Project name: 1AM

Status: done

Started: 2026-02-25 02:17:46
Settings
Chain sequence(s) A: NILRGESLNKSLPILHEWKFFDYDFGSDERRQDAILSGEYDYKNNYPSDIDQWHDKIFVTMLRYNGVPSSLNVISKKVGDGGPLLQPYPDWSFAKYDDCSGIVSASKLAIDKCDRLWVLDSGLVNNTQPMCSPKLLTFDLTTSQLLKQVEIPHDVAVNATTGKGRLSSLAVQSLDCNTNSDTMVYIADEKGEGLIVYHNSDDSFHRLTSNTFDYDPKFTKMTIDGESYTAQDGISGMALSPMTNNLYYSPVASTSLYYVNTEQFRTSDYQQNDIHYEGVQNILDTQSSAKVVSKSGVLFFGLVGDSALGCWNEHRTLERHNIRTVAQSDETLQMIASMKIKEALPHVPIFDRYINREYILVLSNKMQKMVNNDFNFDDVNFRIMNANVNELILNTRCENPDNDR
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:07:40)
[INFO]       Auto_mut: Residue number 349 from chain A and a score of 2.295 (isoleucine) selected  
                       for automated muatation                                                     (00:07:43)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 2.067 (isoleucine) selected    
                       for automated muatation                                                     (00:07:43)
[INFO]       Auto_mut: Residue number 350 from chain A and a score of 1.955 (phenylalanine)        
                       selected for automated muatation                                            (00:07:43)
[INFO]       Auto_mut: Residue number 36 from chain A and a score of 1.660 (leucine) selected for  
                       automated muatation                                                         (00:07:43)
[INFO]       Auto_mut: Residue number 3 from chain A and a score of 1.567 (leucine) selected for   
                       automated muatation                                                         (00:07:43)
[INFO]       Auto_mut: Residue number 347 from chain A and a score of 1.548 (valine) selected for  
                       automated muatation                                                         (00:07:43)
[INFO]       Auto_mut: Mutating residue number 349 from chain A (isoleucine) into glutamic acid    (00:07:43)
[INFO]       Auto_mut: Mutating residue number 349 from chain A (isoleucine) into aspartic acid    (00:07:43)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (isoleucine) into glutamic acid      (00:07:43)
[INFO]       Auto_mut: Mutating residue number 349 from chain A (isoleucine) into arginine         (00:11:02)
[INFO]       Auto_mut: Mutating residue number 349 from chain A (isoleucine) into lysine           (00:11:03)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (isoleucine) into lysine             (00:11:04)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (isoleucine) into aspartic acid      (00:14:24)
[INFO]       Auto_mut: Mutating residue number 350 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 350 from chain A (phenylalanine) into glutamic acid (00:14:28)
[INFO]       Auto_mut: Mutating residue number 350 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 350 from chain A (phenylalanine) into aspartic acid (00:14:59)
[INFO]       Auto_mut: Mutating residue number 350 from chain A (phenylalanine) into lysine        (00:17:35)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (isoleucine) into arginine           (00:17:41)
[INFO]       Auto_mut: Mutating residue number 350 from chain A (phenylalanine) into arginine      (00:18:15)
[INFO]       Auto_mut: Mutating residue number 36 from chain A (leucine) into glutamic acid        (00:20:59)
[INFO]       Auto_mut: Mutating residue number 36 from chain A (leucine) into aspartic acid        (00:21:01)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into glutamic acid         (00:21:40)
[INFO]       Auto_mut: Mutating residue number 36 from chain A (leucine) into arginine             (00:24:05)
[INFO]       Auto_mut: Mutating residue number 36 from chain A (leucine) into lysine               (00:24:19)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into lysine                (00:25:04)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into aspartic acid         (00:27:27)
[INFO]       Auto_mut: Mutating residue number 347 from chain A (valine) into glutamic acid        (00:28:13)
[INFO]       Auto_mut: Mutating residue number 347 from chain A (valine) into aspartic acid        (00:29:13)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into arginine              (00:30:37)
[INFO]       Auto_mut: Mutating residue number 347 from chain A (valine) into lysine               (00:31:23)
[INFO]       Auto_mut: Mutating residue number 347 from chain A (valine) into arginine             (00:32:25)
