Project name: B93tp

Status: done

Started: 2025-08-07 21:01:48
Settings
Chain sequence(s) A: MARESEFRLTKAQREEVSKLSRSVKAKTTRLLKNYGQDFTAYISPKSPDDFKSLNEFNAFKKRAENFTDRSNRDFQFVQNQYGVVISKSELDEILRDTKKAQETAEKILDKFNDVEVISGGKSTGFTVGENKELLAKPDKGFGRIEDFDFESVRTQEGLDRFAARAKNRSKEAYYEESLRRLQDNFIRSVEGTFNSDADDVVEKLRNLPADDFYELFSIYDEISFENFDSENALGMASESILERVRMYVNAYFDGKSDMSLKGF
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]                                                (00:00:08)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:08)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:08)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:08)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:08)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:06:55)
[INFO]       Auto_mut: Residue number 264 from chain A and a score of 1.095 (phenylalanine)        
                       selected for automated muatation                                            (00:06:57)
[INFO]       Auto_mut: Residue number 134 from chain A and a score of 0.697 (leucine) selected for 
                       automated muatation                                                         (00:06:57)
[INFO]       Auto_mut: Residue number 135 from chain A and a score of 0.680 (leucine) selected for 
                       automated muatation                                                         (00:06:57)
[INFO]       Auto_mut: Residue number 234 from chain A and a score of 0.587 (leucine) selected for 
                       automated muatation                                                         (00:06:57)
[INFO]       Auto_mut: Residue number 236 from chain A and a score of 0.548 (methionine) selected  
                       for automated muatation                                                     (00:06:57)
[INFO]       Auto_mut: Residue number 42 from chain A and a score of 0.511 (tyrosine) selected for 
                       automated muatation                                                         (00:06:57)
[INFO]       Auto_mut: Mutating residue number 134 from chain A (leucine) into glutamic acid       (00:06:57)
[INFO]       Auto_mut: Mutating residue number 264 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 264 from chain A (phenylalanine) into aspartic acid (00:06:57)
[INFO]       Auto_mut: Mutating residue number 264 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 264 from chain A (phenylalanine) into glutamic acid (00:06:57)
[INFO]       Auto_mut: Mutating residue number 264 from chain A (phenylalanine) into lysine        (00:10:11)
[INFO]       Auto_mut: Mutating residue number 264 from chain A (phenylalanine) into arginine      (00:10:14)
[INFO]       Auto_mut: Mutating residue number 134 from chain A (leucine) into lysine              (00:10:19)
[INFO]       Auto_mut: Mutating residue number 134 from chain A (leucine) into aspartic acid       (00:13:45)
[INFO]       Auto_mut: Mutating residue number 135 from chain A (leucine) into glutamic acid       (00:13:55)
[INFO]       Auto_mut: Mutating residue number 135 from chain A (leucine) into aspartic acid       (00:14:01)
[INFO]       Auto_mut: Mutating residue number 134 from chain A (leucine) into arginine            (00:17:02)
[INFO]       Auto_mut: Mutating residue number 135 from chain A (leucine) into lysine              (00:17:36)
[INFO]       Auto_mut: Mutating residue number 135 from chain A (leucine) into arginine            (00:17:44)
[INFO]       Auto_mut: Mutating residue number 234 from chain A (leucine) into glutamic acid       (00:20:36)
[INFO]       Auto_mut: Mutating residue number 234 from chain A (leucine) into aspartic acid       (00:21:27)
[INFO]       Auto_mut: Mutating residue number 236 from chain A (methionine) into glutamic acid    (00:21:39)
[INFO]       Auto_mut: Mutating residue number 234 from chain A (leucine) into lysine              (00:24:00)
[INFO]       Auto_mut: Mutating residue number 234 from chain A (leucine) into arginine            (00:24:53)
[INFO]       Auto_mut: Mutating residue number 236 from chain A (methionine) into lysine           (00:25:03)
[INFO]       Auto_mut: Mutating residue number 236 from chain A (methionine) into aspartic acid    (00:27:21)
[INFO]       Auto_mut: Mutating residue number 42 from chain A (tyrosine) into glutamic acid       (00:28:11)
[INFO]       Auto_mut: Mutating residue number 42 from chain A (tyrosine) into aspartic acid       (00:28:27)
[INFO]       Auto_mut: Mutating residue number 236 from chain A (methionine) into arginine         (00:30:28)
[INFO]       Auto_mut: Mutating residue number 42 from chain A (tyrosine) into lysine              (00:31:27)
[INFO]       Auto_mut: Mutating residue number 42 from chain A (tyrosine) into arginine            (00:31:46)
[INFO]       Auto_mut: Effect of mutation residue number 264 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.8882 kcal/mol, Difference in average    
                       score from the base case: -0.0246                                           (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 264 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.1628 kcal/mol, Difference in average score     
                       from the base case: -0.0236                                                 (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 264 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.9347 kcal/mol, Difference in average    
                       score from the base case: -0.0243                                           (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 264 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.0173 kcal/mol, Difference in average score   
                       from the base case: -0.0248                                                 (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 134 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.0359 kcal/mol, Difference in average score from  
                       the base case: -0.0457                                                      (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 134 from chain A (leucine) into lysine:   
                       Energy difference: 0.2662 kcal/mol, Difference in average score from the    
                       base case: -0.0394                                                          (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 134 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.4291 kcal/mol, Difference in average score from  
                       the base case: -0.0417                                                      (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 134 from chain A (leucine) into arginine: 
