ChExVis

Results for PDB structure: 1K4D (with probe radius: 0.00Å)
Please cite the paper ChExVis: a tool for molecular channel extraction and visualization if you are using results from this server.

Parameters used:
* Auto End Points for pore computation: 14
* Inside Points for TM-pore computation: 1
* Outside Points for TM-pore computation: 5
* Transmembrane Classification: TMHMM (Dataset not available on OPM database)

Comment: The functionally significant channel we were interested in finding was found to be the fifth most important trans-membrane pore by ChExVis with the score of 0.835 in the set of 5 trans-membrane pores. However, this pore was the widest and striaghtest in the set. Low rank was due to its short length compared to other four pores.

Without using transmembrane classification data, the same channel was ranked 17th with score of 0.758 in the set of 91 pores between automatically selected 14 boundary points.

How to view: Select Rank 5 pore in "Trans-membrane Pores" table or Rank 17 pore in "Pores" table to view this pore.

Click on any table row below to view the corresponding channel.
Pores

Rank	Pt 1	Pt 2	Length	Bottle-neck	Straightness	Score
1	7	8	146.478	1.792	0.669	0.822
2	6	9	146.482	1.791	0.669	0.822
3	1	3	142.131	1.688	0.683	0.801
4	2	4	142.127	1.688	0.683	0.801
5	4	7	144.301	1.689	0.621	0.786
6	3	6	144.305	1.689	0.621	0.786
7	1	9	144.308	1.688	0.621	0.786
8	2	8	144.303	1.688	0.621	0.786
9	4	6	144.302	1.689	0.606	0.781
10	3	8	144.302	1.689	0.606	0.781
11	1	7	144.305	1.688	0.606	0.781
12	2	9	144.305	1.688	0.606	0.781
13	9	14	131.061	1.792	0.596	0.762
14	7	14	131.056	1.792	0.596	0.762
15	8	14	131.056	1.792	0.596	0.762
16	6	14	131.059	1.791	0.596	0.762
17	5	14	65.126	1.865	1.000	0.758
18	10	14	91.757	1.865	0.795	0.750
19	12	14	91.758	1.865	0.795	0.750
20	11	14	91.758	1.865	0.795	0.750
21	13	14	91.760	1.865	0.795	0.750
22	4	14	128.879	1.689	0.607	0.746
23	3	14	128.884	1.689	0.607	0.746
24	1	14	128.885	1.688	0.607	0.746
25	2	14	128.882	1.688	0.607	0.746
26	9	11	107.181	1.792	0.621	0.717
27	7	10	107.179	1.792	0.621	0.717
28	8	12	107.179	1.792	0.621	0.717
29	6	13	107.181	1.791	0.621	0.716
30	10	12	67.880	2.248	0.683	0.715
31	11	13	67.880	2.248	0.683	0.715
32	1	4	97.018	1.590	0.704	0.691
33	1	2	97.020	1.589	0.704	0.691
34	2	3	97.019	1.589	0.704	0.691
35	3	4	97.018	1.589	0.704	0.691
36	6	8	122.950	1.590	0.474	0.673
37	6	7	122.949	1.589	0.474	0.673
38	7	9	122.948	1.589	0.474	0.673
39	8	9	122.945	1.589	0.474	0.673
40	4	11	105.001	1.689	0.549	0.672
41	3	10	105.004	1.689	0.549	0.672
42	1	12	105.006	1.688	0.549	0.672
43	2	13	105.004	1.688	0.549	0.672
44	4	12	105.002	1.689	0.526	0.664
45	3	11	105.004	1.689	0.526	0.664
46	1	13	105.007	1.688	0.526	0.664
47	2	10	105.005	1.688	0.526	0.664
48	4	10	55.251	1.689	0.817	0.649
49	3	13	55.249	1.689	0.817	0.649
50	1	11	55.252	1.688	0.817	0.649
51	2	12	55.253	1.688	0.817	0.649
52	5	12	32.806	2.248	0.717	0.647
53	5	10	32.808	2.248	0.717	0.647
54	5	11	32.805	2.248	0.717	0.647
55	5	13	32.806	2.248	0.717	0.647
56	9	10	107.180	1.792	0.399	0.643
57	7	13	107.179	1.792	0.399	0.643
58	8	11	107.178	1.792	0.399	0.642
59	6	12	107.180	1.791	0.399	0.642
60	5	9	79.654	1.792	0.567	0.636
61	5	7	79.652	1.792	0.567	0.636
62	5	8	79.651	1.792	0.567	0.636
63	5	6	79.654	1.791	0.567	0.636
64	9	12	107.181	1.792	0.361	0.630
65	7	11	107.178	1.792	0.361	0.630
66	8	13	107.178	1.792	0.361	0.630
67	6	10	107.180	1.791	0.361	0.630
68	12	13	67.880	2.248	0.357	0.607
69	10	13	67.880	2.248	0.357	0.607
70	11	12	67.879	2.248	0.357	0.607
71	10	11	67.879	2.248	0.357	0.607
72	1	10	40.504	1.616	0.817	0.604
73	2	11	40.505	1.615	0.817	0.604
74	3	12	40.506	1.615	0.817	0.604
75	4	13	40.504	1.615	0.817	0.604
76	4	5	77.475	1.689	0.506	0.595
77	3	5	77.477	1.689	0.506	0.595
78	1	5	77.480	1.688	0.506	0.595
79	2	5	77.478	1.688	0.506	0.595
80	1	8	53.456	1.590	0.615	0.562
81	2	6	53.456	1.589	0.615	0.562
82	3	7	53.457	1.589	0.615	0.562
83	4	9	53.454	1.589	0.615	0.562
84	4	8	69.491	1.761	0.408	0.555
85	2	7	69.492	1.761	0.408	0.555
86	3	9	69.491	1.761	0.408	0.555
87	1	6	69.493	1.761	0.408	0.555
88	6	11	40.957	1.560	0.497	0.490
89	9	13	40.955	1.559	0.497	0.490
90	8	10	40.955	1.559	0.497	0.490
91	7	12	40.955	1.559	0.497	0.490

Trans-membrane Pores

Rank	Out Pt	In Pt	Length	Bottle-neck	Straightness	Score
1	4	1	128.879	1.689	0.607	0.837
2	3	1	128.884	1.689	0.607	0.837
3	1	1	128.885	1.688	0.607	0.837
4	2	1	128.882	1.688	0.607	0.837
5	5	1	65.126	1.865	1.000	0.835

3D Channel view in JSMol

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Channel properties

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