Project name: VPS35N [mutate: KA1A]

Status: done

Started: 2026-04-22 17:05:42
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                                                       (00:15:20)
[INFO]       CABS:     Running CABS flex simulation                                                (00:15:32)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:38:18)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:38:22)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:38:27)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:38:32)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:38:37)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:38:42)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:38:46)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:38:51)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:38:56)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:39:01)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:39:04)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:39:07)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:39:10)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:39:20)
[INFO]       Main:     Simulation completed successfully.                                          (01:39:24)
Show buried residues

Minimal score value
-5.077
Maximal score value
2.2915
Average score
-0.8715
Total score value
-398.2954

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 -0.2798 mutated: KA1A
2 L A 0.3124
3 L A -0.5761
4 D A -2.2800
5 E A -2.4158
6 A A 0.0000
7 I A -1.2777
8 Q A -1.8939
9 A A -1.0428
10 V A 0.0000
11 K A -0.9916
12 V A 1.0285
13 Q A -0.0144
14 S A 0.0000
15 F A 0.8642
16 Q A -0.8985
17 M A 0.0000
18 K A -2.1399
19 R A -3.2912
20 C A -3.2754
21 L A -2.8877
22 D A -4.1264
23 K A -4.0784
24 N A -3.7928
25 K A -3.2171
26 L A 0.0000
27 M A -1.9592
28 D A -2.7723
29 A A 0.0000
30 L A 0.0000
31 K A -2.4863
32 H A -1.9682
33 A A 0.0000
34 S A -1.6314
35 N A -2.0899
36 M A 0.0000
37 L A 0.0000
38 G A -1.3573
39 E A -1.0617
40 L A 0.0000
41 R A -0.8510
42 T A -0.1200
43 S A -0.1182
44 M A 0.1825
45 L A -0.1177
46 S A -0.2680
47 P A 0.0000
48 K A -1.4492
49 S A -0.5301
50 Y A 0.0000
51 Y A 0.3289
52 E A -0.6700
53 L A 0.0000
54 Y A 0.1790
55 M A 0.5397
56 A A -0.5958
57 I A 0.0000
58 S A -0.6708
59 D A -1.5797
60 E A -0.9650
61 L A 0.0000
62 H A -0.0164
63 Y A 1.0233
64 L A 0.0000
65 E A 0.0000
66 V A 1.8794
67 Y A 1.1834
68 L A 0.0000
69 T A -0.3789
70 D A -1.7535
71 E A -1.8051
72 F A -1.4890
73 A A -1.8162
74 K A -2.7088
75 G A -2.1799
76 R A -2.6741
77 K A -2.5402
78 V A 0.0000
79 A A -1.1014
80 D A -1.9652
81 L A 0.0000
82 Y A -0.3688
83 E A -1.2704
84 L A -0.8511
85 V A 0.0000
86 Q A -0.8696
87 Y A 0.1665
88 A A -0.7637
89 G A -0.9948
90 N A -1.6018
91 I A -0.8180
92 I A 0.0000
93 P A 0.0000
94 R A -0.7583
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 0.3573
106 V A 0.0000
107 K A -1.3363
108 S A -0.4641
109 F A -0.0286
110 P A -1.5431
