CSHB - BACSU - GREMLIN Contacts

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CSHB - DEAD-box ATP-dependent RNA helicase CshB

UniProt:	P54475	Sequences: MKETKFELYELKPFIIDAVHRLGFYEPTDIQKRLIPAVLKKESVIGQSQTGTGKTHAYLLPLLNKIDPAKDVVQVVITAPTRELANQIYQEALKITQGEEGSQIRSKCFIGGTDKQKSIDKLKIQPHLVVGTPGRIADLIKEQALSVHKAESLVIDEADLMLDMGFLADVDYIGSRMPEDLQMLVFSATIPEKLKPFLKKYMENPKYAHVEPKQVTAAKIEHILIPSKHRDKDKLLFDIMSHLNPYLGIVFANTKNTADHIAQYLTGKGMKIGLLHGGLTPRERKKVMKQINDLEFTYIIATDLAARGIDIKGVSHVINYELPDDLDFYVHRVGRTARAGSSGQAMTIYELTDEDALVRLEKMGIEFEYLELEKGEWKKGDDRQRRKKRKKTPNEADEIAHRLVKKPKKVKPGYKKKMSYEMEKIKKKQRRNQSKKRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	438 (356)
Sequences:	45128 (25936)
Seq/√Len:	1374.6

ECOLI - DEAD RHLE SRMB RECQ DBPA RHLB RECG YFJK YEJH RAPA LHR
BACSU - CSHB DBPA CSHA RECG RECQ RECS YPRA YFML COMFA YQHH YWQA
HALSA - Q9HN80 HELS Q9HNB2 RAD25 Q9HMW5 Q9HQA5 O51997 O52003
SULSO - Q981C8 HELS HELX Q97Y93 Q97X74 Q97WW1 Q980C0 Q97WT0 Q97X64 Q97YC4 Q97ZF9 Q97ZF3 Q97ZV2 Q97YQ4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_L	92_A	3.818	1.00
62_L	75_V	3.758	1.00
273_G	296_F	3.200	1.00
38_V	184_L	3.078	1.00
290_Q	295_E	3.048	1.00
89_Y	93_L	2.693	1.00
289_K	293_D	2.670	1.00
286_K	290_Q	2.581	1.00
79_A	88_I	2.579	1.00
271_K	297_T	2.573	1.00
262_A	266_T	2.536	1.00
273_G	290_Q	2.524	1.00
255_K	278_G	2.471	1.00
105_R	127_H	2.375	1.00
262_A	272_I	2.372	1.00
262_A	274_L	2.345	1.00
107_K	126_P	2.294	1.00
252_A	258_A	2.260	1.00
131_G	136_I	2.185	1.00
167_L	170_V	2.168	1.00
259_D	274_L	2.145	1.00
285_K	289_K	2.064	1.00
237_F	268_K	2.061	1.00
30_I	46_G	2.048	1.00
248_G	316_H	2.038	1.00
343_G	347_T	2.007	1.00
273_G	287_V	1.938	1.00
89_Y	106_S	1.925	1.00
139_L	144_A	1.924	1.00
252_A	261_I	1.921	1.00
89_Y	108_C	1.920	1.00
222_H	333_V	1.895	1.00
221_E	344_Q	1.883	1.00
39_L	64_N	1.862	1.00
246_Y	315_S	1.860	1.00
252_A	300_I	1.834	1.00
280_T	283_E	1.826	1.00
42_E	206_K	1.799	1.00
247_L	313_G	1.797	1.00
158_A	185_V	1.760	1.00
74_Q	151_E	1.757	1.00
169_D	172_Y	1.755	1.00
58_Y	186_F	1.738	1.00
233_D	264_Y	1.729	1.00
91_E	94_K	1.728	1.00
168_A	171_D	1.727	1.00
333_V	345_A	1.726	1.00
65_K	152_S	1.705	1.00
75_V	152_S	1.700	1.00
235_L	238_D	1.696	1.00
170_V	173_I	1.671	1.00
258_A	274_L	1.656	1.00
166_F	170_V	1.649	1.00
167_L	171_D	1.648	1.00
357_L	361_E	1.609	1.00
