5170.58
731_W735_K0.5160.57
583_L623_G0.5160.57
778_L851_F0.5160.57
499_S505_P0.5160.57
316_G339_N0.5150.57
494_A506_Y0.5150.57
483_A488_D0.5150.57
170_L202_N0.5150.57
862_M866_P0.5140.57
535_V540_R0.5140.57
661_A665_S0.5140.57
291_R352_A0.5140.57
80_P194_P0.5130.57
565_N689_A0.5130.57
678_I683_T0.5130.57
366_D484_Q0.5120.57
573_D602_L0.5110.57
127_T166_V0.5110.57
341_D354_S0.5110.57
569_F573_D0.5110.57
906_A910_H0.5100.56
840_E845_A0.5100.56
675_R681_S0.5100.56
521_D527_V0.5100.56
798_G818_L0.5090.56
873_A877_S0.5090.56
497_A506_Y0.5090.56
90_L165_A0.5080.56
558_K569_F0.5080.56
915_E918_G0.5080.56
500_L505_P0.5080.56
456_I461_P0.5080.56
88_H201_G0.5080.56
148_A152_P0.5070.56
518_K522_H0.5060.56
737_V740_D0.5050.56
78_E225_Y0.5050.56
553_I603_M0.5040.56
318_R336_I0.5040.56
83_Y159_A0.5040.56
833_K920_A0.5040.56
341_D350_V0.5030.55
572_N578_L0.5030.55
108_A111_L0.5020.55
45_Q240_P0.5020.55
90_L93_M0.5020.55
145_L818_L0.5020.55
580_L589_V0.5010.55
304_R448_M0.5010.55
654_F815_G0.5010.55
674_E677_K0.5010.55
729_S742_K0.5000.55
564_R678_I0.5000.55
397_D405_I0.5000.55
330_Q371_A0.5000.55
235_I254_R0.5000.55
526_I714_T0.5000.55
481_I485_T0.5000.55
522_H525_L0.5000.55
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  
1q2lA 1 0.973 100 0.235 Contact Map
3cwwA 3 0.9699 100 0.276 Contact Map
2fgeA 1 0.9272 100 0.411 Contact Map
4l3tA 1 0.8794 100 0.422 Contact Map
3s5mA 1 0.9252 100 0.451 Contact Map
3eoqA 2 0.4189 100 0.634 Contact Map
3amiA 2 0.4304 100 0.639 Contact Map
4nnzA 2 0.4044 100 0.646 Contact Map
1hr6B 1 0.4439 100 0.654 Contact Map
4xeaA 2 0.4231 100 0.657 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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