111 Q A -2.4920
112 S A 0.0000
113 R A 0.0000
114 K A 0.0000
115 D A -3.0583
116 I A -1.3480
117 L A 0.0000
118 K A -2.7394
119 D A -2.6632
120 L A 0.0000
121 V A 0.0000
122 E A -3.0256
123 M A 0.0000
124 C A 0.0000
125 R A -2.8329
126 G A -1.9119
127 V A 0.0000
128 Q A -1.6473
129 H A -0.9671
130 P A -0.8341
131 L A 0.0000
132 R A -0.5088
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 -0.3557
139 Y A 0.0000
140 L A 0.0000
141 L A 0.0000
142 Q A -2.1996
143 C A 0.0000
144 T A 0.0000
145 R A -3.3460
146 N A -3.3284
147 I A 0.0000
148 L A 0.0000
149 P A -2.7113
150 D A -3.5656
151 E A -2.9067
152 G A -1.5559
153 E A 0.0000
154 P A -1.8356
155 T A 0.0000
156 D A -3.7368
157 E A -4.1657
158 E A -3.8586
159 T A -2.3031
160 T A -1.6124
161 G A -1.0545
162 D A 0.0000
163 I A -0.0467
164 S A -0.3168
165 D A -0.5364
166 S A 0.0000
167 M A 0.0000
168 D A -0.2691
169 F A 0.0000
170 V A 0.0000
171 L A 0.3344
172 L A 0.5921
173 N A 0.0000
174 F A 0.0000
175 A A -0.3454
176 E A 0.0000
177 M A 0.0000
178 N A 0.0000
179 K A -1.8559
180 L A 0.0000
181 W A 0.0000
182 V A -1.3954
183 R A -1.9126
184 M A 0.0000
185 Q A -3.1760
186 H A -2.7046
187 Q A 0.0000
188 G A -1.9291
189 H A -1.9011
190 S A -2.4339
191 R A -4.2953
192 D A -5.0278
193 R A -5.0770
194 E A -4.5868
195 K A -4.3182
196 R A 0.0000
197 E A -3.3241
198 R A -3.3156
199 E A 0.0000
200 R A 0.0000
201 Q A -1.4939
202 E A -1.3578
203 L A 0.0000
204 R A 0.0000
205 I A 1.6142
206 L A 0.9487
207 V A 0.0000
208 G A 1.1365
209 T A 1.0082
210 N A 0.0000
211 L A 0.0000
212 V A 1.0546
213 R A -0.3880
214 L A 0.0000
215 S A -0.7373
216 Q A -1.3291
217 L A -1.3641
218 E A -2.3525
219 G A -1.8903
220 V A 0.0000
221 N A -2.7038
222 V A -2.0710
223 E A -2.7825
224 R A -2.2267
225 Y A 0.0000
226 K A -2.2244
227 Q A -1.8368
228 I A -0.6967
229 V A 0.0000
230 L A 0.0000
231 T A -0.9277
232 G A 0.0000
233 I A 0.0000
234 L A 0.0000
235 E A -2.1426
236 Q A 0.0000
237 V A 0.0000
238 V A -1.6746
239 N A -2.3165
240 C A 0.0000
241 R A -2.4251
242 D A -1.4605
243 A A -0.6426
244 L A 0.1839
245 A A 0.0000
246 Q A 0.0000
247 E A -0.3663
248 Y A 0.9007
249 L A 0.0000
250 M A 0.0000
251 E A -0.7671
252 C A 0.0000
253 I A 0.0000
254 I A 0.0000
255 Q A -1.2549
256 V A 0.0000
257 F A 0.0000
258 P A -1.3538
259 D A -0.9648
260 E A -1.5398
261 F A 0.0000
262 H A 0.0000
263 L A 0.0000
264 Q A -1.1453
265 T A 0.0000
266 L A 0.0000
267 N A -0.8282
268 P A -1.0347
269 F A 0.0000
270 L A 0.0000
271 R A -2.3843
272 A A 0.0000
273 C A 0.0000
274 A A -2.2242
275 E A -2.5206
276 L A 0.0000
277 H A -2.3393
278 Q A 0.0000
279 N A -1.9932
280 V A 0.0000
281 N A -1.7032
282 V A 0.0000
283 K A -1.4635
284 N A -1.5976
285 I A 0.0000
286 I A 0.0000
287 I A -0.3762
288 A A -0.6923
289 L A 0.0000
290 I A 0.0000
291 D A -0.8814
292 R A -0.9559
293 L A 0.0000
294 A A 0.0000
295 L A -0.3334
296 F A -1.2876
297 A A 0.0000
298 H A -2.5401
299 R A -3.2330
300 E A -3.7467
301 D A -3.3546
302 G A -2.3024
303 P A -1.5719