316_H	346_M	1.606	1.00
86_N	285_K	1.605	1.00
258_A	276_H	1.604	1.00
264_Y	268_K	1.601	1.00
319_N	333_V	1.581	1.00
223_I	344_Q	1.573	1.00
107_K	121_K	1.555	1.00
174_G	177_M	1.549	1.00
257_T	321_E	1.548	1.00
114_D	117_K	1.546	1.00
301_A	305_A	1.541	1.00
32_K	36_P	1.539	1.00
36_P	40_K	1.524	1.00
261_I	320_Y	1.507	1.00
86_N	90_Q	1.507	1.00
270_M	298_Y	1.496	1.00
305_A	309_I	1.496	1.00
34_L	57_A	1.484	1.00
317_V	336_T	1.483	1.00
205_P	210_V	1.482	1.00
38_V	44_V	1.481	1.00
237_F	241_S	1.480	1.00
353_D	356_A	1.458	1.00
254_T	257_T	1.452	1.00
265_L	300_I	1.445	1.00
21_R	101_G	1.439	1.00
91_E	310_D	1.437	1.00
46_G	186_F	1.434	1.00
24_F	56_H	1.426	1.00
116_Q	120_D	1.425	1.00
92_A	128_L	1.408	1.00
66_I	75_V	1.403	1.00
313_G	341_S	1.403	1.00
38_V	61_P	1.397	1.00
58_Y	154_V	1.376	1.00
72_V	149_K	1.375	1.00
62_L	154_V	1.372	1.00
257_T	260_H	1.366	1.00
222_H	329_Y	1.363	1.00
73_V	151_E	1.356	1.00
322_L	347_T	1.348	1.00
195_K	199_K	1.346	1.00
248_G	318_I	1.343	1.00
217_A	220_I	1.342	1.00
195_K	207_Y	1.340	1.00
74_Q	127_H	1.332	1.00
279_L	287_V	1.328	1.00
287_V	296_F	1.327	1.00
239_I	242_H	1.317	1.00
92_A	106_S	1.315	1.00
290_Q	296_F	1.312	1.00
266_T	272_I	1.311	1.00
283_E	286_K	1.303	1.00
159_D	307_R	1.300	1.00
357_L	360_L	1.298	1.00
37_A	44_V	1.297	1.00
62_L	152_S	1.295	1.00
236_L	318_I	1.292	1.00
137_A	172_Y	1.289	1.00
79_A	85_A	1.288	1.00
343_G	346_M	1.277	1.00
354_E	357_L	1.261	1.00
90_Q	94_K	1.260	1.00
126_P	129_V	1.257	1.00
168_A	172_Y	1.255	1.00
84_L	308_G	1.248	1.00
35_I	39_L	1.246	1.00
319_N	347_T	1.245	1.00
76_V	150_A	1.241	1.00
283_E	287_V	1.239	1.00
49_Q	52_T	1.238	1.00
160_L	163_D	1.233	1.00
241_S	268_K	1.228	1.00
356_A	359_R	1.222	1.00
115_K	119_I	1.220	1.00
205_P	208_A	1.215	1.00
287_V	299_I	1.199	1.00
22_L	94_K	1.197	1.00
262_A	300_I	1.196	1.00
37_A	206_K	1.195	1.00
248_G	298_Y	1.193	1.00
353_D	357_L	1.192	1.00
316_H	344_Q	1.187	1.00
204_N	207_Y	1.186	1.00
171_D	200_K	1.176	1.00
325_D	328_F	1.175	1.00
354_E	358_V	1.174	1.00
243_L	246_Y	1.170	1.00
90_Q	93_L	1.168	1.00
63_L	96_T	1.162	1.00
153_L	183_M	1.146	1.00
97_Q	101_G	1.143	1.00
353_D	360_L	1.140	1.00
85_A	108_C	1.139	1.00
319_N	332_R	1.139	1.00
65_K	151_E	1.137	1.00
349_Y	352_T	1.120	1.00
279_L	283_E	1.120	1.00
206_K	210_V	1.119	1.00
19_V	24_F	1.116	1.00
37_A	40_K	1.105	1.00
