Color ConSurf Grade
      No Conservation data available
      1
      2
      3
      4
      5
      6
      7
      8
      9

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

Hub: the hub being considered.

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

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

Community: the id of the community the link belong to, otherwise 0.

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

Index Hub Avg Int. Strength Num Of Links Community ConSurf
1R:R:Y36 4.95415
2R:R:L39 6.7875417
3R:R:N50 5.8675409
4R:R:F60 3.7125405
5R:R:S73 6.6275419
6R:R:F79 4.16407
7R:R:V81 4.2325417
8R:R:G82 3.1775417
9R:R:V85 5.422517
10R:R:M86 4.18857717
11R:R:S89 5.005416
12R:R:R92 4.53415
13R:R:W98 3.42429718
14R:R:H108 4.538515
15R:R:D112 8.335416
16R:R:T113 6.404514
17R:R:S114 3.95515
18R:R:F115 4.922517
19R:R:F117 3.95515
20R:R:L120 4.2925417
21R:R:F121 3.218515
22R:R:H122 6.832518
23R:R:Y131 11.675408
24R:R:Y140 5.08167627
25R:R:F144 8.9125426
26R:R:I153 4.7325418
27R:R:W157 3.11111919
28R:R:Y163 5.5615
29R:R:I167 5.22415
30R:R:F168 5.39375815
31R:R:Y169 5.2975405
32R:R:N173 4.5825414
33R:R:E174 5.525414
34R:R:P193 4.815413
35R:R:L194 4.1825414
36R:R:F203 2.5475406
37R:R:F206 8.0525418
38R:R:P209 5.3075419
39R:R:L216 6.9775406
40R:R:Y217 4.852539
41R:R:I220 3.2925409
42R:R:F221 2.0275405
43R:R:E232 5.44504
44R:R:K246 2.85475
45R:R:F267 4.825409
46R:R:W271 5.93571718
47R:R:Y274 5.578516
48R:R:I275 5.85417
49R:R:D281 4.245483
50R:R:Y293 4.0125404
51R:R:W298 6.56833615
52R:R:Y301 7.72286718
53R:R:A305 1.9975447
54R:R:N307 6.048519
55R:R:Y311 5.004519
56R:R:Y315 6.67458
57R:R:F318 4.694509
58L:L:?1 7.73444910
   

Color ConSurf Grade
      No Conservation data available
      1
      2
      3
      4
      5
      6
      7
      8
      9

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.

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

Int. Strength: the interaction strength between the two nodes.

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

Community: the id of the community the link belong to, otherwise 0.