[INFO]       Auto_mut: Effect of mutation residue number 349 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.2955 kcal/mol, Difference in average   
                       score from the base case: -0.0110                                           (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 349 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.3390 kcal/mol, Difference in average score    
                       from the base case: -0.0105                                                 (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 349 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.2951 kcal/mol, Difference in average    
                       score from the base case: -0.0108                                           (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 349 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.5953 kcal/mol, Difference in average score  
                       from the base case: -0.0110                                                 (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (isoleucine) into glutamic 
                       acid: Energy difference: -1.1235 kcal/mol, Difference in average score from 
                       the base case: -0.0110                                                      (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (isoleucine) into lysine:  
                       Energy difference: -0.1695 kcal/mol, Difference in average score from the   
                       base case: -0.0097                                                          (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (isoleucine) into aspartic 
                       acid: Energy difference: -0.4034 kcal/mol, Difference in average score from 
                       the base case: -0.0105                                                      (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (isoleucine) into          
                       arginine: Energy difference: -0.1351 kcal/mol, Difference in average score  
                       from the base case: -0.0098                                                 (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 350 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.0745 kcal/mol, Difference in average   
                       score from the base case: -0.0107                                           (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 350 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.1537 kcal/mol, Difference in average score     
                       from the base case: -0.0103                                                 (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 350 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -1.1620 kcal/mol, Difference in average   
                       score from the base case: -0.0106                                           (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 350 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.0195 kcal/mol, Difference in average score  
                       from the base case: -0.0065                                                 (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 36 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.7270 kcal/mol, Difference in average score from  
                       the base case: -0.0121                                                      (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 36 from chain A (leucine) into lysine:    
                       Energy difference: 0.2464 kcal/mol, Difference in average score from the    
                       base case: -0.0086                                                          (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 36 from chain A (leucine) into aspartic   
                       acid: Energy difference: 1.2600 kcal/mol, Difference in average score from  
                       the base case: -0.0105                                                      (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 36 from chain A (leucine) into arginine:  
                       Energy difference: 0.0653 kcal/mol, Difference in average score from the    
                       base case: -0.0085                                                          (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into glutamic    
                       acid: Energy difference: 0.0179 kcal/mol, Difference in average score from  