204_N	208_A	1.102	1.00
323_P	329_Y	1.100	1.00
247_L	294_L	1.098	1.00
259_D	276_H	1.096	1.00
243_L	344_Q	1.095	1.00
291_I	299_I	1.091	1.00
358_V	361_E	1.082	1.00
197_F	200_K	1.082	1.00
245_P	248_G	1.081	1.00
172_Y	175_S	1.079	1.00
207_Y	210_V	1.071	1.00
20_H	25_Y	1.070	1.00
48_S	52_T	1.070	1.00
120_D	123_K	1.069	1.00
236_L	320_Y	1.065	1.00
78_T	136_I	1.063	1.00
239_I	243_L	1.060	1.00
294_L	297_T	1.056	1.00
174_G	178_P	1.055	1.00
29_D	33_R	1.055	1.00
55_T	88_I	1.054	1.00
367_F	371_E	1.048	1.00
234_K	237_F	1.047	1.00
87_Q	310_D	1.041	1.00
29_D	32_K	1.034	1.00
34_L	46_G	1.033	1.00
107_K	129_V	1.033	1.00
275_L	305_A	1.032	1.00
235_L	239_I	1.031	1.00
275_L	304_L	1.031	1.00
258_A	300_I	1.026	1.00
89_Y	130_V	1.026	1.00
78_T	131_G	1.013	1.00
172_Y	176_R	1.007	1.00
353_D	358_V	1.004	1.00
21_R	97_Q	1.002	1.00
239_I	318_I	1.001	1.00
35_I	60_L	0.998	1.00
141_K	172_Y	0.993	1.00
276_H	279_L	0.990	1.00
233_D	320_Y	0.988	1.00
65_K	182_Q	0.988	1.00
241_S	270_M	0.988	1.00
44_V	184_L	0.983	1.00
170_V	177_M	0.980	1.00
359_R	362_K	0.977	1.00
243_L	316_H	0.972	1.00
238_D	242_H	0.970	1.00
92_A	130_V	0.970	1.00
353_D	361_E	0.969	1.00
250_V	298_Y	0.967	1.00
67_D	70_K	0.964	1.00
47_Q	209_H	0.963	1.00
119_I	123_K	0.963	1.00
270_M	297_T	0.962	1.00
198_L	201_Y	0.956	1.00
166_F	169_D	0.954	1.00
261_I	300_I	0.954	1.00
289_K	292_N	0.952	1.00
41_K	182_Q	0.952	1.00
368_E	371_E	0.951	1.00
375_G	378_K	0.951	1.00
211_E	214_Q	0.948	1.00
239_I	346_M	0.948	1.00
137_A	169_D	0.948	1.00
56_H	91_E	0.944	1.00
263_Q	266_T	0.943	1.00
286_K	289_K	0.943	1.00
263_Q	267_G	0.941	1.00
240_M	248_G	0.938	1.00
169_D	173_I	0.936	1.00
191_P	194_L	0.934	1.00
33_R	37_A	0.934	1.00
232_K	235_L	0.934	1.00
85_A	130_V	0.934	1.00
199_K	202_M	0.933	1.00
140_I	176_R	0.928	1.00
197_F	202_M	0.927	1.00
153_L	174_G	0.926	1.00
207_Y	211_E	0.925	1.00
206_K	209_H	0.923	1.00
116_Q	119_I	0.922	1.00
370_L	374_K	0.921	1.00
256_N	260_H	0.921	1.00
204_N	210_V	0.916	1.00
220_I	337_A	0.914	1.00
26_E	32_K	0.911	1.00
173_I	177_M	0.906	1.00
364_G	367_F	0.906	1.00
264_Y	267_G	0.905	1.00
287_V	290_Q	0.902	1.00
237_F	264_Y	0.898	1.00
208_A	211_E	0.897	1.00
292_N	313_G	0.896	1.00
231_D	234_K	0.895	1.00
258_A	262_A	0.893	1.00
233_D	237_F	0.889	1.00
66_I	127_H	0.889	1.00
117_K	121_K	0.889	1.00
245_P	297_T	0.887	1.00
41_K	44_V	0.886	1.00
