Project name: Pyp1

Status: done

Started: 2026-07-15 13:23:10
Settings
Chain sequence(s) A: MGSSHHHHHHTGGTTSLHSVPDAFTNPDVATLYQKFLRLQSLEHQRLVSCSDRNSQWSTVDSLSNTSYKKNRYTDIVPYNCTRVHLKRTSPSELDYINASFIKTETSNYIACQGSISRSISDFWHMVWDNVENIGTIVMLGSLFEAGREMCTAYWPSNGIGDKQVYGDYCVKQISEENVDNSRFILRKFEIQNANFPSVKKVHHYQYPNWSDCNSPENVKSMVEFLKYVNNSHGSGNTIVHCSAGVGRTGTFIVLDTILRFPESKLSGFNPSVADSSDVVFQLVDHIRKQRMKMVQTFTQFKYVYDLIDSLQKSQVHFPVLT
input PDB
Selected Chain(s) A
Distance of aggregation 10 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                                          (00:05:15)
[INFO]       Auto_mut: Residue number 48 from chain A and a score of 1.094 (valine) selected for   
                       automated muatation                                                         (00:05:17)
[INFO]       Auto_mut: Residue number 24 from chain A and a score of 0.921 (phenylalanine)         
                       selected for automated muatation                                            (00:05:17)
[INFO]       Auto_mut: Residue number 144 from chain A and a score of 0.910 (phenylalanine)        
                       selected for automated muatation                                            (00:05:17)
[INFO]       Auto_mut: Residue number 160 from chain A and a score of 0.862 (isoleucine) selected  
                       for automated muatation                                                     (00:05:17)
[INFO]       Auto_mut: Residue number 165 from chain A and a score of 0.728 (valine) selected for  
                       automated muatation                                                         (00:05:17)
[INFO]       Auto_mut: Residue number 196 from chain A and a score of 0.722 (phenylalanine)        
                       selected for automated muatation                                            (00:05:17)
[INFO]       Auto_mut: Mutating residue number 48 from chain A (valine) into glutamic acid         (00:05:17)
[INFO]       Auto_mut: Mutating residue number 48 from chain A (valine) into aspartic acid         (00:05:17)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 24 from chain A (phenylalanine) into glutamic acid  (00:05:17)
[INFO]       Auto_mut: Mutating residue number 48 from chain A (valine) into lysine                (00:07:52)
[INFO]       Auto_mut: Mutating residue number 48 from chain A (valine) into arginine              (00:07:52)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (phenylalanine) into lysine         (00:07:58)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 24 from chain A (phenylalanine) into aspartic acid  (00:10:35)
[INFO]       Auto_mut: Mutating residue number 144 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 144 from chain A (phenylalanine) into glutamic acid (00:10:43)
[INFO]       Auto_mut: Mutating residue number 144 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 144 from chain A (phenylalanine) into aspartic acid (00:10:48)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (phenylalanine) into arginine       (00:13:02)
[INFO]       Auto_mut: Mutating residue number 144 from chain A (phenylalanine) into arginine      (00:13:12)
[INFO]       Auto_mut: Mutating residue number 144 from chain A (phenylalanine) into lysine        (00:13:19)
[INFO]       Auto_mut: Mutating residue number 160 from chain A (isoleucine) into glutamic acid    (00:15:37)
[INFO]       Auto_mut: Mutating residue number 160 from chain A (isoleucine) into aspartic acid    (00:15:52)
[INFO]       Auto_mut: Mutating residue number 165 from chain A (valine) into glutamic acid        (00:16:04)
[INFO]       Auto_mut: Mutating residue number 160 from chain A (isoleucine) into lysine           (00:18:06)
[INFO]       Auto_mut: Mutating residue number 160 from chain A (isoleucine) into arginine         (00:18:16)
[INFO]       Auto_mut: Mutating residue number 165 from chain A (valine) into lysine               (00:18:29)
[INFO]       Auto_mut: Mutating residue number 165 from chain A (valine) into aspartic acid        (00:20:47)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 196 from chain A (phenylalanine) into glutamic acid (00:20:53)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 196 from chain A (phenylalanine) into aspartic acid (00:21:12)