304 G A -1.8468
305 I A 0.0000
306 P A -1.4999
307 A A -1.7773
308 D A -2.6189
309 I A 0.0000
310 K A -2.3509
311 L A 0.0000
312 F A 0.0000
313 D A -1.5684
314 I A -0.9609
315 F A 0.0000
316 S A -0.9423
317 Q A -1.5242
318 Q A -1.3207
319 V A 0.0000
320 A A -0.8413
321 T A -1.6023
322 V A 0.0000
323 I A 0.0000
324 Q A -2.8331
325 S A -2.5115
326 R A -3.3587
327 Q A -3.3646
328 D A -3.2446
329 M A -2.3610
330 P A -1.4885
331 S A 0.0000
332 E A -2.1671
333 D A -1.7200
334 V A 0.0000
335 V A 0.0000
336 S A -1.0230
337 L A 0.0000
338 Q A 0.0000
339 V A 0.0000
340 S A 0.0000
341 L A 0.0000
342 I A 0.0000
343 N A -0.8207
344 L A 0.0000
345 A A 0.0000
346 M A -0.5948
347 K A -0.6551
348 C A 0.0000
349 Y A -0.0962
350 P A -1.0931
351 D A -2.7319
352 R A -3.3153
353 V A 0.0000
354 D A -2.5137
355 Y A -1.5012
356 V A 0.0000
357 D A 0.0000
358 K A -1.8855
359 V A 0.0000
360 L A 0.0000
361 E A -1.6617
362 T A -1.4967
363 T A 0.0000
364 V A 0.0000
365 E A -2.8723
366 I A 0.0000
367 F A 0.0000
368 N A -2.8982
369 K A -3.2851
370 L A -2.4238
371 N A -2.4172
372 L A 0.0000
373 E A -2.2811
374 H A -1.6668
375 I A -0.6372
376 A A -0.7826
377 T A -0.9282
378 S A -0.8627
379 S A -0.9008
380 A A -1.1257
381 V A 0.0000
382 S A -1.5075
383 K A -2.7352
384 E A -2.3946
385 L A 0.0000
386 T A -1.9755
387 R A -2.9654
388 L A 0.0000
389 L A 0.0000
390 K A -2.2541
391 I A -1.3986
392 P A 0.0000
393 V A 0.0000
394 D A -2.2560
395 T A -1.9050
396 Y A 0.0000
397 N A -2.5190
398 N A -1.9535
399 I A 0.0000
400 L A -0.3710
401 T A -1.4496
402 V A 0.0000
403 L A 0.0000
404 K A -1.9561
405 L A 0.0000
406 K A -1.8718
407 H A -1.3535
408 F A 0.0000
409 H A -1.0466
410 P A -0.7802
411 L A 0.0000
412 F A 0.0000
413 E A -0.5211
414 Y A 0.0940
415 F A 0.0000
416 D A -0.7505
417 Y A -0.0267
418 E A -1.4991
419 S A -1.1189
420 R A 0.0000
421 K A -0.4370
422 S A -0.0276
423 M A 0.0000
424 S A 0.0000
425 C A 1.4794
426 Y A 1.1248
427 V A 0.0000
428 L A 2.2915
429 S A 0.8847
430 N A 0.2585
431 V A 1.2185
432 L A 1.0785
433 D A -0.6366
434 Y A 0.1530
435 N A -0.7827
436 T A -0.1693
437 E A -0.7018
438 I A 1.2466
439 V A 0.1816
440 S A -0.7549
441 Q A -1.9963
442 D A -2.8326
443 Q A -1.5750
444 V A -1.2610
445 D A -2.3372
446 S A -1.8340
447 I A 0.0000
448 M A 0.3011
449 N A -0.8396
450 L A 0.0000
451 V A 0.0000
452 S A 0.3343
453 T A 0.0000
454 L A 1.5883
455 I A 1.6193
456 Q A -0.4335
457 D A -1.3940
Download PDB file
View in 3Dmol

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, -0.8715 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_6 -0.8715 View CSV PDB
model_2 -0.8763 View CSV PDB
model_1 -0.8993 View CSV PDB
model_10 -0.9004 View CSV PDB
model_5 -0.9147 View CSV PDB
model_11 -0.9177 View CSV PDB
CABS_average -0.9253 View CSV PDB
model_3 -0.9322 View CSV PDB
model_0 -0.9465 View CSV PDB
model_8 -0.9489 View CSV PDB
model_4 -0.9595 View CSV PDB
model_7 -0.9648 View CSV PDB
input -0.969 View CSV PDB
model_9 -0.9717 View CSV PDB