Orange: nodes, hubs and links specific of opsins_off network

Green: nodes, hubs and links shared by both networks

Purple: nodes, hubs and links specific of opsins_on network

Index: hub id, click on each number to highlight the corresponding hub in the 3D visualization.

Hub: the hub being considered.

Owner: the name of the network the hub belong to or "Shared" if the corresponding hub is present in both networks.

Avg Int. Strength: the average interaction strength of all the links of the corresponding hub in the corresponding network.

Num Of Links: the number of links of the corresponding hub in the corresponding network.

ConSurf: this column reports the ConSurf conservation grades of each hub.


Index Hub Owner opsins_off Avg Int. Strength opsins_on Avg Int. Strength opsins_off Num Of Links opsins_on Num Of Links ConSurf
11x30 opsins_off00423
21x39 opsins_off66.66670427
31x47 opsins_off00436
41x59 opsins_off33.33330435
52x38 opsins_off00416
62x41 opsins_off33.33330425
72x57 opsins_off33.333350537
8E1x51 opsins_off66.66670424
93x31 opsins_off00524
103x50 opsins_off1000639
114x41 opsins_off33.33330435
125x42 opsins_off66.666750434
13I3 opsins_off66.66670500
146x31 opsins_off33.33330514
157x39 opsins_off1000425
167x42 opsins_off1000427
178x47 opsins_off00428
188x49 opsins_off00416
198x54 opsins_off00436
20CT opsins_off10001210
21NT Shared1001001290
221x60 Shared66.66670545
23I1x50 Shared66.66670447
243x30 Shared66.66670446
253x37 Shared66.66670446
263x41 Shared100100665
273x51 Shared66.6667100447
28I2x56 Shared33.333350447
294x50 Shared66.666750459
30E2 Shared10010029290
315x39 Shared100100546
325x461 Shared100100656
336x44 Shared050449
346x48 Shared66.6667100648
35E3 Shared100100670
367x53 Shared100100459
378x50 Shared0100448
38Lig Shared1001001060
391x38 opsins_on050144
401x50 opsins_on050349
412x42 opsins_on050347
422x45 opsins_on66.6667100349
432x50 opsins_on050149
44E1x50 opsins_on66.6667100368
453x28 opsins_on33.33330345
463x42 opsins_on33.333350348
47I2x50 opsins_on00248
484x56 opsins_on33.333350155
495x43 opsins_on33.33330145
505x46 opsins_on00244
515x58 opsins_on050349
526x30 opsins_on050157
536x51 opsins_on33.333350346
547x54 opsins_on00147
   
Orange: nodes, hubs and links specific of opsins_off network

Green: nodes, hubs and links shared by both networks

Purple: nodes, hubs and links specific of opsins_on network

Index: link id, click on each number to highlight the corresponding link in the 3D visualization.

Node1 Node2: the two nodes of the corresponding link.

Owner: the name of the network the link belong to or "Shared" if the corresponding link is present in both networks.

Recurrence: the relative Recurrence in the filtered pool of shortest paths.

Hub1?, Hub2?: "Yes" if the corresponding node has more than 3 links, otherwise "No".

ConSurf1, ConSurf2: these columns report the ConSurf conservation grades of the two nodes involved in a link.


