Project name: VPS35N [mutate: KA1A]

Status: done

Started: 2026-04-22 17:05:44
Chain sequence(s) A: KLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYMAISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLALFAHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQD
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Mutated residues KA1A
Energy difference between WT (input) and mutated protein (by FoldX) 0.024353 kcal/mol
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:13)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:13)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:13)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:13)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:13)
[INFO]       FoldX:    Building mutant model                                                       (00:15:24)
[INFO]       CABS:     Running CABS flex simulation                                                (00:15:37)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:38:24)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:38:29)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:38:34)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:38:38)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:38:42)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:38:46)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:38:51)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:38:56)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:39:01)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:39:04)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:39:07)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:39:11)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:39:14)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:39:22)
[INFO]       Main:     Simulation completed successfully.                                          (01:39:26)
Show buried residues

Minimal score value
-4.397
Maximal score value
1.9794
Average score
-0.8877
Total score value
-405.6602

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 A A -0.0976 mutated: KA1A
2 L A 0.5030
3 L A -0.2251
4 D A -2.1444
5 E A -2.2344
6 A A -1.2342
7 I A -1.2928
8 Q A -1.6879
9 A A -1.0828
10 V A 0.0000
11 K A -0.0202
12 V A 1.4163
13 Q A 0.2972
14 S A 0.0000
15 F A 0.7744
16 Q A -0.9678
17 M A 0.0000
18 K A -2.9794
19 R A -3.5400
20 C A 0.0000
21 L A -3.1972
22 D A -4.2440
23 K A -4.1874
24 N A -3.3216
25 K A -2.8260
26 L A 0.0000
27 M A -0.1173
28 D A -1.4996
29 A A 0.0000
30 L A -0.0632
31 K A -0.5169
32 H A -0.9336
33 A A 0.0000
34 S A 0.0000
35 N A -1.2112
36 M A 0.0000
37 L A 0.0000
38 G A -1.3693
39 E A -1.4229
40 L A 0.0000
41 R A 0.0000
42 T A 0.0651
43 S A -0.1467
44 M A 0.5526
45 L A 0.1888
46 S A -0.1781
47 P A 0.0000
48 K A -0.6989
49 S A -0.0260
50 Y A 0.0000
51 Y A 0.4104
52 E A -0.1255
53 L A 0.0000
54 Y A 0.2237
55 M A 0.6344
56 A A -0.1388
57 I A 0.0000
58 S A -0.5459
59 D A -1.4460
60 E A -0.8067
61 L A 0.0000
62 H A -0.0979
63 Y A 1.0461
64 L A 0.0000
65 E A 0.0000
66 V A 1.1689
67 Y A 0.5831
68 L A 0.0000
69 T A -1.1053
70 D A -1.9628
71 E A 0.0000
72 F A 0.0000
73 A A -2.0363
74 K A -2.7544
75 G A -2.4142
76 R A -3.0327
77 K A -2.7187