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

Index Node1 Node2 Recurrence Int. Strength Hub1? Hub2? Community ConSurf1 ConSurf2
1R:R:C186 R:R:C22 49.36837.28NoNo038
2R:R:C22 R:R:V187 51.87725.12NoNo083
3R:R:A183 R:R:C186 46.85041.81NoNo023
4R:R:A183 R:R:K24 44.32353.21NoNo025
5R:R:K24 R:R:S96 41.78763.06NoNo053
6R:R:S96 R:R:Y27 31.55473.82NoNo031
7R:R:Y27 R:R:Y291 26.38449.93NoNo012
8R:R:G188 R:R:V187 54.37721.84NoNo043
9R:R:G188 R:R:W98 59.35041.41NoYes048
10R:R:H108 R:R:W98 66.97133.17YesYes158
11R:R:H108 R:R:S89 37.54.18YesYes156
12R:R:S89 R:R:W298 16.37543.71YesYes165
13R:R:H108 R:R:V85 45.19279.69YesYes157
14R:R:V85 R:R:Y301 23.78585.05YesYes178
15R:R:M86 R:R:Y301 40.71684.79YesYes178
16R:R:G82 R:R:M86 16.51435.24YesYes177
17R:R:A46 R:R:G82 13.79481.95NoYes077
18R:R:A305 R:R:A46 11.85041.79YesNo077
19R:R:S89 R:R:Y301 23.20798.9YesYes168
20R:R:M86 R:R:W298 23.74553.49YesYes175
21R:R:D78 R:R:S304 50.31818.83NoNo099
22R:R:M86 R:R:S304 46.50993.07YesNo179
23R:R:D78 R:R:N307 52.93912.69NoYes099
24R:R:N307 R:R:Y311 1006.98YesYes199
25R:R:I126 R:R:Y311 98.1724.84NoYes099
26R:R:I126 R:R:V71 96.89961.54NoNo098
27R:R:I57 R:R:V71 95.47941.54NoNo078
28R:R:F318 R:R:I57 92.79125.02YesNo097
29R:R:A312 R:R:F318 37.36564.16NoYes079
30R:R:A312 R:R:V53 35.47943.39NoNo079
31R:R:F313 R:R:V53 33.58423.93NoNo059
32R:R:F313 R:R:I322 31.680112.56NoNo057
33R:R:A56 R:R:I322 23.9741.62NoNo077
34R:R:A321 R:R:A56 22.02511.79NoNo077
35R:R:A321 R:R:F60 20.05824.16NoYes075
36R:R:F60 R:R:L324 12.13713.65YesNo054
37R:R:F115 R:R:W157 14.3284.01YesYes179
38R:R:I153 R:R:W157 16.11112.35YesYes189
39R:R:G150 R:R:I153 20.69891.76NoYes048
40R:R:G150 R:R:S149 19.90141.86NoNo047
41R:R:F69 R:R:S149 19.11742.64NoNo057
42R:R:F69 R:R:V146 16.75183.93NoNo053
43R:R:P66 R:R:V146 15.98573.53NoNo063
44R:R:P66 R:R:T65 15.39873.5NoNo068
45R:R:T65 R:R:T67 24.26974.71NoNo088
46R:R:F318 R:R:N68 16.18734.83YesNo099
47R:R:T67 R:R:Y140 13.67382.5NoYes287
48R:R:H122 R:R:W157 10.10754.23YesYes189
49R:R:H122 R:R:L74 17.64786.43YesNo189
50R:R:L74 R:R:N307 11.38449.61NoYes199
51R:R:D112 R:R:V85 18.46334.38YesYes167
52R:R:E294 R:R:R92 11.415810.47NoYes045
53R:R:D112 R:R:T113 11.97134.34YesYes164
54R:R:F168 R:R:T113 12.39710.38YesYes154
55R:R:C110 R:R:F168 13.16761.4NoYes065
56R:R:C110 R:R:Y169 10.99464.03NoYes065
57L:L:?1 R:R:F168 33.68737.52YesYes105
58L:L:?1 R:R:Y301 32.76885.17YesYes108
59R:R:T113 R:R:Y163 14.18014.99YesYes145
60R:R:S164 R:R:T113 13.61113.2NoYes074
61R:R:S114 R:R:S164 13.45884.89YesNo057
62L:L:?1 R:R:C116 23.57082.8YesNo007
63R:R:E294 R:R:Y293 11.84143.37NoYes044
64R:R:Y274 R:R:Y293 13.91131.99YesYes064
65R:R:I275 R:R:Y274 12.32533.63YesYes176
66R:R:V300 R:R:W271 29.33249.81NoYes178
67L:L:?1 R:R:V300 23.45436.57YesNo107
68R:R:C116 R:R:W271 23.22582.61NoYes078
69R:R:F117 R:R:Y163 20.45257.22YesYes155
70R:R:F117 R:R:F121 16.51883.22YesYes155
71R:R:F267 R:R:W271 10.47048.02YesYes098
72R:R:H122 R:R:S156 12.02069.76YesNo087
73R:R:F121 R:R:S156 11.8283.96YesNo057
74R:R:F121 R:R:F159 11.62192.14YesNo054
75R:R:F318 R:R:W317 49.82537.02YesNo096
76R:R:W317 R:R:Y315 46.061817.36NoYes568
77R:R:R130 R:R:Y315 40.74823.09NoYes098
78R:R:I220 R:R:R130 38.89792.51YesNo099
79R:R:I220 R:R:Y217 19.72222.42YesYes099
80R:R:I220 R:R:Y131 13.98753.63YesYes098
81R:R:F168 R:R:N173 16.73397.25YesYes154
82L:L:?1 R:R:A192 15.93192.78YesNo104
83R:R:A192 R:R:P193 16.79661.87NoYes143
84R:R:N195 R:R:W198 10.33156.78NoNo046
85R:R:I310 R:R:Y311 10.11654.84NoYes089
86R:R:N303 R:R:W271 61.88623.39NoYes098
87R:R:N303 R:R:S270 15.85574.47NoNo098
88R:R:C299 R:R:S270 10.60483.44NoNo078
89R:R:P289 R:R:Y291 23.78589.74NoNo042
90R:R:P289 R:R:T288 18.56183.5NoNo046
91R:R:D281 R:R:T288 10.622810.12YesNo836
92R:R:N68 R:R:T65 14.6647.31NoNo098
93R:R:F117 R:R:W271 19.78492YesYes158
94R:R:N303 R:R:N307 52.69712.72NoYes099
95R:R:S114 R:R:W157 11.65322.47YesYes159
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.

ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

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.


Links and nodes colored according to ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

Node1 Node2 LinkStrength Comm IsNode1Hub? IsNode2Hub? Node1Cons Node2Cons Node1Shell Node2Shell
R:R:S89 R:R:V85 3.23 1 Yes Yes 6 7 2 2
R:R:D112 R:R:V85 4.38 1 Yes Yes 6 7 1 2
R:R:V85 R:R:Y301 5.05 1 Yes Yes 7 8 2 1
R:R:M86 R:R:W298 3.49 1 Yes Yes 7 5 2 2
R:R:M86 R:R:Y301 4.79 1 Yes Yes 7 8 2 1
R:R:S89 R:R:W298 3.71 1 Yes Yes 6 5 2 2
R:R:S89 R:R:Y301 8.9 1 Yes Yes 6 8 2 1
R:R:F168 R:R:T109 5.19 1 Yes No 5 5 1 2
R:R:D112 R:R:T113 4.34 1 Yes Yes 6 4 1 1
R:R:D112 R:R:Y301 12.64 1 Yes Yes 6 8 1 1
L:L:?1 R:R:D112 11.98 1 Yes Yes 0 6 0 1
R:R:T113 R:R:Y163 4.99 1 Yes Yes 4 5 1 2
R:R:S164 R:R:T113 3.2 0 No Yes 7 4 2 1
R:R:F168 R:R:T113 10.38 1 Yes Yes 5 4 1 1
L:L:?1 R:R:T113 9.11 1 Yes Yes 0 4 0 1
R:R:C116 R:R:W271 2.61 0 No Yes 7 8 1 2
L:L:?1 R:R:C116 2.8 1 Yes No 0 7 0 1
R:R:I167 R:R:Y163 6.04 1 Yes Yes 5 5 2 2
R:R:F168 R:R:I167 3.77 1 Yes Yes 5 5 1 2
R:R:F168 R:R:N173 7.25 1 Yes Yes 5 4 1 2
R:R:A192 R:R:F168 2.77 1 No Yes 4 5 1 1
R:R:F168 R:R:L194 4.87 1 Yes Yes 5 4 1 2
L:L:?1 R:R:F168 7.52 1 Yes Yes 0 5 0 1
R:R:L194 R:R:N173 4.12 1 Yes Yes 4 4 2 2
R:R:A192 R:R:P193 1.87 1 No Yes 4 3 1 2
L:L:?1 R:R:A192 2.78 1 Yes No 0 4 0 1
R:R:I275 R:R:W271 4.7 1 Yes Yes 7 8 2 2
R:R:V300 R:R:W271 9.81 1 No Yes 7 8 1 2
R:R:I275 R:R:Y274 3.63 1 Yes Yes 7 6 2 1
R:R:A278 R:R:Y274 4 0 No Yes 5 6 2 1
R:R:Y274 R:R:Y293 1.99 1 Yes Yes 6 4 1 2
R:R:V300 R:R:Y274 3.79 1 No Yes 7 6 1 1
L:L:?1 R:R:Y274 14.48 1 Yes Yes 0 6 0 1
R:R:V297 R:R:Y293 5.05 1 No Yes 6 4 1 2
R:R:V297 R:R:Y301 8.83 1 No Yes 6 8 1 1
L:L:?1 R:R:V297 9.2 1 Yes No 0 6 0 1
R:R:W298 R:R:Y301 8.68 1 Yes Yes 5 8 2 1
L:L:?1 R:R:V300 6.57 1 Yes No 0 7 0 1
L:L:?1 R:R:Y301 5.17 1 Yes Yes 0 8 0 1
R:R:C110 R:R:F168 1.4 0 No Yes 6 5 2 1

Location and physicochemical properties of the interaction partners of this ligand

