Project name: Charged mutations

Status: done

Started: 2025-03-17 08:57:30
Chain sequence(s) A: DILPCVPFSVAKSVKSLYLGRMFSGTPVIRLRFKRLQPTRLVAEFDFRTFDPEGILLFAGGHQDSTWIVLALRAGRLELQLRYNGVGRVTSSGPVINHGMWQTISVEELARNLVIKVNRDAVMKIAVAGDLFQPERGLYHLNLTVGGIPFHEKDLVQPINPRLDGCMRSWNWLNGEDTTIQETVKVNTRMQCFSVTERGSFYPGSGFAFYSLDYMRTPLDVGTESTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYHSTKKLKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPAAA
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
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 minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:06:39)
[INFO]       AutoMut:  Residue number 5 from chain A and a score of 1.254 (cysteine) selected for  
                       automated mutation                                                          (00:06:41)
[INFO]       AutoMut:  Residue number 6 from chain A and a score of 1.005 (valine) selected for    
                       automated mutation                                                          (00:06:41)
[INFO]       AutoMut:  Residue number 89 from chain A and a score of 0.963 (valine) selected for   
                       automated mutation                                                          (00:06:41)
[INFO]       AutoMut:  Residue number 209 from chain A and a score of 0.742 (phenylalanine)        
                       selected for automated mutation                                             (00:06:41)
[INFO]       AutoMut:  Residue number 342 from chain A and a score of 0.580 (leucine) selected for 
                       automated mutation                                                          (00:06:41)
[INFO]       AutoMut:  Residue number 4 from chain A and a score of 0.577 (proline) selected for   
                       automated mutation                                                          (00:06:41)
[INFO]       AutoMut:  Mutating residue number 5 from chain A (cysteine) into glutamic acid        (00:06:41)
[INFO]       AutoMut:  Mutating residue number 5 from chain A (cysteine) into aspartic acid        (00:06:41)
[INFO]       AutoMut:  Mutating residue number 6 from chain A (valine) into glutamic acid          (00:06:41)
[INFO]       AutoMut:  Mutating residue number 6 from chain A (valine) into lysine                 (00:06:49)
[INFO]       AutoMut:  Mutating residue number 5 from chain A (cysteine) into arginine             (00:06:50)
[INFO]       AutoMut:  Mutating residue number 5 from chain A (cysteine) into lysine               (00:06:54)
[INFO]       AutoMut:  Mutating residue number 6 from chain A (valine) into aspartic acid          (00:06:59)
[INFO]       AutoMut:  Mutating residue number 89 from chain A (valine) into glutamic acid         (00:07:04)
[INFO]       AutoMut:  Mutating residue number 6 from chain A (valine) into arginine               (00:07:07)
[INFO]       AutoMut:  Mutating residue number 89 from chain A (valine) into lysine                (00:07:14)
[INFO]       AutoMut:  Mutating residue number 89 from chain A (valine) into aspartic acid         (00:07:16)
[INFO]       AutoMut:  Mutating residue number 209 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 209 from chain A (phenylalanine) into glutamic acid (00:07:20)
[INFO]       AutoMut:  Mutating residue number 89 from chain A (valine) into arginine              (00:07:27)
[INFO]       AutoMut:  Mutating residue number 209 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 209 from chain A (phenylalanine) into aspartic acid (00:07:37)
[INFO]       AutoMut:  Mutating residue number 209 from chain A (phenylalanine) into lysine        (00:07:39)
[INFO]       AutoMut:  Mutating residue number 342 from chain A (leucine) into glutamic acid       (00:07:42)
[INFO]       AutoMut:  Mutating residue number 209 from chain A (phenylalanine) into arginine      (00:07:52)
[INFO]       AutoMut:  Mutating residue number 342 from chain A (leucine) into lysine              (00:07:54)
[INFO]       AutoMut:  Mutating residue number 342 from chain A (leucine) into aspartic acid       (00:08:03)
[INFO]       AutoMut:  Mutating residue number 4 from chain A (proline) into glutamic acid         (00:08:12)
[INFO]       AutoMut:  Mutating residue number 342 from chain A (leucine) into arginine            (00:08:13)
[INFO]       AutoMut:  Mutating residue number 4 from chain A (proline) into aspartic acid         (00:08:13)