78 V A -0.8673
79 A A 0.0000
80 D A -1.6727
81 L A -0.2639
82 Y A 0.1203
83 E A -0.7729
84 L A 1.2373
85 V A 0.0000
86 Q A -0.1242
87 Y A 0.9588
88 A A -0.2765
89 G A -0.8383
90 N A -1.3383
91 I A -0.9665
92 I A 0.0000
93 P A 0.0000
94 R A -1.6199
95 L A 0.0000
96 Y A 0.0000
97 L A 0.0000
98 L A 0.0000
99 I A 0.0000
100 T A 0.0000
101 V A 0.0000
102 G A 0.0000
103 V A 0.0000
104 V A 0.0000
105 Y A -0.4679
106 V A 0.0000
107 K A -1.7905
108 S A -0.4248
109 F A 0.1212
110 P A -1.3110
111 Q A -2.0815
112 S A -1.7145
113 R A 0.0000
114 K A -1.9486
115 D A -1.7861
116 I A 0.0000
117 L A 0.0000
118 K A -1.3564
119 D A -1.6865
120 L A 0.0000
121 V A -1.4296
122 E A -2.6860
123 M A -1.8476
124 C A 0.0000
125 R A -3.0963
126 G A -2.1912
127 V A 0.0000
128 Q A -2.3769
129 H A -1.5670
130 P A 0.0000
131 L A 0.0000
132 R A -0.3748
133 G A 0.0000
134 L A 0.0000
135 F A 0.0000
136 L A 0.0000
137 R A 0.0000
138 N A -0.3762
139 Y A 0.0000
140 L A 0.0000
141 L A 0.0000
142 Q A -1.0970
143 C A 0.0000
144 T A -1.1518
145 R A -1.8080
146 N A -2.1110
147 I A 0.0000
148 L A -1.7118
149 P A -1.8457
150 D A -2.2839
151 E A -2.7503
152 G A -1.8359
153 E A 0.0000
154 P A -2.3350
155 T A 0.0000
156 D A -3.6752
157 E A -3.9266
158 E A -3.4521
159 T A -2.6119
160 T A -2.1123
161 G A -2.3349
162 D A -2.1558
163 I A -1.1866
164 S A -1.2205
165 D A -0.8686
166 S A 0.0000
167 M A 0.0000
168 D A -0.1807
169 F A 0.0000
170 V A 0.0000
171 L A 0.6478
172 L A 0.9513
173 N A 0.0000
174 F A 0.0000
175 A A -0.1618
176 E A 0.0000
177 M A 0.0000
178 N A 0.0000
179 K A -2.2554
180 L A 0.0000
181 W A 0.0000
182 V A -1.1926
183 R A -1.8436
184 M A 0.0000
185 Q A -2.5032
186 H A -2.3059
187 Q A -1.7783
188 G A -1.9890
189 H A -1.9468
190 S A -2.4922
191 R A -3.7609
192 D A -4.3970
193 R A -4.0242
194 E A -4.2026
195 K A -3.9892
196 R A 0.0000
197 E A -3.3698
198 R A -3.6973
199 E A 0.0000
200 R A 0.0000
201 Q A -1.9351
202 E A -1.4004
203 L A 0.0000
204 R A -0.2223
205 I A 0.5794
206 L A 0.0000
207 V A 0.0000
208 G A -0.0015
209 T A 0.2431
210 N A 0.0000
211 L A 0.0000
212 V A -0.4263
213 R A -1.0491
214 L A 0.0000
215 S A -1.5504
216 Q A -1.9802
217 L A -1.5173
218 E A -2.6803
219 G A -2.3506
220 V A 0.0000
221 N A -3.6023
222 V A 0.0000
223 E A -3.9075
224 R A -3.8332
225 Y A 0.0000
226 K A -3.2655
227 Q A -2.8625
228 I A -1.2030
229 V A 0.0000
230 L A 0.0000
231 T A -0.9221
232 G A 0.0000
233 I A 0.0000
234 L A -0.9989
235 E A -1.8800
236 Q A -1.6439
237 V A 0.0000
238 V A -1.6465
239 N A -2.2265
240 C A -2.0005
241 R A -2.7898
242 D A -1.8345
243 A A -1.7240
244 L A 0.0000
245 A A 0.0000
246 Q A 0.0000
247 E A -2.1071
248 Y A -0.8072
249 L A 0.0000
250 M A 0.0000
251 E A -2.2669
252 C A 0.0000
253 I A 0.0000
254 I A 0.0000
255 Q A -1.7311
256 V A 0.0000
257 F A 0.0000
258 P A -1.9202
259 D A -2.0504
260 E A -2.5774
261 F A 0.0000
262 H A 0.0000
263 L A 0.0000
264 Q A -1.5517
265 T A 0.0000
266 L A 0.0000
267 N A -1.0597
268 P A -1.1741
269 F A 0.0000
270 L A 0.0000
271 R A -2.2713
272 A A 0.0000
273 C A 0.0000
274 A A 0.0000
275 E A -2.5278
276 L A 0.0000
277 H A -2.4587
278 Q A -2.3406
279 N A -2.5790
280 V A 0.0000
281 N A -2.4115
282 V A 0.0000
283 K A 0.0000
284 N A -1.8766
285 I A 0.0000
