Project name: test

Status: done

Started: 2025-06-27 16:04:04
Settings
Chain sequence(s) A: LALQAKQYGDFDRYVLALSWQTGFCQSQHDRNRNERDECRLQTETTNKADFLTVHGLWPGLPKSVAARGVDERRWMRFGCATRPIPNLPEARASRMCSSPETGLSLETAAKLSEVMPGAGGRSCLERYEYAKHGACFGFDPDAYFGTMVRLNQEIKESEAGKFLADNYGKTVSRRDFDAAFAKSWGKENVKAVKLTCQGNPAYLTEIQISIKADAINAPLSANSFLPQPHPGNCGKTFVIDKAGY
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                                          (00:05:22)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.139 (leucine) selected for   
                       automated muatation                                                         (00:05:25)
[INFO]       Auto_mut: Residue number 106 from chain A and a score of 0.390 (leucine) selected for 
                       automated muatation                                                         (00:05:25)
[INFO]       Auto_mut: Residue number 245 from chain A and a score of 0.373 (tyrosine) selected    
                       for automated muatation                                                     (00:05:25)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 0.122 (alanine) selected for   
                       automated muatation                                                         (00:05:25)
[INFO]       Auto_mut: Residue number 15 from chain A and a score of -0.036 (valine) selected for  
                       automated muatation                                                         (00:05:25)
[INFO]       Auto_mut: Residue number 24 from chain A and a score of -0.077 (phenylalanine)        
                       selected for automated muatation                                            (00:05:25)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (leucine) into glutamic acid         (00:05:25)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (leucine) into aspartic acid         (00:05:25)
[INFO]       Auto_mut: Mutating residue number 106 from chain A (leucine) into glutamic acid       (00:05:25)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (leucine) into arginine              (00:08:22)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (leucine) into lysine                (00:08:24)
[INFO]       Auto_mut: Mutating residue number 106 from chain A (leucine) into lysine              (00:08:26)
[INFO]       Auto_mut: Mutating residue number 106 from chain A (leucine) into aspartic acid       (00:10:56)
[INFO]       Auto_mut: Mutating residue number 245 from chain A (tyrosine) into glutamic acid      (00:11:07)
[INFO]       Auto_mut: Mutating residue number 245 from chain A (tyrosine) into aspartic acid      (00:11:08)
[INFO]       Auto_mut: Mutating residue number 106 from chain A (leucine) into arginine            (00:13:21)
[INFO]       Auto_mut: Mutating residue number 245 from chain A (tyrosine) into arginine           (00:13:45)
[INFO]       Auto_mut: Mutating residue number 245 from chain A (tyrosine) into lysine             (00:13:49)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (alanine) into glutamic acid         (00:16:00)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (alanine) into aspartic acid         (00:16:22)
[INFO]       Auto_mut: Mutating residue number 15 from chain A (valine) into glutamic acid         (00:16:51)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (alanine) into lysine                (00:18:23)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (alanine) into arginine              (00:18:54)
[INFO]       Auto_mut: Mutating residue number 15 from chain A (valine) into lysine                (00:19:33)
[INFO]       Auto_mut: Mutating residue number 15 from chain A (valine) into aspartic acid         (00:21:09)
[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  (00:21:22)
[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  (00:22:58)
[INFO]       Auto_mut: Mutating residue number 15 from chain A (valine) into arginine              (00:23:44)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (phenylalanine) into lysine         (00:24:18)
[INFO]       Auto_mut: Mutating residue number 24 from chain A (phenylalanine) into arginine       (00:25:45)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (leucine) into glutamic    
                       acid: Energy difference: 0.0605 kcal/mol, Difference in average score from  
                       the base case: -0.0158                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (leucine) into lysine:     
                       Energy difference: -0.5350 kcal/mol, Difference in average score from the   
                       base case: 0.0001                                                           (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (leucine) into aspartic    
                       acid: Energy difference: -0.4578 kcal/mol, Difference in average score from 
                       the base case: -0.0154                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (leucine) into arginine:   