Index Node1 Node2 Owner opsins_off Recurrence opsins_on Recurrence opsins_off Hub1? opsins_on Hub1? opsins_off Hub2? opsins_on Hub2? ConSurf1 ConSurf2
11x39 2x57 opsins_off10.34550YesNoYesNo77
21x39 7x39 opsins_off18.74050YesNoYesNo75
37x39 E2 opsins_off27.77350YesNoYesYes50
47x39 7x42 opsins_off11.07750YesNoYesNo57
5E2 Lig opsins_off48.54220YesYesYesYes00
61x39 2x61 opsins_off10.17790.949832YesNoNoNo76
71x43 2x57 opsins_off11.62540NoNoYesNo67
81x53 7x50 opsins_off15.60010NoNoNoNo99
91x53 8x50 opsins_off18.06990NoNoYesYes98
107x53 8x50 opsins_off29.70760YesYesYesYes98
112x43 7x53 opsins_off44.12590NoNoYesYes89
122x43 6x40 opsins_off44.48580NoNoNoNo88
136x40 7x49 opsins_off45.01330NoNoNoNo89
142x46 7x49 opsins_off47.07420NoNoNoNo99
153x42 4x49 opsins_off96.04990NoYesNoNo87
162x45 4x49 opsins_off96.31161.44997NoYesNoNo97
172x45 4x50 opsins_off96.81058.71082NoYesYesYes99
182x52 4x50 opsins_off97.91452.92408NoNoYesYes69
192x52 3x31 opsins_off98.29890NoNoYesNo64
203x30 3x31 opsins_off99.50930YesYesYesNo64
213x30 4x61 opsins_off99.82831.21087YesYesNoNo65
223x26 4x61 opsins_off1000NoNoNoNo75
233x26 E2 opsins_off99.97961.10558NoNoYesYes70
241x56 8x50 opsins_off10.0470NoNoYesYes78
252x40 I1x50 opsins_off10.43960NoNoYesYes87
262x40 7x53 opsins_off14.18520NoNoYesYes89
278x49 CT opsins_off11.84620YesNoYesNo60
288x47 8x49 opsins_off11.4661.12751YesNoYesNo86
297x53 8x47 opsins_off17.98410YesYesYesNo98
302x38 3x49 opsins_off18.59330YesNoNoNo68
313x49 3x50 opsins_off27.03740NoNoYesNo89
323x50 6x37 opsins_off48.48090YesNoNoNo98
333x46 6x37 opsins_off48.8980NoNoNoNo98
342x37 2x38 opsins_off15.66552.19799NoNoYesNo76
352x37 2x40 opsins_off15.66964.3938NoNoNoNo78
363x37 Lig opsins_off21.45980YesYesYesYes60
373x37 3x41 opsins_off13.39190.0438722YesYesYesYes65
383x41 5x461 opsins_off11.02026.3834YesYesYesYes56
395x42 5x461 opsins_off13.5760YesNoYesYes46
405x42 E2 opsins_off15.3676.10042YesNoYesYes40
413x41 5x50 opsins_off10.27191.86676YesYesNoNo59
423x50 6x34 opsins_off41.66840YesNoNoNo96
433x55 5x61 opsins_off12.67232.32303NoNoNoNo78
443x54 5x61 opsins_off13.89491.16261NoNoNoNo88
453x54 5x65 opsins_off17.51380NoNoNoNo88
465x65 6x34 opsins_off40.65020NoNoNoNo86
475x49 5x50 opsins_off12.7540.934477NoNoNoNo59
485x69 6x35 opsins_off10.35780NoNoNoNo57
495x69 6x31 opsins_off11.39640NoNoYesNo54
505x65 6x31 opsins_off24.39580NoNoYesNo84
51E2 E3 Shared10.108412.7778YesYesYesYes00
522x57 7x42 Shared20.936418.2048YesNoYesNo77
537x42 Lig Shared14.491919.069YesNoYesYes70
542x46 3x42 Shared47.84328.9929NoNoNoYes98
552x42 3x46 Shared49.360114.9341NoYesNoNo79
562x42 3x42 Shared51.60516.4937NoYesNoYes78
576x48 Lig Shared15.9967100YesYesYesYes80
58E2 NT Shared20.490736.585YesYesYesYes00
591x38 1x42 opsins_on2.9155612.9269NoYesNoNo47
601x42 2x57 opsins_on5.8270315.5856NoNoYesNo77
61E2x52 Lig opsins_on045.4779NoNoYesYes40
62E2 E2x52 opsins_on1.2594644.3372YesYesNoNo04
636x51 Lig opsins_on1.3616846.5988NoYesYesYes60
646x51 E2 opsins_on0.74013544.9909NoYesYesYes60
651x43 2x58 opsins_on011.262NoNoNoNo68
662x58 2x59 opsins_on1.279913.5017NoNoNoNo85
672x59 3x28 opsins_on015.7369NoNoNoYes55
683x28 E2x50 opsins_on028.8218NoYesNoNo59
69E1x50 E2x50 opsins_on0.012267430.8268NoYesNoNo89
70E1x50 NT opsins_on022.2278NoYesYesYes80
711x50 2x50 opsins_on1.3412442.4858NoYesNoYes99
722x50 7x49 opsins_on047.6035NoYesNoNo99
737x45 7x49 opsins_on063.0969NoNoNoNo99
746x47 7x45 opsins_on063.3624NoNoNoNo89
756x47 6x48 opsins_on7.307365.2269NoNoYesYes88
761x50 7x50 opsins_on9.2414634.7643NoYesNoNo99
778x50 I1x50 opsins_on020.576YesYesYesYes87
787x54 8x50 opsins_on026.5931NoYesYesYes78
797x50 7x54 opsins_on033.843NoNoNoYes97
802x42 3x49 opsins_on021.5237NoYesNoNo78
812x46 2x50 opsins_on025.0817NoNoNoYes99
822x46 3x43 opsins_on022.1532NoNoNoNo98
833x43 7x49 opsins_on032.2241NoNoNoNo89
843x43 7x53 opsins_on027.3477NoNoYesYes89
853x50 5x58 opsins_on016.8513YesNoNoYes99
863x47 5x58 opsins_on030.2433NoNoNoYes99
873x47 5x54 opsins_on034.2291NoNoNoNo98
885x54 6x44 opsins_on034.7226NoNoYesYes89
896x44 6x48 opsins_on4.8742636.7429YesYesYesYes98
903x49 I2x56 opsins_on7.7734614.3265NoNoYesYes87
914x42 I2x56 opsins_on010.1674NoNoYesYes77
922x45 3x42 opsins_on013.0278NoYesNoYes98
932x64 E1x50 opsins_on021.7628NoNoNoYes58
943x47 5x57 opsins_on1.3003522.3814NoNoNoNo98
953x51 5x57 opsins_on2.5966121.3394YesYesNoNo78
965x58 6x37 opsins_on017.8933NoYesNoNo98
975x58 6x40 opsins_on011.5186NoYesNoNo98
986x30 6x34 opsins_on014.5612NoYesNoNo76
995x62 6x34 opsins_on015.6755NoNoNoNo56
1005x62 6x37 opsins_on016.7899NoNoNoNo58
1012x64 E2 opsins_on1.1204322.717NoNoYesYes50
1025x43 Lig opsins_on010.5776NoYesYesYes50