210_V	214_Q	0.885	1.00
353_D	359_R	0.879	1.00
168_A	173_I	0.878	1.00
66_I	104_I	0.876	1.00
192_E	196_P	0.876	1.00
73_V	149_K	0.870	1.00
221_E	342_S	0.865	1.00
281_P	285_K	0.861	1.00
37_A	42_E	0.856	1.00
306_A	328_F	0.856	1.00
209_H	212_P	0.854	1.00
282_R	286_K	0.847	1.00
57_A	61_P	0.847	1.00
356_A	360_L	0.846	1.00
374_K	378_K	0.842	1.00
250_V	318_I	0.842	1.00
373_E	376_E	0.839	1.00
62_L	128_L	0.837	1.00
223_I	226_P	0.837	1.00
194_L	197_F	0.835	1.00
348_I	351_L	0.834	1.00
58_Y	88_I	0.833	1.00
118_S	121_K	0.833	1.00
232_K	239_I	0.832	1.00
355_D	360_L	0.831	1.00
152_S	184_L	0.828	1.00
46_G	184_L	0.828	1.00
271_K	296_F	0.826	1.00
371_E	375_G	0.825	1.00
152_S	182_Q	0.823	1.00
206_K	211_E	0.822	1.00
119_I	144_A	0.822	1.00
77_I	92_A	0.821	1.00
117_K	120_D	0.820	1.00
166_F	171_D	0.820	1.00
291_I	314_V	0.819	1.00
171_D	175_S	0.818	1.00
138_D	142_E	0.815	1.00
229_H	257_T	0.814	1.00
113_T	118_S	0.814	1.00
147_V	150_A	0.809	1.00
239_I	316_H	0.809	1.00
233_D	268_K	0.804	1.00
355_D	358_V	0.799	1.00
110_I	113_T	0.796	1.00
104_I	127_H	0.792	1.00
115_K	142_E	0.791	1.00
187_S	190_I	0.789	1.00
189_T	331_H	0.788	1.00
257_T	320_Y	0.788	1.00
170_V	174_G	0.787	1.00
205_P	209_H	0.786	1.00
228_K	231_D	0.785	1.00
253_N	321_E	0.782	1.00
30_I	211_E	0.781	1.00
62_L	92_A	0.777	1.00
166_F	173_I	0.777	1.00
260_H	264_Y	0.775	1.00
84_L	87_Q	0.774	1.00
219_K	342_S	0.774	1.00
113_T	117_K	0.774	1.00
223_I	346_M	0.773	1.00
41_K	65_K	0.769	1.00
366_E	371_E	0.767	1.00
75_V	128_L	0.767	1.00
294_L	313_G	0.766	1.00
137_A	141_K	0.763	1.00
363_M	367_F	0.762	1.00
86_N	108_C	0.762	1.00
232_K	321_E	0.760	1.00
113_T	121_K	0.758	1.00
363_M	366_E	0.757	1.00
154_V	184_L	0.755	1.00
233_D	260_H	0.754	1.00
251_F	305_A	0.754	1.00
253_N	324_D	0.753	1.00
63_L	67_D	0.751	1.00
358_V	362_K	0.751	1.00
36_P	39_L	0.750	1.00
344_Q	347_T	0.750	1.00
225_I	235_L	0.747	1.00
303_D	328_F	0.744	1.00
30_I	33_R	0.739	1.00
75_V	154_V	0.738	1.00
251_F	332_R	0.738	1.00
91_E	95_I	0.735	1.00
259_D	263_Q	0.734	1.00
236_L	250_V	0.734	1.00
61_P	152_S	0.733	1.00
319_N	323_P	0.733	1.00
118_S	122_L	0.733	1.00
355_D	359_R	0.732	1.00
161_M	166_F	0.730	1.00
249_I	301_A	0.728	1.00
159_D	331_H	0.726	1.00
365_I	368_E	0.726	1.00
106_S	109_F	0.725	1.00
121_K	126_P	0.724	1.00
366_E	370_L	0.722	1.00
234_K	238_D	0.722	1.00
222_H	226_P	0.719	1.00
