26 S proteasome of S. pombe - Identifying key residues for the interaction
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Run Tutorial2 (Tutorial2)
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Please cite the following papers in your work:
G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato and A.M.J.J. Bonvin.
The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes. J. Mol. Biol., Advanced Online Publication (2016).

G.C.P. van Zundert and A.M.J.J. Bonvin (2015)
DisVis: Quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes..
Bioinformatics 31, 3222-3224.
and add the following acknowledgment:
The H2020 e-Infrastructure projects West-Life (grant no. 675858), EGI-Engage-MobrainCC (grant no. 654142) and INDIGO-DataCloud (grant no. 653549) are acknowledged for the use of their web portals, which make use of the EGI infrastructure.
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Accessible Interaction Space
The accessible interaction space consistent with at least N restraints is depicted below. Use the slider to adjust N and the arrows on the side of the images to change the view.
Current Level (N): 4
Images were generated with UCSF Chimera.
Accessible Complexes
The table below lists the number of complexes consistent with at least N restraints as raw number and as fraction of all complexes.
Number of consistent restraints (N) Number of accessible complexes consistent with at least N restraints Fraction of accessible complexes consistent with at least N restraints
0 960879791 100.00 %
1 193019087 20.09 %
2 107393137 11.18 %
3 58184829 6.06 %
4 3253159 0.34 %
5 203095 0.02 %
6 64812 0.01 %
7 14112 0.00 %
z-Score
IMPORTANT! Complexes consistent with all restraints you provided exist indicating that there are no false positives among your restraints. The tables listing z-Scores and Violations can thus be ignored but are provided as part of the DisVis output nevertheless.
# Restraint Average violated fraction Standard deviation Z-score
1 A27(CA)-A18(CA) 0.44 0.37 0.83
2 A122(CA)-A125(CA) 0.48 0.23 1.45
3 A122(CA)-A128(CA) 0.45 0.29 1.02
4 A122(CA)-A127(CA) 0.36 0.33 -0.30
5 A55(CA)-A169(CA) 0.33 0.24 -0.79
6 A55(CA)-A179(CA) 0.30 0.23 -1.26
7 A54(CA)-A179(CA) 0.32 0.22 -0.94
Violations
IMPORTANT! Complexes consistent with all restraints you provided exist indicating that there are no false positives among your restraints. The tables listing z-Scores and Violations can thus be ignored but are provided as part of the DisVis output nevertheless.
Number of consistent restraints (N) Restraint 1 Restraint 2 Restraint 3 Restraint 4 Restraint 5 Restraint 6 Restraint 7
1 0.76 0.76 0.86 0.82 0.66 0.64 0.64
2 0.90 0.69 0.76 0.69 0.61 0.38 0.40
3 0.91 0.60 0.61 0.58 0.41 0.41 0.42
4 0.10 0.48 0.47 0.43 0.43 0.49 0.51
5 0.30 0.51 0.29 0.02 0.11 0.15 0.24
6 0.12 0.34 0.19 0.00 0.09 0.01 0.03
Interaction analysis
The tables below shows how often a selected residues of the fixed and scanning chain are involved in the interaction in the complexes consistent with a specific number of restraints. The higher the interaction fraction of a specific residue is, the more likely it is involved in the complex interaction. Column 1 shows the residue ID, while each following column indicates the minimum number of restraints N. Each row thus represents the frequency that a residue of the receptor is found at the interface in complexes that are consistent with at least N restraints.