[INFO]       Auto_mut: Mutating residue number 165 from chain A (valine) into arginine             (00:23:25)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (phenylalanine) into lysine        (00:23:32)
[INFO]       Auto_mut: Mutating residue number 196 from chain A (phenylalanine) into arginine      (00:23:44)
[INFO]       Auto_mut: Effect of mutation residue number 48 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.0641 kcal/mol, Difference in average score from 
                       the base case: -0.0289                                                      (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 48 from chain A (valine) into lysine:     
                       Energy difference: -0.2131 kcal/mol, Difference in average score from the   
                       base case: -0.0228                                                          (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 48 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.3214 kcal/mol, Difference in average score from  
                       the base case: -0.0343                                                      (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 48 from chain A (valine) into arginine:   
                       Energy difference: -0.3315 kcal/mol, Difference in average score from the   
                       base case: -0.0286                                                          (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 1.4739 kcal/mol, Difference in average    
                       score from the base case: -0.0278                                           (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (phenylalanine) into      
                       lysine: Energy difference: 1.1667 kcal/mol, Difference in average score     
                       from the base case: -0.0224                                                 (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 1.4141 kcal/mol, Difference in average    
                       score from the base case: -0.0239                                           (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (phenylalanine) into      
                       arginine: Energy difference: 0.9295 kcal/mol, Difference in average score   
                       from the base case: -0.0298                                                 (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 144 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.2090 kcal/mol, Difference in average    
                       score from the base case: -0.0510                                           (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 144 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.7912 kcal/mol, Difference in average score     
                       from the base case: -0.0406                                                 (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 144 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.5004 kcal/mol, Difference in average    
                       score from the base case: -0.0457                                           (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 144 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.7987 kcal/mol, Difference in average score   
                       from the base case: -0.0343                                                 (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 160 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.0937 kcal/mol, Difference in average   
                       score from the base case: -0.0357                                           (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 160 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.1689 kcal/mol, Difference in average score    
                       from the base case: -0.0426                                                 (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 160 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.6336 kcal/mol, Difference in average    