76_V	153_L	0.719	1.00
371_E	374_K	0.718	1.00
212_P	215_V	0.716	1.00
367_F	370_L	0.716	1.00
202_M	205_P	0.715	1.00
303_D	332_R	0.710	1.00
288_M	311_I	0.703	1.00
238_D	241_S	0.701	1.00
192_E	195_K	0.696	1.00
205_P	211_E	0.695	1.00
235_L	348_I	0.695	1.00
250_V	320_Y	0.694	1.00
199_K	204_N	0.689	1.00
188_A	334_G	0.687	1.00
109_F	118_S	0.684	1.00
314_V	336_T	0.680	1.00
200_K	204_N	0.679	1.00
246_Y	316_H	0.678	1.00
160_L	307_R	0.677	1.00
133_P	155_I	0.676	1.00
33_R	36_P	0.673	1.00
227_S	235_L	0.672	1.00
288_M	292_N	0.668	1.00
131_G	145_L	0.666	1.00
348_I	352_T	0.666	1.00
19_V	60_L	0.665	1.00
62_L	77_I	0.665	1.00
232_K	236_L	0.660	1.00
193_K	196_P	0.659	1.00
151_E	181_L	0.655	1.00
45_I	190_I	0.654	1.00
262_A	265_L	0.652	1.00
374_K	377_W	0.652	1.00
135_R	138_D	0.651	1.00
105_R	125_Q	0.651	1.00
246_Y	341_S	0.650	1.00
222_H	227_S	0.649	1.00
247_L	297_T	0.648	1.00
50_T	334_G	0.648	1.00
275_L	279_L	0.647	1.00
56_H	60_L	0.646	1.00
361_E	366_E	0.642	1.00
86_N	110_I	0.641	1.00
368_E	372_L	0.639	1.00
197_F	201_Y	0.637	1.00
108_C	111_G	0.633	1.00
373_E	378_K	0.627	1.00
81_T	307_R	0.626	1.00
82_R	132_T	0.625	1.00
240_M	243_L	0.623	1.00
208_A	212_P	0.619	1.00
247_L	315_S	0.618	1.00
46_G	57_A	0.616	1.00
96_T	106_S	0.615	1.00
59_L	96_T	0.614	1.00
60_L	63_L	0.612	1.00
282_R	285_K	0.611	1.00
158_A	190_I	0.610	1.00
93_L	97_Q	0.609	1.00
275_L	301_A	0.603	1.00
173_I	176_R	0.603	1.00
274_L	279_L	0.602	1.00
163_D	168_A	0.600	1.00
236_L	240_M	0.600	1.00
43_S	185_V	0.599	1.00
323_P	332_R	0.599	1.00
353_D	362_K	0.598	1.00
350_E	353_D	0.595	1.00
204_N	211_E	0.591	1.00
205_P	214_Q	0.590	1.00
315_S	341_S	0.590	1.00
86_N	89_Y	0.589	1.00
167_L	173_I	0.589	1.00
252_A	320_Y	0.589	1.00
56_H	95_I	0.589	1.00
171_D	174_G	0.588	1.00
66_I	128_L	0.588	1.00
90_Q	289_K	0.587	1.00
194_L	198_L	0.586	1.00
72_V	127_H	0.585	1.00
85_A	110_I	0.584	1.00
77_I	88_I	0.583	1.00
178_P	181_L	0.581	1.00
364_G	368_E	0.580	1.00
94_K	97_Q	0.579	1.00
47_Q	190_I	0.578	1.00
220_I	345_A	0.576	1.00
249_I	299_I	0.574	1.00
196_P	199_K	0.574	1.00
168_A	175_S	0.573	1.00
356_A	361_E	0.573	1.00
82_R	112_G	0.573	1.00
373_E	377_W	0.572	1.00
134_G	137_A	0.570	1.00
170_V	175_S	0.569	1.00
90_Q	292_N	0.568	1.00
96_T	102_S	0.568	1.00
365_I	369_Y	0.567	1.00
240_M	270_M	0.566	1.00
219_K	222_H	0.566	1.00
140_I	147_V	0.566	1.00