                       Energy difference: -0.7591 kcal/mol, Difference in average score from the   
                       base case: -0.0093                                                          (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.1212 kcal/mol, Difference in average score from 
                       the base case: -0.0258                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain A (leucine) into lysine:   
                       Energy difference: -0.1685 kcal/mol, Difference in average score from the   
                       base case: -0.0243                                                          (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.4316 kcal/mol, Difference in average score from  
                       the base case: -0.0254                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 106 from chain A (leucine) into arginine: 
                       Energy difference: -0.2809 kcal/mol, Difference in average score from the   
                       base case: -0.0365                                                          (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 245 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 3.6257 kcal/mol, Difference in average score from  
                       the base case: -0.0080                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 245 from chain A (tyrosine) into lysine:  
                       Energy difference: 2.4305 kcal/mol, Difference in average score from the    
                       base case: -0.0114                                                          (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 245 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 3.8742 kcal/mol, Difference in average score from  
                       the base case: -0.0194                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 245 from chain A (tyrosine) into          
                       arginine: Energy difference: 2.1686 kcal/mol, Difference in average score   
                       from the base case: -0.0111                                                 (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (alanine) into glutamic    
                       acid: Energy difference: -0.7456 kcal/mol, Difference in average score from 
                       the base case: 0.0063                                                       (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (alanine) into lysine:     
                       Energy difference: -0.3297 kcal/mol, Difference in average score from the   
                       base case: 0.0061                                                           (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (alanine) into aspartic    
                       acid: Energy difference: -0.7078 kcal/mol, Difference in average score from 
                       the base case: 0.0067                                                       (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (alanine) into arginine:   
                       Energy difference: -0.2005 kcal/mol, Difference in average score from the   
                       base case: -0.0034                                                          (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain A (valine) into glutamic    
                       acid: Energy difference: 1.5526 kcal/mol, Difference in average score from  
                       the base case: 0.0250                                                       (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain A (valine) into lysine:     
                       Energy difference: 1.1730 kcal/mol, Difference in average score from the    
                       base case: 0.0264                                                           (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain A (valine) into aspartic    
                       acid: Energy difference: 2.7107 kcal/mol, Difference in average score from  
                       the base case: 0.0207                                                       (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain A (valine) into arginine:   
                       Energy difference: 0.4139 kcal/mol, Difference in average score from the    
                       base case: 0.0266                                                           (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 1.4462 kcal/mol, Difference in average    
                       score from the base case: 0.0060                                            (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (phenylalanine) into      
                       lysine: Energy difference: 0.6531 kcal/mol, Difference in average score     
                       from the base case: 0.0017                                                  (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 0.4300 kcal/mol, Difference in average    