                       score from the base case: -0.0434                                           (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 160 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.6576 kcal/mol, Difference in average score  
                       from the base case: -0.0444                                                 (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 165 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.4491 kcal/mol, Difference in average score from 
                       the base case: -0.0301                                                      (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 165 from chain A (valine) into lysine:    
                       Energy difference: -0.3682 kcal/mol, Difference in average score from the   
                       base case: -0.0335                                                          (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 165 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.3481 kcal/mol, Difference in average score from  
                       the base case: -0.0276                                                      (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 165 from chain A (valine) into arginine:  
                       Energy difference: -0.2928 kcal/mol, Difference in average score from the   
                       base case: -0.0328                                                          (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.3856 kcal/mol, Difference in average   
                       score from the base case: -0.0132                                           (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.1295 kcal/mol, Difference in average score    
                       from the base case: -0.0211                                                 (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.5025 kcal/mol, Difference in average    
                       score from the base case: -0.0182                                           (00:26:24)
[INFO]       Auto_mut: Effect of mutation residue number 196 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.0875 kcal/mol, Difference in average score  
                       from the base case: -0.0227                                                 (00:26:24)
[INFO]       Main:     Simulation completed successfully.                                          (00:26:31)
Show buried residues
Minimal score value
-3.5963
Maximal score value
1.0942
Average score
-0.6672
Total score value
-214.8485
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 M A -0.3884
2 G A -0.4365
3 S A 0.0000
4 S A 0.0000
5 H A -1.4075
6 H A -1.7869
7 H A -1.7050
8 H A 0.0000
9 H A -1.6983
10 H A -1.1962
11 T A -0.7574
12 G A -0.6446
13 G A 0.0000
14 T A -0.5827
15 T A -0.1519
16 S A -0.2430
17 L A -0.1855
18 H A -0.8436
19 S A -0.9414
20 V A 0.0000
21 P A -1.0497
22 D A -1.7474
23 A A 0.0000
24 F A 0.9210
25 T A -0.1819
26 N A -1.0388
27 P A -1.0171
28 D A -1.9274
29 V A 0.0000
30 A A -0.7737
31 T A -0.9764
32 L A 0.0000
33 Y A 0.0000
34 Q A -1.2173
35 K A 0.0000
36 F A 0.0000
37 L A -0.0692
38 R A -0.6254
39 L A 0.0000
40 Q A -0.5881
41 S A -0.5521
42 L A -0.1564
43 E A 0.0000
44 H A -0.9433
45 Q A -0.8017
46 R A 0.0000
47 L A 0.3965
48 V A 1.0942
49 S A -0.4076
50 C A -0.6191
51 S A -1.0302
52 D A -2.4957
53 R A -3.4218
54 N A -2.8541
55 S A -1.9115
56 Q A -1.8644
57 W A -0.9464
58 S A 0.0000
59 T A 0.0000
60 V A -1.0829
61 D A -0.9998
62 S A 0.0000
63 L A -0.1751
64 S A -0.7905
65 N A -1.4899
66 T A -0.9966
67 S A 0.0000
68 Y A -0.8264
69 K A -2.1944
70 K A -1.5354
71 N A -1.0108
72 R A -0.9499
73 Y A 0.0000
74 T A -1.0166
75 D A -1.6411
76 I A 0.0000
77 V A 0.0000
78 P A 0.0000
79 Y A 0.0000
80 N A -0.7016
81 C A 0.3113
82 T A -0.0508
83 R A 0.0000
84 V A 0.0000
85 H A -1.7568
86 L A 0.0000
87 K A -2.7527
88 R A -1.9786
89 T A -0.9971
90 S A -0.9706
91 P A -0.8634
92 S A -0.9522
93 E A -1.6321