[INFO]       AutoMut:  Mutating residue number 4 from chain A (proline) into arginine              (00:08:33)
[INFO]       AutoMut:  Mutating residue number 4 from chain A (proline) into lysine                (00:08:38)
[INFO]       AutoMut:  Effect of mutation residue number 5 from chain A (cysteine) into glutamic   
                       acid: Energy difference: -0.6823 kcal/mol, Difference in average score from 
                       the base case: -0.0171                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 5 from chain A (cysteine) into lysine:    
                       Energy difference: -0.2358 kcal/mol, Difference in average score from the   
                       base case: -0.0213                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 5 from chain A (cysteine) into aspartic   
                       acid: Energy difference: -1.2967 kcal/mol, Difference in average score from 
                       the base case: -0.0182                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 5 from chain A (cysteine) into arginine:  
                       Energy difference: -0.5610 kcal/mol, Difference in average score from the   
                       base case: -0.0204                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 6 from chain A (valine) into glutamic     
                       acid: Energy difference: -0.1019 kcal/mol, Difference in average score from 
                       the base case: -0.0120                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 6 from chain A (valine) into lysine:      
                       Energy difference: 0.6148 kcal/mol, Difference in average score from the    
                       base case: -0.0171                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 6 from chain A (valine) into aspartic     
                       acid: Energy difference: 0.8647 kcal/mol, Difference in average score from  
                       the base case: -0.0128                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 6 from chain A (valine) into arginine:    
                       Energy difference: 1.3832 kcal/mol, Difference in average score from the    
                       base case: -0.0198                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 89 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.5726 kcal/mol, Difference in average score from  
                       the base case: -0.0281                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 89 from chain A (valine) into lysine:     
                       Energy difference: -0.3774 kcal/mol, Difference in average score from the   
                       base case: -0.0212                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 89 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.9091 kcal/mol, Difference in average score from  
                       the base case: -0.0262                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 89 from chain A (valine) into arginine:   
                       Energy difference: -0.7279 kcal/mol, Difference in average score from the   
                       base case: -0.0222                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 209 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.0144 kcal/mol, Difference in average   
                       score from the base case: -0.0130                                           (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 209 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.8614 kcal/mol, Difference in average score    
                       from the base case: -0.0132                                                 (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 209 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.4290 kcal/mol, Difference in average    
                       score from the base case: -0.0106                                           (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 209 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.3979 kcal/mol, Difference in average score  
                       from the base case: -0.0186                                                 (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 342 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.2743 kcal/mol, Difference in average score from 