286 I A 0.0000
287 I A -0.2978
288 A A -0.7755
289 L A 0.0000
290 I A 0.0000
291 D A -0.7154
292 R A -0.8945
293 L A 0.0000
294 A A -0.6201
295 L A -0.2246
296 F A -1.1030
297 A A 0.0000
298 H A -2.5165
299 R A -3.0877
300 E A -3.4390
301 D A -3.4204
302 G A -2.1958
303 P A -1.9604
304 G A -1.2452
305 I A 0.0000
306 P A -0.9608
307 A A -1.3125
308 D A -2.2083
309 I A -1.4541
310 K A -1.9096
311 L A 0.0000
312 F A -0.7183
313 D A -1.2720
314 I A -0.8908
315 F A 0.0000
316 S A 0.0000
317 Q A -1.3348
318 Q A -1.4989
319 V A 0.0000
320 A A -0.9717
321 T A -1.4405
322 V A 0.0000
323 I A 0.0000
324 Q A -2.1213
325 S A -2.0601
326 R A -2.5068
327 Q A -2.6360
328 D A -2.7011
329 M A 0.0000
330 P A -1.6738
331 S A 0.0000
332 E A -1.6154
333 D A -1.7255
334 V A 0.0000
335 V A 0.0000
336 S A -1.1005
337 L A 0.0000
338 Q A 0.0000
339 V A 0.0000
340 S A -0.3922
341 L A 0.0000
342 I A 0.0000
343 N A -0.6156
344 L A 0.0000
345 A A 0.0000
346 M A -0.3742
347 K A -0.9578
348 C A 0.0000
349 Y A 0.2123
350 P A -0.4078
351 D A -1.2137
352 R A -1.8432
353 V A 0.0000
354 D A -2.3507
355 Y A 0.0000
356 V A 0.0000
357 D A 0.0000
358 K A -2.1957
359 V A 0.0000
360 L A 0.0000
361 E A -1.9592
362 T A -1.7098
363 T A 0.0000
364 V A 0.0000
365 E A -2.8976
366 I A 0.0000
367 F A 0.0000
368 N A -3.2330
369 K A -3.1288
370 L A -2.3906
371 N A -2.9601
372 L A -2.0446
373 E A -3.0258
374 H A -1.9981
375 I A 0.0000
376 A A -0.7923
377 T A -0.9513
378 S A -0.5277
379 S A -0.7837
380 A A -1.0408
381 V A 0.0000
382 S A 0.0000
383 K A -2.3427
384 E A -2.0487
385 L A 0.0000
386 T A -1.6767
387 R A -2.5083
388 L A 0.0000
389 L A 0.0000
390 K A -1.9203
391 I A 0.0000
392 P A 0.0000
393 V A 0.0000
394 D A -2.2339
395 T A -1.6091
396 Y A 0.0000
397 N A -2.2882
398 N A -1.8824
399 I A 0.0000
400 L A 0.0000
401 T A -1.0895
402 V A 0.0000
403 L A 0.0000
404 K A -2.4083
405 L A 0.0000
406 K A -2.6270
407 H A -2.1379
408 F A 0.0000
409 H A -1.7815
410 P A -1.3867
411 L A 0.0000
412 F A 0.0000
413 E A -1.6090
414 Y A -1.4526
415 F A 0.0000
416 D A -1.6085
417 Y A -0.6770
418 E A -1.9124
419 S A 0.0000
420 R A -1.2220
421 K A -1.2957
422 S A -0.7021
423 M A 0.0000
424 S A 0.0000
425 C A 0.9856
426 Y A 0.8043
427 V A 0.0000
428 L A 1.9794
429 S A 0.8562
430 N A 0.0771
431 V A 1.3675
432 L A 1.2615
433 D A -0.9045
434 Y A 0.3425
435 N A -1.4039
436 T A 0.0000
437 E A -0.8365
438 I A 1.1754
439 V A 1.2330
440 S A -0.2425
441 Q A -1.5192
442 D A -2.3810
443 Q A -1.2501
444 V A -0.5398
445 D A -2.0626
446 S A -1.8376
447 I A 0.0000
448 M A -0.1033
449 N A -1.2151
450 L A 0.0000
451 V A 0.0000
452 S A -0.6162
453 T A -0.4040
454 L A 0.7138
455 I A 1.1827
456 Q A -1.0147
457 D A -1.7837
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.8877 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A4D Score
model_0 -0.8877 View CSV PDB
model_1 -0.89 View CSV PDB
model_6 -0.9005 View CSV PDB
model_3 -0.9034 View CSV PDB
model_4 -0.9074 View CSV PDB
model_10 -0.9164 View CSV PDB
CABS_average -0.9201 View CSV PDB
model_2 -0.9228 View CSV PDB
model_11 -0.9305 View CSV PDB
model_8 -0.9335 View CSV PDB
model_7 -0.9378 View CSV PDB
model_5 -0.9519 View CSV PDB
model_9 -0.9587 View CSV PDB
input -0.969 View CSV PDB