94 L A -0.9759
95 D A -1.6753
96 Y A 0.0000
97 I A 0.0000
98 N A 0.0000
99 A A 0.0000
100 S A 0.0000
101 F A 0.1523
102 I A 0.0000
103 K A -2.3261
104 T A -2.0442
105 E A -2.4255
106 T A -1.4504
107 S A -1.4006
108 N A -1.6597
109 Y A 0.0000
110 I A 0.0000
111 A A 0.0000
112 C A 0.0000
113 Q A 0.0000
114 G A 0.0000
115 S A 0.0000
116 I A -0.8889
117 S A -0.9830
118 R A -2.2305
119 S A 0.0000
120 I A -0.4006
121 S A -0.4123
122 D A 0.0000
123 F A 0.0000
124 W A 0.0000
125 H A -1.0710
126 M A 0.0000
127 V A 0.0000
128 W A -1.2886
129 D A -2.3809
130 N A -1.5064
131 V A 0.0000
132 E A -2.9635
133 N A -2.1862
134 I A -1.4047
135 G A 0.0000
136 T A 0.0000
137 I A 0.0000
138 V A 0.0000
139 M A 0.0000
140 L A 0.0000
141 G A 0.0000
142 S A 0.2645
143 L A 0.6309
144 F A 0.9100
145 E A -0.2285
146 A A -0.4835
147 G A -1.0299
148 R A -1.7771
149 E A -1.1140
150 M A 0.0000
151 C A 0.0000
152 T A -0.0581
153 A A -0.0387
154 Y A 0.0000
155 W A 0.0000
156 P A 0.0000
157 S A -1.0243
158 N A -1.4953
159 G A -0.4541
160 I A 0.8619
161 G A -0.0887
162 D A -1.3426
163 K A -1.9605
164 Q A -0.9673
165 V A 0.7276
166 Y A 0.1901
167 G A -0.5734
168 D A -1.2064
169 Y A 0.0000
170 C A -0.1759
171 V A 0.0000
172 K A -1.2083
173 Q A 0.0000
174 I A -0.0775
175 S A -0.6425
176 E A -1.9948
177 E A -3.1883
178 N A -3.2461
179 V A -2.7735
180 D A -3.5963
181 N A -3.1980
182 S A 0.0000
183 R A -3.4715
184 F A 0.0000
185 I A -1.6340
186 L A -1.2838
187 R A 0.0000
188 K A -0.9001
189 F A 0.0000
190 E A -0.9664
191 I A 0.0000
192 Q A -0.3877
193 N A 0.0000
194 A A -0.4370
195 N A -0.8675
196 F A 0.7216
197 P A 0.2463
198 S A 0.0657
199 V A 0.2198
200 K A -1.1212
201 K A -1.3982
202 V A 0.0000
203 H A -0.6481
204 H A 0.0000
205 Y A 0.0000
206 Q A 0.0000
207 Y A 0.0000
208 P A -0.7203
209 N A -1.7060
210 W A 0.0000
211 S A -0.4591
212 D A -0.4029
213 C A 0.2388
214 N A -0.6575
215 S A -1.1108
216 P A -1.7084
217 E A -2.6514
218 N A -2.1900
219 V A 0.0000
220 K A -2.8400
221 S A -2.7920
222 M A 0.0000
223 V A -1.4285
224 E A -2.3795
225 F A 0.0000
226 L A 0.0000
227 K A -1.4095
228 Y A -0.8238
229 V A 0.0000
230 N A -1.3817
231 N A -1.7769
232 S A -1.2220
233 H A -1.5293
234 G A -1.5411
235 S A -1.5616
236 G A -1.8597
237 N A -1.2923
238 T A -0.5287
239 I A 0.0000
240 V A 0.0000
241 H A 0.0000
242 C A 0.0000
243 S A 0.0000
244 A A 0.0000
245 G A 0.0000
246 V A 0.0000
247 G A 0.0000
248 R A 0.0000
249 T A 0.0000
250 G A 0.0000
251 T A 0.0000
252 F A 0.0000
253 I A 0.0000
254 V A 0.0000
255 L A 0.0000
256 D A 0.0000
257 T A 0.0000
258 I A 0.0000
259 L A 0.0000
260 R A -0.9386
261 F A 0.0000
262 P A -1.2238
263 E A -1.6887
264 S A -1.2982
265 K A -1.7050
266 L A 0.0000
267 S A -1.0402
268 G A -0.8648
269 F A -0.7068
270 N A -1.1253
271 P A -0.9624
272 S A -0.6479
273 V A -0.0323
274 A A -0.1421
275 D A -0.5391
276 S A -0.4727
277 S A -0.4382
278 D A 0.0000
279 V A -0.2444
280 V A 0.0000
281 F A 0.0000
282 Q A -0.8552
283 L A 0.0000
284 V A 0.0000
285 D A 0.0000
286 H A -1.4271
287 I A 0.0000
288 R A 0.0000
289 K A -1.0863
290 Q A -0.6806
291 R A 0.0000
292 M A 0.0000
293 K A -0.5976
294 M A 0.0000
295 V A 0.0000
296 Q A 0.0000
297 T A -0.2787
298 F A 0.0000
299 T A -0.2900
300 Q A 0.0000
301 F A 0.0000
302 K A -0.5654
303 Y A 0.0000
304 V A 0.0000
305 Y A 0.0000
306 D A -0.9922
307 L A 0.0000
308 I A 0.0000
309 D A -1.8948
310 S A -1.7999
311 L A 0.0000
312 Q A -2.7011
313 K A -2.8021
314 S A -2.0361
315 Q A -2.3223
316 V A -1.2371
317 H A -1.4511
318 F A 0.0000
319 P A -0.8801
320 V A 0.0000
321 L A 0.0000
322 T A -0.5755
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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
IR160A -0.6576 -0.0444 View CSV PDB
VK165A -0.3682 -0.0335 View CSV PDB
VE165A -0.4491 -0.0301 View CSV PDB
IK160A -0.1689 -0.0426 View CSV PDB
VR48A -0.3315 -0.0286 View CSV PDB
VE48A -0.0641 -0.0289 View CSV PDB
FR196A -0.0875 -0.0227 View CSV PDB
FK196A -0.1295 -0.0211 View CSV PDB
FK144A 0.7912 -0.0406 View CSV PDB
FR144A 0.7987 -0.0343 View CSV PDB
FR24A 0.9295 -0.0298 View CSV PDB
FK24A 1.1667 -0.0224 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018