                       the base case: -0.0130                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 342 from chain A (leucine) into lysine:   
                       Energy difference: 0.1502 kcal/mol, Difference in average score from the    
                       base case: -0.0140                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 342 from chain A (leucine) into aspartic  
                       acid: Energy difference: -0.0626 kcal/mol, Difference in average score from 
                       the base case: -0.0104                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 342 from chain A (leucine) into arginine: 
                       Energy difference: -0.4819 kcal/mol, Difference in average score from the   
                       base case: -0.0127                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 4 from chain A (proline) into glutamic    
                       acid: Energy difference: 2.1538 kcal/mol, Difference in average score from  
                       the base case: -0.0085                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 4 from chain A (proline) into lysine:     
                       Energy difference: 2.4902 kcal/mol, Difference in average score from the    
                       base case: -0.0130                                                          (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 4 from chain A (proline) into aspartic    
                       acid: Energy difference: 0.8605 kcal/mol, Difference in average score from  
                       the base case: -0.0082                                                      (00:09:09)
[INFO]       AutoMut:  Effect of mutation residue number 4 from chain A (proline) into arginine:   
                       Energy difference: 2.6163 kcal/mol, Difference in average score from the    
                       base case: -0.0126                                                          (00:09:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:18)
Show buried residues
Minimal score value
-3.5529
Maximal score value
1.2538
Average score
-0.7527
Total score value
-301.0718
Download the table (csv)

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 D A -1.4556
2 I A 0.0000
3 L A 0.5586
4 P A 0.5770
5 C A 1.2538
6 V A 1.0052
7 P A 0.3140
8 F A 0.2979
9 S A -0.0623
10 V A 0.3584
11 A A -0.2053
12 K A -1.3970
13 S A -1.1508
14 V A -0.5937
15 K A -1.9780
16 S A 0.0000
17 L A 0.0000
18 Y A 0.0000
19 L A 0.0000
20 G A 0.0000
21 R A -1.8864
22 M A -0.7140
23 F A 0.0000
24 S A -0.6933
25 G A -0.6041
26 T A 0.0000
27 P A 0.0000
28 V A 0.0000
29 I A -0.2681
30 R A -1.8747
31 L A -1.6435
32 R A -2.5889
33 F A -1.4430
34 K A -1.7504
35 R A -0.8691
36 L A 0.1172
37 Q A -0.8478
38 P A -0.6935
39 T A -0.5150
40 R A -0.8013
41 L A 0.0000
42 V A -0.0290
43 A A 0.0000
44 E A -1.6325
45 F A 0.0000
46 D A 0.0000
47 F A 0.0000
48 R A -1.1192
49 T A 0.0000
50 F A 0.0000
51 D A -2.7045
52 P A 0.0000
53 E A -1.2671
54 G A 0.0000
55 I A 0.0000
56 L A 0.0000
57 L A 0.0000
58 F A 0.0000
59 A A 0.0000
60 G A 0.0000
61 G A 0.0000
62 H A -2.4464
63 Q A -2.7164
64 D A -2.8718
65 S A -2.2877
66 T A 0.0000
67 W A 0.0000
68 I A 0.0000
69 V A 0.0000
70 L A 0.0000
71 A A 0.0000
72 L A 0.0000
73 R A -1.9104
74 A A -1.8269
75 G A -1.8931
76 R A -2.4304
77 L A 0.0000
78 E A -0.7340
79 L A 0.0000
80 Q A 0.0000
81 L A 0.0000
82 R A -1.1740
83 Y A -1.3601
84 N A -2.0986
85 G A -1.1476
86 V A -0.6333
87 G A -0.6099
88 R A -0.1620
89 V A 0.9631
90 T A 0.0000
91 S A -0.4599
92 S A 0.0000
93 G A -1.2152
94 P A -1.1257
95 V A 0.0000
96 I A 0.0000
97 N A -1.6353
98 H A -1.7413
99 G A -0.8969
100 M A 0.1227
101 W A 0.1348
102 Q A 0.0000
103 T A -1.4067
104 I A 0.0000
105 S A -1.3513
106 V A 0.0000
107 E A -1.3631
108 E A 0.0000
109 L A 0.1726
110 A A -0.6569
111 R A -1.9158
112 N A -1.3367
113 L A 0.0000
114 V A 0.0000
115 I A 0.0000
116 K A -2.9534
117 V A 0.0000
118 N A -2.1836
119 R A -3.1959
120 D A -3.0339
121 A A -2.0202
122 V A -1.1894
123 M A 0.0000
124 K A -1.8488
125 I A -0.7530
126 A A -0.7968
127 V A 0.0000
128 A A -0.8315
129 G A -0.9701
130 D A -1.3888
131 L A 0.0000
132 F A 0.0000
133 Q A -1.5473
134 P A -1.5411
135 E A -2.1174
136 R A -2.2711
137 G A -1.3453
138 L A -1.0534
139 Y A -1.0033
140 H A -1.5241
141 L A 0.0000
142 N A -1.8294
143 L A 0.0000
144 T A 0.0000
145 V A 0.0000
146 G A 0.0000
147 G A 0.0000
148 I A -0.1152
149 P A -0.7330
150 F A -0.5885