Interactions of this ligand

Similarities between the interactions of this ligand and those of other networks

PDB Summary
PDB 8IW4_nogp
Class
SubFamily
Type
SubType
Species
Ligand
Other Ligand(s)
Protein Partners
PDB Resolution
Date
D.O.I.
Net Summary
Imin 1.76
Number of Linked Nodes 285
Number of Links 342
Number of Hubs 58
Number of Links mediated by Hubs 214
Number of Communities 8
Number of Nodes involved in Communities 79
Number of Links involved in Communities 119
Path Summary
Number Of Nodes in MetaPath 96
Number Of Links MetaPath 95
Number of Shortest Paths 62690
Length Of Smallest Path 3
Average Path Length 13.6335
Length of Longest Path 38
Minimum Path Strength 1.185
Average Path Strength 4.76933
Maximum Path Strength 16.905
Minimum Path Correlation 0.7
Average Path Correlation 0.932708
Maximum Path Correlation 1
Minimum % Of Corr. Nodes 3.125
Average % Of Corr. Nodes 53.1468
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 47.785
Maximum Path Hubs % 100
AnnotationTypeLinks
Gene OntologyMolecular Function
Gene OntologyBiological Process
Gene OntologyCellular Component
SCOP2Domain Identifier
SCOP2Family Identifier
Membrane Protein Annotations-• Orientations of Proteins in Membranes database (OPM)   • Protein Data Bank of Transmembrane Proteins (PDBTM)   • MemProtMD


Details about the values in these tables can be found in the corresponding documentation page .
CodeSPD
PDB ResiduesL:L:?1
Environment DetailsOpen EMBL-EBI Page
CodeSPD
NameSpermidine
Synonyms4-azaoctamethylenediamine
Identifier
FormulaC7 H19 N3
Molecular Weight145.246
SMILES
PubChem1102
Formal Charge0
Total Atoms29
Total Chiral Atoms0
Total Bonds28
Total Aromatic Bonds0

PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtQ5QD04
Sequence
>8IW4_nogp_Chain_R
CIKSSYAPW PRAILYGVL GLGALLAVF GNLLVIIAI LHFKQLHTP 
TNFLVASLA CADFLVGVT VMPFSTVRS VESCWYFGE SYCKFHTCF 
DTSFCFASL FHLCCISID RYIAVTDPL TYPTKFTVS VSGLCIALS 
WFFSVTYSF SIFYTGANE EGIEELVAL TCVGGCQAP LNQNWVLLC 
FLLFFLPTV VMVFLYGRI FLVAKYQAR KIEGYKERV AKRERKAAK 
TLGIAMAAF LVSWLPYII DAVIDAYMN FITPAYVYE ILVWCVYYN 
SAMNPLIYA FFYPWFRKA IKLIVSGK


Click on each residue to open a popup with some information about it.

ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  




This receptor, from the same or other species and bound to the same or other ligands, is also present in the following networks:
Show PDB Class SubFamily Type SubType Species Orthosteric Ligand Other Ligand(s) Protein Partners Resolution Date DOI
8ITFAOrphanOrphanTAA9Mus musculusDMCHA-chim(NtGi1-Gs)/β1/γ23.462023-05-31doi.org/10.1038/s41586-023-06106-4
8ITF (No Gprot) AOrphanOrphanTAA9Mus musculusDMCHA-3.462023-05-31doi.org/10.1038/s41586-023-06106-4
8IW1AOrphanOrphanTAA9Mus musculus--chim(NtGi1-Gs)/β1/γ23.42023-05-31doi.org/10.1038/s41586-023-06106-4
8IW1 (No Gprot) AOrphanOrphanTAA9Mus musculus--3.42023-05-31doi.org/10.1038/s41586-023-06106-4
8IW4AOrphanOrphanTAA9Mus musculusSpermidine-chim(NtGi1-Gs)/β1/γ23.492023-05-31doi.org/10.1038/s41586-023-06106-4
8IW4 (No Gprot) AOrphanOrphanTAA9Mus musculusSpermidine-3.492023-05-31doi.org/10.1038/s41586-023-06106-4
8IW7AOrphanOrphanTAA9Mus musculus2-Phenylethylamine-chim(NtGi1-Gs)/β1/γ22.972023-05-31doi.org/10.1038/s41586-023-06106-4
8IW7 (No Gprot) AOrphanOrphanTAA9Mus musculus2-Phenylethylamine-2.972023-05-31doi.org/10.1038/s41586-023-06106-4
8IW9AOrphanOrphanTAA9Mus musculus--chim(NtGi1-Gs)/β1/γ23.082023-05-31doi.org/10.1038/s41586-023-06106-4
8IW9 (No Gprot) AOrphanOrphanTAA9Mus musculus--3.082023-05-31doi.org/10.1038/s41586-023-06106-4
8IWEAOrphanOrphanTAA9Mus musculusSpermidine--3.42023-05-31doi.org/10.1038/s41586-023-06106-4
8IWMAOrphanOrphanTAA9Mus musculus2-Phenylethylamine--3.172023-05-31doi.org/10.1038/s41586-023-06106-4




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).

Download 8IW4_nogp.zip



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