                       the base case: -0.0115                                                      (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into lysine:     
                       Energy difference: -0.4987 kcal/mol, Difference in average score from the   
                       base case: -0.0082                                                          (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into aspartic    
                       acid: Energy difference: -0.1074 kcal/mol, Difference in average score from 
                       the base case: -0.0088                                                      (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into arginine:   
                       Energy difference: -0.5341 kcal/mol, Difference in average score from the   
                       base case: -0.0087                                                          (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 347 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.9090 kcal/mol, Difference in average score from 
                       the base case: -0.0101                                                      (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 347 from chain A (valine) into lysine:    
                       Energy difference: -0.9897 kcal/mol, Difference in average score from the   
                       base case: -0.0102                                                          (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 347 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.5287 kcal/mol, Difference in average score from 
                       the base case: -0.0100                                                      (00:36:11)
[INFO]       Auto_mut: Effect of mutation residue number 347 from chain A (valine) into arginine:  
                       Energy difference: -1.0374 kcal/mol, Difference in average score from the   
                       base case: -0.0082                                                          (00:36:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:36:25)
Show buried residues
Minimal score value
-2.3784
Maximal score value
2.2952
Average score
-0.337
Total score value
-136.1488
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 N A -0.9179
2 I A 2.0674
3 L A 1.5669
4 R A -1.6405
5 G A -1.1270
6 E A -1.9412
7 S A -0.4564
8 L A 0.2491
9 N A -1.3044
10 K A -0.9355
11 S A -0.2395
12 L A 0.0000
13 P A -0.0508
14 I A 1.1716
15 L A 0.8783
16 H A -0.2138
17 E A -0.7237
18 W A 0.0000
19 K A -0.5864
20 F A 0.0823
21 F A 0.0000
22 D A 0.0000
23 Y A 0.0000
24 D A -0.1965
25 F A 0.0000
26 G A -0.4808
27 S A -0.4916
28 D A -2.1908
29 E A -2.3784
30 R A -1.6843
31 R A -1.0400
32 Q A -1.0239
33 D A -1.9179
34 A A 0.0000
35 I A 1.0484
36 L A 1.6603
37 S A -0.0090
38 G A -0.8412
39 E A -1.9060
40 Y A 0.0000
41 D A -0.3496
42 Y A 0.2239
43 K A -1.3541
44 N A -0.5755
45 N A 0.0000
46 Y A 0.0000
47 P A 0.0000
48 S A -0.0206
49 D A 0.0000
50 I A 0.0000
51 D A 0.0000
52 Q A -0.1055
53 W A 0.0371
54 H A -0.9835
55 D A -2.0202
56 K A -0.8964
57 I A 0.0000
58 F A 0.0000
59 V A 0.0000
60 T A 0.0000
61 M A 0.0000
62 L A 0.1838
63 R A 0.0000
64 Y A -0.0755
65 N A -1.2294
66 G A 0.0000
67 V A 0.0000
68 P A 0.0000
69 S A 0.0000
70 S A 0.0000
71 L A 0.0000
72 N A 0.0000
73 V A 0.0000
74 I A 0.2504
75 S A -0.2984
76 K A -1.8999
77 K A -1.0513
78 V A 1.5389
79 G A -0.1712
80 D A -1.8213
81 G A 0.0000
82 G A -0.0646
83 P A 0.2707
84 L A 0.1732
85 L A 0.0000
86 Q A -0.3029
87 P A 0.0000
88 Y A 0.0000
89 P A -0.2627
90 D A -1.1352
91 W A 0.0206
92 S A -0.0704
93 F A 0.2709
94 A A -0.2489
95 K A -1.6549
96 Y A -0.3800
97 D A -2.0762
98 D A -2.0657
99 C A -0.0410
100 S A -0.1601
101 G A 0.0000
102 I A 0.0000
103 V A 0.0000
104 S A 0.0000
105 A A 0.0000
106 S A 0.0000
107 K A -0.2264
108 L A 0.0000
109 A A 0.0000
110 I A 0.3182
111 D A 0.0000
112 K A -1.6716
113 C A -0.2740
114 D A -0.7055
115 R A 0.0000
116 L A 0.0000
117 W A 0.0000
118 V A 0.0000
119 L A 0.0000
120 D A 0.0000
121 S A 0.0000
122 G A 0.0000
123 L A 0.1806
124 V A 0.0000
125 N A -0.3781
126 N A -0.4972
127 T A -0.3662
128 Q A -1.2585
129 P A -0.3397
130 M A 0.6115
131 C A 0.1644
132 S A -0.1422
133 P A -0.0592
134 K A 0.0000
135 L A 0.0000
136 L A 0.0000
137 T A 0.0000
138 F A 0.0000
139 D A -0.3596
140 L A 0.0000
141 T A -0.0832
142 T A -0.0875
143 S A -0.2822
144 Q A -1.0868
145 L A 0.5784
146 L A 0.8631
147 K A -0.3194
148 Q A -0.6169
149 V A 0.0000