234_K	264_Y	0.565	1.00
88_I	130_V	0.563	1.00
93_L	106_S	0.563	1.00
236_L	261_I	0.562	1.00
363_M	368_E	0.562	1.00
250_V	261_I	0.561	1.00
255_K	259_D	0.558	1.00
250_V	300_I	0.558	1.00
171_D	177_M	0.557	1.00
76_V	131_G	0.557	1.00
34_L	38_V	0.557	1.00
292_N	312_K	0.556	1.00
217_A	222_H	0.556	1.00
216_T	219_K	0.552	1.00
208_A	214_Q	0.552	1.00
376_E	379_K	0.551	1.00
34_L	37_A	0.551	1.00
335_R	338_R	0.551	1.00
43_S	205_P	0.550	1.00
103_Q	106_S	0.549	1.00
86_N	289_K	0.547	1.00
200_K	203_E	0.545	1.00
249_I	314_V	0.544	1.00
131_G	135_R	0.544	1.00
37_A	208_A	0.543	1.00
30_I	48_S	0.539	1.00
363_M	370_L	0.535	1.00
28_T	339_A	0.535	1.00
50_T	188_A	0.532	1.00
197_F	204_N	0.532	1.00
307_R	331_H	0.532	1.00
274_L	287_V	0.530	1.00
43_S	182_Q	0.529	1.00
253_N	257_T	0.527	1.00
108_C	113_T	0.527	1.00
215_V	218_A	0.527	1.00
19_V	56_H	0.526	1.00
255_K	276_H	0.525	1.00
197_F	203_E	0.525	1.00
74_Q	149_K	0.525	1.00
206_K	212_P	0.525	1.00
220_I	225_I	0.525	1.00
180_D	183_M	0.524	1.00
204_N	212_P	0.524	1.00
79_A	130_V	0.523	1.00
177_M	180_D	0.520	1.00
43_S	183_M	0.520	1.00
233_D	261_I	0.519	1.00
284_R	288_M	0.519	1.00
196_P	200_K	0.519	1.00
118_S	139_L	0.515	1.00
218_A	222_H	0.515	1.00
355_D	361_E	0.515	1.00
354_E	361_E	0.513	1.00
27_P	56_H	0.511	1.00
211_E	215_V	0.511	1.00
77_I	130_V	0.510	1.00
82_R	281_P	0.509	1.00
370_L	377_W	0.509	1.00
365_I	373_E	0.508	1.00
247_L	314_V	0.508	1.00
318_I	348_I	0.508	1.00
306_A	332_R	0.508	1.00
349_Y	357_L	0.507	1.00
365_I	370_L	0.505	1.00
167_L	174_G	0.503	1.00
329_Y	333_V	0.503	1.00
90_Q	285_K	0.502	1.00
109_F	129_V	0.502	1.00
205_P	212_P	0.502	1.00
271_K	290_Q	0.501	1.00
364_G	371_E	0.501	1.00
153_L	181_L	0.501	1.00
369_Y	373_E	0.500	1.00
169_D	174_G	0.500	1.00

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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
4pxaA	1	0.8607	100	0.254	Contact Map
4nhoA	1	0.8493	100	0.255	Contact Map
4c9bA	1	0.8516	100	0.257	Contact Map
4ljyA	1	0.8904	100	0.259	Contact Map
4d25A	1	0.8516	100	0.263	Contact Map
3eiqA	1	0.8082	100	0.267	Contact Map
1s2mA	1	0.8584	100	0.267	Contact Map
2db3A	1	0.8493	100	0.267	Contact Map
4ct4B	1	0.8584	100	0.274	Contact Map
4kbfA	2	0.8242	100	0.279	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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