                       score from the base case: 0.0022                                            (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain A (phenylalanine) into      
                       arginine: Energy difference: -0.7677 kcal/mol, Difference in average score  
                       from the base case: 0.0016                                                  (00:28:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:28:45)
Show buried residues
Minimal score value
-4.3822
Maximal score value
1.1391
Average score
-1.1141
Total score value
-272.96
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 L A 1.1391
2 A A 0.1222
3 L A 0.0000
4 Q A -1.9271
5 A A -2.1895
6 K A -2.7875
7 Q A -2.4062
8 Y A -1.4946
9 G A -2.3134
10 D A -2.2204
11 F A 0.0000
12 D A -2.9799
13 R A -1.8669
14 Y A 0.0000
15 V A -0.0357
16 L A 0.0000
17 A A 0.0000
18 L A 0.0000
19 S A -0.1422
20 W A 0.0000
21 Q A -0.4356
22 T A 0.0000
23 G A 0.0000
24 F A -0.0768
25 C A 0.0000
26 Q A -1.2083
27 S A -1.7831
28 Q A -2.8919
29 H A -3.3450
30 D A -3.6344
31 R A -4.2288
32 N A -4.2326
33 R A -4.3822
34 N A -3.4310
35 E A -2.9692
36 R A -2.8013
37 D A -2.8133
38 E A 0.0000
39 C A 0.0000
40 R A -2.0835
41 L A -0.1838
42 Q A -0.9007
43 T A -1.0458
44 E A -2.5108
45 T A -1.5279
46 T A -1.1371
47 N A -1.8863
48 K A -2.0526
49 A A 0.0000
50 D A -2.0110
51 F A 0.0000
52 L A 0.0000
53 T A 0.0000
54 V A 0.0000
55 H A -0.3335
56 G A 0.0000
57 L A 0.0000
58 W A 0.0000
59 P A 0.0000
60 G A -1.0733
61 L A -1.6107
62 P A 0.0000
63 K A -2.4611
64 S A -1.5780
65 V A 0.0000
66 A A -1.9145
67 A A -1.5135
68 R A -2.5548
69 G A -2.0827
70 V A 0.0000
71 D A -2.8689
72 E A -3.5343
73 R A -3.7004
74 R A -3.5603
75 W A 0.0000
76 M A -1.4882
77 R A -2.1808
78 F A -1.4592
79 G A 0.0000
80 C A 0.0000
81 A A 0.0000
82 T A 0.0000
83 R A -2.3309
84 P A -1.7277
85 I A -1.1567
86 P A -0.9830
87 N A -1.7036
88 L A -0.7920
89 P A -1.1001
90 E A -1.7805
91 A A -1.7041
92 R A -2.6681
93 A A -1.5494
94 S A -1.6418
95 R A -2.4284
96 M A -1.5809
97 C A -1.4208
98 S A -1.2920
99 S A -1.4488
100 P A -1.2836
101 E A -2.1337
102 T A -1.3975
103 G A -1.0025
104 L A -0.6388
105 S A -0.1779
106 L A 0.3903
107 E A -1.4707
108 T A -1.0388
109 A A -0.8763
110 A A -1.3238
111 K A -2.3190
112 L A 0.0000
113 S A -1.7907
114 E A -2.4535
115 V A 0.0000
116 M A 0.0000
117 P A -0.8371
118 G A 0.0000
119 A A -0.7942
120 G A -1.1075
121 G A -1.6244
122 R A -2.3393
123 S A -1.6210
124 C A 0.0000
125 L A -0.4666
126 E A -0.5048
127 R A -1.0535
128 Y A -1.0479
129 E A 0.0000
130 Y A -0.3011
131 A A 0.0000
132 K A -0.6023
133 H A 0.0000
134 G A 0.0000
135 A A -0.4718
136 C A 0.0000
137 F A 0.0000
138 G A -1.3930
139 F A 0.0000
140 D A -1.4343
141 P A -0.8273
142 D A -0.6459
143 A A 0.0000
144 Y A 0.0000
145 F A 0.0000
146 G A -0.6317
147 T A 0.0000
148 M A 0.0000
149 V A 0.0000
150 R A -1.1397
151 L A 0.0000
152 N A 0.0000
153 Q A -1.7448
154 E A -1.5583
155 I A 0.0000
156 K A 0.0000
157 E A -2.6895
158 S A 0.0000
159 E A -2.3998
160 A A 0.0000
161 G A 0.0000
162 K A -2.4287
163 F A -1.5589
164 L A 0.0000
165 A A -1.8963
166 D A -2.5047
167 N A -1.7877
168 Y A -1.5780
169 G A -1.7902
170 K A -1.9344
171 T A -0.7399
172 V A 0.0000
173 S A -1.6045
174 R A -2.0987
175 R A -2.6861
176 D A -1.8363
177 F A 0.0000
178 D A -1.9075
179 A A -1.7763
180 A A 0.0000
181 F A 0.0000
182 A A -2.3296
183 K A -2.3180
184 S A -1.5813
185 W A -1.4554
186 G A -2.1240
187 K A -3.2363
188 E A -3.1979
189 N A 0.0000
190 V A 0.0000
191 K A -2.8688
192 A A 0.0000
193 V A 0.0000
194 K A -1.5129
195 L A 0.0000
196 T A -0.7539
197 C A 0.0000
198 Q A -1.2914
199 G A -1.6406
200 N A -1.6181
201 P A -1.1782
202 A A -1.2492
203 Y A 0.0000
204 L A 0.0000
205 T A -0.0783
206 E A -0.3179
207 I A 0.0000
208 Q A -0.4371
209 I A 0.0000
210 S A 0.0000
211 I A 0.0000
212 K A -2.0267
213 A A -2.2934
214 D A -2.5147
215 A A -1.7427
216 I A 0.0000
217 N A -0.9778
218 A A -0.6995
219 P A -0.5110
220 L A 0.0000
221 S A -0.5670
222 A A -1.0613
223 N A -1.5061
224 S A 0.0000
225 F A 0.0000
226 L A -1.0900
227 P A -1.4828
228 Q A -1.2073
229 P A -1.3489
230 H A -1.9907
231 P A -1.8291
232 G A -1.6120
233 N A -2.0137
234 C A 0.0000
235 G A -1.8432
236 K A -2.6062
237 T A -1.4430
238 F A 0.0000
239 V A -0.7306
240 I A 0.0000
241 D A -1.1300
242 K A -2.2841
243 A A 0.0000
244 G A -0.8542
245 Y A 0.3735
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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
LR106A -0.2809 -0.0365 View CSV PDB
LK106A -0.1685 -0.0243 View CSV PDB
LD1A -0.4578 -0.0154 View CSV PDB
LR1A -0.7591 -0.0093 View CSV PDB
AR2A -0.2005 -0.0034 View CSV PDB
YR245A 2.1686 -0.0111 View CSV PDB
YD245A 3.8742 -0.0194 View CSV PDB
FR24A -0.7677 0.0016 View CSV PDB
AE2A -0.7456 0.0063 View CSV PDB
FK24A 0.6531 0.0017 View CSV PDB
VR15A 0.4139 0.0266 View CSV PDB
VK15A 1.173 0.0264 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018