Fixed chain
4 5 6 7
6 0.800 0.327 0.327 0.339
7 0.749 0.399 0.481 0.564
10 0.889 0.959 1.197 1.864
13 0.554 0.698 1.015 1.146
15 0.390 0.282 0.428 0.340
17 0.334 0.101 0.138 0.057
18 0.324 0.040 0.051 0.015
19 0.352 0.079 0.112 0.053
33 0.366 0.399 0.212 0.074
43 0.001 0.000 0.000 0.000
54 0.374 0.318 0.272 0.125
55 0.691 0.609 0.553 0.338
57 0.574 0.367 0.416 0.406
58 0.658 0.812 1.044 1.196
60 0.348 0.705 0.883 1.017
62 0.139 0.362 0.428 0.486
72 0.017 0.028 0.027 0.042
82 0.417 0.688 0.595 0.624
83 0.797 1.334 1.358 1.666
97 0.097 0.335 0.305 0.251
98 0.154 0.522 0.469 0.302
101 0.088 0.241 0.182 0.156
102 0.091 0.218 0.136 0.052
104 0.021 0.027 0.015 0.016
125 1.019 1.776 2.234 3.306
126 0.917 1.725 2.226 2.840
127 0.788 1.661 2.075 2.022
128 0.659 1.312 1.537 0.926
129 0.639 1.315 1.330 0.735
130 0.714 1.421 1.426 1.003
131 0.814 1.601 1.866 2.021
133 1.095 1.933 2.322 3.074
149 0.002 0.000 0.000 0.000
150 0.005 0.000 0.000 0.000
162 0.227 0.010 0.017 0.024
164 0.082 0.000 0.000 0.000
165 0.031 0.000 0.000 0.000
176 0.178 0.018 0.011 0.004
180 0.097 0.002 0.000 0.000
184 0.040 0.000 0.000 0.000
189 0.002 0.000 0.000 0.000
193 0.000 0.000 0.000 0.000
208 0.295 0.048 0.024 0.003
209 0.323 0.035 0.014 0.002
210 0.242 0.008 0.001 0.000
214 0.058 0.006 0.005 0.001
223 0.000 0.000 0.000 0.000
224 0.001 0.001 0.002 0.001
228 0.011 0.010 0.009 0.003
231 0.013 0.015 0.022 0.021
233 0.009 0.004 0.006 0.001
234 0.002 0.000 0.000 0.000
237 0.004 0.000 0.000 0.000
241 0.004 0.000 0.000 0.000
244 0.020 0.000 0.000 0.000
245 0.011 0.000 0.000 0.000
Scanning chain
4 5 6 7
1 0.527 0.403 0.305 0.141
2 0.648 0.789 0.637 0.337
3 0.599 0.915 0.770 0.514
5 0.528 0.783 0.760 0.605
8 0.442 0.522 0.573 0.447
11 0.724 1.253 1.903 2.617
13 1.051 2.030 2.510 2.704
15 1.222 1.820 2.021 2.102
16 1.378 1.981 2.147 1.870
17 1.421 2.206 2.468 2.042
31 0.194 0.282 0.143 0.045
41 0.128 0.229 0.261 0.403
53 0.111 0.086 0.070 0.032
54 0.079 0.070 0.058 0.018
55 0.034 0.029 0.018 0.002
56 0.037 0.023 0.010 0.000
58 0.030 0.018 0.008 0.001
60 0.031 0.020 0.008 0.002
61 0.013 0.016 0.006 0.000
68 0.003 0.010 0.002 0.000
79 0.105 0.043 0.010 0.001
82 0.031 0.022 0.004 0.000
90 0.025 0.007 0.002 0.001
93 0.008 0.004 0.001 0.000
94 0.030 0.021 0.018 0.033
97 0.007 0.010 0.006 0.011
98 0.028 0.061 0.072 0.153
99 0.034 0.102 0.122 0.220
100 0.011 0.036 0.032 0.033
107 0.198 0.288 0.347 0.427
114 0.504 0.538 0.692 0.698
121 0.922 1.493 2.145 2.635
122 0.813 0.989 1.443 2.459
123 0.711 0.556 0.735 1.528
124 0.618 0.163 0.093 0.193
139 0.117 0.330 0.429 0.492
140 0.212 0.515 0.705 0.903
152 0.521 0.603 0.805 0.827
154 0.487 0.555 0.756 0.909
157 0.353 0.299 0.389 0.383
166 0.349 0.323 0.245 0.061
173 0.652 0.477 0.487 0.356
174 0.613 0.495 0.487 0.293
177 0.425 0.533 0.538 0.491
179 0.114 0.159 0.145 0.085
181 0.017 0.034 0.023 0.001
183 0.004 0.009 0.003 0.000
185 0.001 0.006 0.002 0.000
200 0.157 0.186 0.120 0.005
201 0.145 0.201 0.122 0.015
202 0.093 0.134 0.080 0.014
207 0.003 0.016 0.008 0.000
208 0.004 0.013 0.006 0.000
218 0.004 0.013 0.006 0.007
225 0.008 0.033 0.015 0.000