151 H A -1.7591
152 E A -2.5641
153 K A -2.1367
154 D A -2.5700
155 L A 0.0000
156 V A -0.6944
157 Q A -0.8014
158 P A -0.8358
159 I A -0.4272
160 N A -0.4751
161 P A 0.0000
162 R A -1.0965
163 L A 0.0000
164 D A 0.0000
165 G A 0.0000
166 C A 0.0000
167 M A 0.0000
168 R A -2.4406
169 S A -1.7096
170 W A 0.0000
171 N A -1.5453
172 W A 0.0000
173 L A 0.0000
174 N A -1.3334
175 G A -1.3278
176 E A -2.3102
177 D A 0.0000
178 T A -1.3138
179 T A -1.1605
180 I A 0.0000
181 Q A -1.6794
182 E A -1.7311
183 T A -0.6460
184 V A 0.0000
185 K A -0.9428
186 V A 0.5038
187 N A -0.6240
188 T A -0.7406
189 R A -1.9258
190 M A -1.3147
191 Q A -1.0998
192 C A 0.0000
193 F A 0.0000
194 S A -0.6159
195 V A 0.1199
196 T A -0.9081
197 E A -2.2690
198 R A -2.5055
199 G A -1.4845
200 S A 0.0000
201 F A 0.0000
202 Y A 0.0000
203 P A -0.5206
204 G A -0.5570
205 S A -0.5343
206 G A -0.6991
207 F A -0.3552
208 A A 0.0000
209 F A 0.7416
210 Y A 0.5026
211 S A -0.0759
212 L A 0.0000
213 D A -2.1065
214 Y A -1.6078
215 M A -1.4801
216 R A -2.1054
217 T A -1.0818
218 P A -0.9487
219 L A -0.2581
220 D A -1.4383
221 V A -0.5354
222 G A -1.3588
223 T A -1.6630
224 E A -2.0866
225 S A -2.0065
226 T A -1.7933
227 W A 0.0000
228 E A -2.7611
229 V A 0.0000
230 E A -2.3234
231 V A 0.0000
232 V A -0.5609
233 A A 0.0000
234 H A -0.8785
235 I A 0.0000
236 R A -1.9610
237 P A 0.0000
238 A A 0.0000
239 A A 0.0000
240 D A 0.0000
241 T A 0.0000
242 G A 0.0000
243 V A 0.0000
244 L A 0.0000
245 F A 0.0000
246 A A 0.0000
247 L A 0.0000
248 W A 0.0271
249 A A 0.0000
250 P A -0.8697
251 D A -1.6326
252 L A -0.0112
253 R A -0.6142
254 A A -0.3178
255 V A 0.0000
256 P A 0.0000
257 L A 0.0000
258 S A 0.0000
259 V A 0.0000
260 A A 0.0000
261 L A 0.0000
262 V A -0.1116
263 D A 0.0000
264 Y A -0.6049
265 H A -0.8930
266 S A -1.1527
267 T A -1.1216
268 K A -1.9836
269 K A -1.7294
270 L A -0.9009
271 K A -1.8539
272 K A -2.1775
273 Q A 0.0000
274 L A -0.8904
275 V A 0.0000
276 V A 0.0000
277 L A 0.0000
278 A A 0.0000
279 V A 0.0000
280 E A 0.0000
281 H A -0.8348
282 T A -0.6035
283 A A 0.0000
284 L A 0.0000
285 A A 0.0000
286 L A -1.4873
287 M A 0.0000
288 E A -3.0541
289 I A 0.0000
290 K A -3.5529
291 V A 0.0000
292 C A 0.0000
293 D A -3.1693
294 G A -2.2883
295 Q A -2.1578
296 E A -2.6527
297 H A 0.0000
298 V A -0.6212
299 V A 0.0000
300 T A -0.9462
301 V A 0.0000
302 S A 0.0000
303 L A 0.0000
304 R A -2.7774
305 D A -2.8441
306 G A -2.5516
307 E A -2.6117
308 A A 0.0000
309 T A -1.3972
310 L A 0.0000
311 E A -2.3490
312 V A 0.0000
313 D A -3.1841
314 G A -2.4576
315 T A -2.9471
316 R A -3.3783
317 G A -2.4046
318 Q A -2.3702
319 S A -1.8035
320 E A -2.1216
321 V A -1.4769
322 S A -0.8101
323 A A -1.1122
324 A A -1.1461
325 Q A -1.9071
326 L A -1.8950
327 Q A -2.6890
328 E A -2.6052
329 R A 0.0000
330 L A 0.0000
331 A A -2.0254
332 V A 0.0000
333 L A 0.0000
334 E A -1.9421
335 R A -2.6752
336 H A 0.0000
337 L A 0.0000
338 R A -1.8844
339 S A 0.0000
340 P A -0.7157
341 V A 0.0000
342 L A 0.5795
343 T A 0.0000
344 F A 0.0000
345 A A 0.0000
346 G A 0.0000
347 G A 0.0000
348 L A 0.0000
349 P A -0.9768
350 D A -1.7701
351 V A 0.0000
352 P A -0.3882
353 V A 0.3483
354 T A 0.0882
355 S A -0.0471
356 A A 0.0000
357 P A 0.0997
358 V A 0.2839
359 T A -0.0087
360 A A 0.0087
361 F A 0.0366
362 Y A 0.0000
363 R A -0.6701
364 G A 0.0000
365 C A 0.0000
366 M A 0.0000
367 T A -0.6422
368 L A 0.0000
369 E A -1.7006
370 V A 0.0000
371 N A -3.1124
372 R A -3.1649
373 R A -2.4066
374 L A -0.2737
375 L A 0.0000
376 D A -0.6063
377 L A 0.0000
378 D A 0.0000
379 E A -1.2973
380 A A -0.3052
381 A A -0.3626
382 Y A 0.0000
383 K A -0.9878
384 H A -0.8577
385 S A -1.0406
386 D A -1.2609
387 I A 0.0000
388 T A 0.0000
389 A A 0.0000
390 H A -1.6159
391 S A 0.0000
392 C A 0.0000
393 P A 0.0000
394 P A -0.5624
395 V A 0.0527
396 E A -1.3938
397 P A -0.8176
398 A A -0.5657
399 A A -0.9135
400 A A -0.5595
Download PDB file
View in 3Dmol

Automated mutations analysis - charged mutations

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
CD5A -1.2967 -0.0182 View CSV PDB
VR89A -0.7279 -0.0222 View CSV PDB
CR5A -0.561 -0.0204 View CSV PDB
VK89A -0.3774 -0.0212 View CSV PDB
FK209A -0.8614 -0.0132 View CSV PDB
FR209A -0.3979 -0.0186 View CSV PDB
LR342A -0.4819 -0.0127 View CSV PDB
LE342A -0.2743 -0.013 View CSV PDB
VE6A -0.1019 -0.012 View CSV PDB
VK6A 0.6148 -0.0171 View CSV PDB
PD4A 0.8605 -0.0082 View CSV PDB
PK4A 2.4902 -0.013 View CSV PDB