150 E A -1.8199
151 I A 0.0000
152 P A -0.2838
153 H A -1.3404
154 D A -1.9729
155 V A 0.0000
156 A A 0.0000
157 V A 0.3381
158 N A -0.0725
159 A A 0.0161
160 T A -0.0664
161 T A -0.1330
162 G A -0.7836
163 K A -1.7866
164 G A -0.5872
165 R A -0.2558
166 L A 0.0000
167 S A -0.0236
168 S A 0.0000
169 L A 0.0000
170 A A 0.0000
171 V A 0.1950
172 Q A -0.0896
173 S A 0.0753
174 L A 0.5874
175 D A -0.5955
176 C A 0.3364
177 N A -1.1492
178 T A -0.5048
179 N A -1.2851
180 S A 0.0000
181 D A -1.5067
182 T A 0.0000
183 M A 0.0000
184 V A 0.0000
185 Y A 0.0000
186 I A 0.0000
187 A A 0.0000
188 D A 0.0000
189 E A -0.4321
190 K A -1.4087
191 G A 0.0000
192 E A -0.2818
193 G A 0.0000
194 L A 0.0000
195 I A 0.0000
196 V A 0.0000
197 Y A 0.0000
198 H A 0.0000
199 N A 0.0000
200 S A -0.5267
201 D A -2.0835
202 D A -1.7324
203 S A -0.2631
204 F A 0.2045
205 H A -0.1404
206 R A -0.3455
207 L A 0.0000
208 T A -0.0766
209 S A -0.2840
210 N A -1.2803
211 T A -0.2447
212 F A 0.0000
213 D A -0.6034
214 Y A 0.1250
215 D A -0.3080
216 P A -0.6233
217 K A -1.6742
218 F A 0.0729
219 T A -0.2661
220 K A -1.7107
221 M A 0.0000
222 T A -0.0359
223 I A 0.0000
224 D A -1.8742
225 G A -1.0929
226 E A -1.7836
227 S A -0.3881
228 Y A 0.0970
229 T A -0.2594
230 A A -0.2329
231 Q A -1.2401
232 D A -0.4537
233 G A 0.0000
234 I A 0.0000
235 S A 0.0000
236 G A -0.0507
237 M A 0.0000
238 A A 0.0000
239 L A 0.2832
240 S A 0.0000
241 P A -0.1612
242 M A 0.4745
243 T A 0.0126
244 N A -0.3585
245 N A -0.2587
246 L A 0.0000
247 Y A 0.0000
248 Y A 0.0000
249 S A 0.0000
250 P A 0.0000
251 V A 0.2051
252 A A 0.0000
253 S A 0.0000
254 T A 0.0000
255 S A 0.0000
256 L A 0.0000
257 Y A 0.0000
258 Y A 0.2016
259 V A 0.0000
260 N A -0.4391
261 T A 0.0000
262 E A -1.8840
263 Q A -0.6832
264 F A 0.0000
265 R A -1.8571
266 T A -0.4250
267 S A -0.4051
268 D A -1.7768
269 Y A -0.3985
270 Q A -1.3428
271 Q A -1.3626
272 N A -1.7586
273 D A -1.9849
274 I A -0.3105
275 H A -0.9084
276 Y A -0.2599
277 E A -1.6957
278 G A -0.4061
279 V A 0.3581
280 Q A -1.3091
281 N A -1.4889
282 I A 0.0000
283 L A 0.0000
284 D A -1.7894
285 T A 0.0000
286 Q A 0.0000
287 S A 0.0000
288 S A -0.0253
289 A A 0.0000
290 K A 0.0000
291 V A 0.1791
292 V A 0.0000
293 S A 0.0000
294 K A -1.7164
295 S A -0.4022
296 G A 0.0000
297 V A 0.0000
298 L A 0.0000
299 F A 0.0000
300 F A 0.0000
301 G A 0.0000
302 L A 0.0000
303 V A 0.0000
304 G A -0.5605
305 D A -0.9288
306 S A 0.0000
307 A A 0.0000
308 L A 0.0000
309 G A 0.0000
310 C A 0.0000
311 W A 0.0000
312 N A 0.0000
313 E A -0.2888
314 H A -0.6242
315 R A -1.1314
316 T A -0.2394
317 L A -0.0335
318 E A -1.2745
319 R A -1.9194
320 H A -1.0023
321 N A 0.0000
322 I A 0.1168
323 R A -0.6035
324 T A -0.1499
325 V A 0.0000
326 A A 0.0000
327 Q A -0.4916
328 S A -0.4506
329 D A -2.1308
330 E A -2.1507
331 T A 0.0000
332 L A 0.0000
333 Q A 0.0000
334 M A 0.0000
335 I A 0.0000
336 A A 0.0097
337 S A 0.0000
338 M A 0.0000
339 K A -0.1864
340 I A 0.2312
341 K A -0.5224
342 E A -1.8581
343 A A -0.1576
344 L A 0.7667
345 P A -0.2812
346 H A -0.7117
347 V A 1.5483
348 P A 0.4205
349 I A 2.2952
350 F A 1.9552
351 D A -1.7655
352 R A -1.9295
353 Y A 1.1517
354 I A 1.0355
355 N A -0.9844
356 R A -1.9987
357 E A 0.0000
358 Y A 0.1937
359 I A 0.0000
360 L A 0.0000
361 V A 0.0000
362 L A 0.0000
363 S A 0.0000
364 N A 0.0000
365 K A 0.0000
366 M A 0.2822
367 Q A 0.0000
368 K A -0.5221
369 M A 0.1787
370 V A 0.8731
371 N A -1.2807
372 N A -1.8135
373 D A -2.0128
374 F A -0.2528
375 N A -0.9273
376 F A -0.2043
377 D A -2.0263
378 D A -1.8569
379 V A -0.0840
380 N A 0.0000
381 F A 0.0000
382 R A 0.0000
383 I A 0.0000
384 M A 0.0000
385 N A -0.3054
386 A A 0.0000
387 N A -0.1352
388 V A 0.0000
389 N A -0.7898
390 E A -1.9041
391 L A 0.0000
392 I A 0.0000
393 L A 1.3033
394 N A -1.0011
395 T A -0.4905
396 R A -1.3242
397 C A 0.0000
398 E A -0.5155
399 N A -0.3532
400 P A -0.3979
401 D A -2.0173
402 N A -1.8882
403 D A -2.3232
404 R A -2.1525
Download PDB file
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
IE2A -1.1235 -0.011 View CSV PDB
FD350A -1.162 -0.0106 View CSV PDB
VK347A -0.9897 -0.0102 View CSV PDB
VE347A -0.909 -0.0101 View CSV PDB
IR349A -0.5953 -0.011 View CSV PDB
ID2A -0.4034 -0.0105 View CSV PDB
LR3A -0.5341 -0.0087 View CSV PDB
IK349A -0.339 -0.0105 View CSV PDB
LK3A -0.4987 -0.0082 View CSV PDB
FE350A -0.0745 -0.0107 View CSV PDB
LR36A 0.0653 -0.0085 View CSV PDB
LK36A 0.2464 -0.0086 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018