Here, those paths that begin and end at given residue pair(s) or that pass through a residue are used to generate a novel metapath. Such a path filtering is particularly recommended if some information on allosteric residues is available. The selection syntax for a residue pair ("Pairs") is C:C:c534,A:A:?600 (the lower-case "c" stands for cytosine and "?" indicates any non standard amino acid or nucleotide residue). Selection of more than one apical residue pair has the following syntax: C:C:c534,A:A:?600,C:C:c534,A:A:E41. Only one residue can be selected as a tail ("Tail"). For midway residue(s), each residue must be separated by a comma as well e.g. A:A:?600,A:A:E41.

Midway



Download PSN data

2D representation of the global metapath, ligand(s) interactions and
histograms of path distribution according to several parameters
(click on the image to enlarge it 🔍):

A 2D representation of the global communication in the network.

Number of shortest communication paths as a function of the average residue correlation.

Number of shortest communication paths as a function of the average interaction strength of their links.

Number of shortest communication paths as a function of the % of hub nodes in each path.

Number of shortest communication paths as a function of the number of nodes in each path.

Number of shortest communication paths as a function of the % of correlated nodes in each path.


2D representation of the interactions of this orthosteric/allosteric ligand.


Node1Node2OwnerNet1LinkStrengthNet2LinkStrengthComm1Comm2Node1ShellNode2Shell
E3NTopsins_off21.696701122
NTNTShared237.28796.071122
E2NTShared78.226745.841112
1x32NTShared12.57679.11122
1x32E2Shared8.596678.611121
1x352x64opsins_off5.0066701022
1x35E2Shared4.943333.6251021
1x357x39opsins_off15.423301022
2x577x42Shared8.275.770021
2x603x28Shared11.294.1150021
2x64E2Shared4.586673.181121
E1x50E2opsins_off4.3333301121
E1x50E2x50Shared7.916674.191122
3x26E2Shared5.036675.3551021
3x287x42opsins_off8.5501011
3x28Ligopsins_off4.9166701010
3x29E2Shared5.316.520021
3x32LigShared6.046673.0550010
3x33E2Shared5.826675.041111
3x33Ligopsins_off8.7801110
3x366x48opsins_off4.6900021
3x373x40opsins_off6.6301112
3x373x41Shared5.813334.991112
3x375x461Shared7.399.631112
3x37Ligopsins_off5.4166701110
3x406x44Shared10.156.540622
3x415x461Shared4.936675.5351122
4x565x461Shared13.26675.6450122
4x594x60Shared7.145.841122
4x595x39opsins_off6.2601122
4x60E2Shared13.966719.1651121
4x605x39Shared6.746.981122
5x38E2Shared4.945.561021
5x39E2Shared29.716717.5751121
5x42E2Shared9.966675.5651121
E2E2x52Shared15.73.811111
E2E2Shared138.603102.6151111
5x36E2Shared35.323318.4150021
E2E2x51Shared7.394.8651112
E2E2x50opsins_off6.0966701112
6x51E2Shared16.67679.4951111
7x34E2Shared17.845.821021
7x35E2Shared15.18334.1450121
7x39E2opsins_off8.0501021
E2Ligopsins_off4.8333301110
5x39E2x52Shared4.186673.2051121
6x55E2Shared8.896671.5150021
6x58E2opsins_off12.0901021
E2E3Shared9.393333.21112
5x37E2opsins_off7.5601021
5x37E3opsins_off9.7701022
5x395x42opsins_off7.2233301122
5x425x461opsins_off11.613301122
5x435x44opsins_off4.9733300112
5x475x51opsins_off4.8733300012
5x47Ligopsins_off6.3533300010
6x446x48Shared16.375.4750621
6x487x41opsins_off6.4833300612
6x487x45opsins_off8.2366700612
6x48LigShared14.09674.5450610
6x517x34opsins_off7.9833301112
6x51LigShared21.7718.321110
6x547x34opsins_off6.5933300122
6x547x37Shared6.484.3350122
6x58E3Shared8.373334.671022
7x397x42opsins_off9.101021
7x42LigShared8.743338.4351010
6x476x48Shared3.483335.8750021
3x304x57Shared3.233335.130122
7x38E2Shared2.783332.220021
5x355x38opsins_off2.4833300022
6x52Ligopsins_off2.0933300010
4x63E2Shared1.821.50021
6x526x53Shared1.31.9450012
E1x50NTopsins_on03.41122
2x593x28opsins_on05.6450021
3x28E2x50opsins_on04.5651012
3x30E2opsins_on06.0350121
3x334x57opsins_on05.6751112
3x374x56opsins_on06.0751112
3x406x48opsins_on013.6650621
4x565x43opsins_on03.330121
4x59E2opsins_on05.41121
E2x52Ligopsins_on05.721110
5x40E2opsins_on05.20021
6x54E2opsins_on03.5950121
5x395x43opsins_on010.911121
5x435x461opsins_on03.5550112
5x43Ligopsins_on05.150110
5x476x52opsins_on05.0050011
5x516x44opsins_on05.910022
6x477x45opsins_on04.3850022
6x517x37opsins_on06.2551112
E3E3opsins_on04.691122
2x64E1x50opsins_on06.041122
2x65E2opsins_on04.250121
6x54E3opsins_on03.750122
5x35E2opsins_on03.0750021
6x517x41opsins_on02.671112
2x563x28opsins_on02.4550021
3x374x53opsins_on02.381112
5x445x47opsins_on02.1450021
6x496x52opsins_on01.820021

Location and physicochemical properties of the interaction partners of this ligand

Interactions of this ligand

Difference Members
Id Description
opsins_off rhodopsin_off
opsins_on rhodopsin_on
opsin1lw_on
Network Difference
Value opsins_off opsins_on
Imin 3.98667 3.075
Number of Linked Nodes 266 258
Number of Specific Nodes 11 (4.14%) 3  (1.16%)
Number of Shared Nodes 255 (95.86%) 255  (98.84%)
Number of Links 317 289
Number of Specific Links 173 (54.57%) 145  (50.17%)
Number of Shared Links 144 (45.43%) 144  (49.83%)
Number of Hubs 38 34
Number of Specific Hubs 20 (52.63%) 16  (47.06%)
Number of Shared Hubs 18 (47.37%) 18  (52.94%)
Average % Shared Neighbours (Jaccard) 35.51
Average % Shared Neighbours (Otsuka) 44.50
Average % Shared Neighbours (Overlap Coefficient) 53.04
Average % Shared Cliques (k3-6) 78.26
Graphlets Similarity 0.643227
Paths Difference
Value opsins_off opsins_on
Number Of Nodes in MetaPath 55 50
Specific Nodes in MetaPath 32 (58.18%) 27  (54.00%)
Shared Nodes in MetaPath 255 (95.86%) 255  (95.86%)
Number Of Links MetaPath 58 52
Specific Links in MetaPath 50 (86.21%) 44  (84.62%)
Shared Links in MetaPath 144 (45.43%) 144  (45.43%)
Number of Shortest Paths 47383 74924
Length Of Smallest Path 3 3
Average Path Length 14.6951 13.7255
Length of Longest Path 32 28
Minimum Path Strength 0.751667 0.6375
Average Path Strength 7.72581 6.36392
Maximum Path Strength 56.775 32.5025
Minimum Path Correlation 0.7 0.7
Average Path Correlation 0.935553 0.919972
Maximum Path Correlation 1 0.995
Minimum % Of Corr. Nodes 4.54545 5
Average % Of Corr. Nodes 57.6049 47.303
Maximum % Of Corr. Nodes 100 100
Minimum Path Hubs % 0 0
Average Path Hubs % 39.5057 44.7774
Maximum Path Hubs % 100 100

Details about the values in these tables can be found in the corresponding documentation page .

You can download a compressed (zip) file with structure(s), 3D outputs (as PyMol and VMD scripts) and numerical data files (as csv and plain text files).

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