                       Energy difference: -0.4748 kcal/mol, Difference in average score from the   
                       base case: -0.0579                                                          (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 135 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.9624 kcal/mol, Difference in average score from  
                       the base case: -0.0283                                                      (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 135 from chain A (leucine) into lysine:   
                       Energy difference: 0.3423 kcal/mol, Difference in average score from the    
                       base case: -0.0246                                                          (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 135 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.7578 kcal/mol, Difference in average score from  
                       the base case: -0.0326                                                      (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 135 from chain A (leucine) into arginine: 
                       Energy difference: 0.2736 kcal/mol, Difference in average score from the    
                       base case: -0.0317                                                          (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 234 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.4127 kcal/mol, Difference in average score from  
                       the base case: -0.0376                                                      (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 234 from chain A (leucine) into lysine:   
                       Energy difference: -0.6711 kcal/mol, Difference in average score from the   
                       base case: -0.0361                                                          (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 234 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.1155 kcal/mol, Difference in average score from  
                       the base case: -0.0370                                                      (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 234 from chain A (leucine) into arginine: 
                       Energy difference: -0.5090 kcal/mol, Difference in average score from the   
                       base case: -0.0384                                                          (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 236 from chain A (methionine) into        
                       glutamic acid: Energy difference: -0.9121 kcal/mol, Difference in average   
                       score from the base case: -0.0267                                           (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 236 from chain A (methionine) into        
                       lysine: Energy difference: -0.2633 kcal/mol, Difference in average score    
                       from the base case: -0.0199                                                 (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 236 from chain A (methionine) into        
                       aspartic acid: Energy difference: -0.7623 kcal/mol, Difference in average   
                       score from the base case: -0.0276                                           (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 236 from chain A (methionine) into        
                       arginine: Energy difference: -0.2044 kcal/mol, Difference in average score  
                       from the base case: -0.0169                                                 (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 42 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.5556 kcal/mol, Difference in average score from  
                       the base case: -0.0265                                                      (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 42 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.3943 kcal/mol, Difference in average score from the    
                       base case: -0.0192                                                          (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 42 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.1145 kcal/mol, Difference in average score from  
                       the base case: -0.0232                                                      (00:35:07)
[INFO]       Auto_mut: Effect of mutation residue number 42 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.3799 kcal/mol, Difference in average score from the    
                       base case: -0.0245                                                          (00:35:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:35:14)
Show buried residues
Minimal score value
-4.1875
Maximal score value
1.0952
Average score
-1.6135
Total score value
-425.9752
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 0.3565
2 A A -0.8356
3 R A -2.7637
4 E A -3.0971
5 S A -2.6448
6 E A -3.2457
7 F A -2.1061
8 R A -3.0783
9 L A 0.0000
10 T A -1.8160
11 K A -2.7574
12 A A -1.9118
13 Q A -2.2869
14 R A -3.1416
15 E A -3.4612
16 E A -3.1229
17 V A 0.0000
18 S A -2.6513
19 K A -3.2535
20 L A 0.0000
21 S A 0.0000
22 R A -3.2892
23 S A -2.3182
24 V A 0.0000
25 K A -2.8278
26 A A -1.9280
27 K A -1.6971
28 T A 0.0000
29 T A -2.2395
30 R A -3.2145
31 L A 0.0000
32 L A -2.0949
33 K A -3.0749
34 N A -2.4992
35 Y A -1.5095
36 G A -1.7266
37 Q A -1.6961
38 D A -1.9970
39 F A -0.5195
40 T A -0.4033
41 A A 0.1962
42 Y A 0.5115
43 I A 0.0000
44 S A -0.5437
45 P A -1.7259
46 K A -2.2199
47 S A -1.8608
48 P A -2.9990
49 D A -3.4808
50 D A -3.6176
51 F A 0.0000
52 K A -3.0901
53 S A -1.6869
54 L A -0.4122
55 N A -1.6354
56 E A -1.9473
57 F A 0.0000
58 N A -1.9443
59 A A -1.9124
60 F A 0.0000
61 K A -3.0547
62 K A -3.7154
63 R A -3.5435
64 A A 0.0000
65 E A -3.9508
66 N A -3.5670
67 F A 0.0000
68 T A 0.0000
69 D A -3.1984
70 R A -3.0341
71 S A -2.1100
72 N A -2.6010
73 R A -2.7821
74 D A -2.5863
75 F A -1.7492
76 Q A -1.7784
77 F A -0.7440
78 V A -0.0705
79 Q A -0.7907
80 N A 0.0000
81 Q A -1.5121
82 Y A -0.6924
83 G A -0.8713
84 V A 0.0000
85 V A -0.4032
86 I A 0.0000
87 S A 0.0000
88 K A -2.0392
89 S A -2.5275
90 E A -3.0432
91 L A -1.7925
92 D A -2.1733
93 E A -3.4230
94 I A 0.0000
95 L A -2.1773
96 R A -3.2991
97 D A -3.2352
98 T A 0.0000
99 K A -3.3465
100 K A -3.1818
101 A A 0.0000
102 Q A -3.4158
103 E A -3.4969
104 T A 0.0000
105 A A 0.0000
106 E A -3.6200
107 K A -3.4953
108 I A -2.6143
109 L A 0.0000
110 D A -3.4991
111 K A -3.2279
112 F A 0.0000
113 N A -2.6556
114 D A -2.8420
115 V A -1.8560
116 E A -2.0172
117 V A 0.0000
118 I A -1.0955
119 S A -1.4804
120 G A -1.3498
121 G A -1.3314
122 K A -2.1758
123 S A -1.3585
124 T A -0.9359
125 G A -0.7349
126 F A -0.1100
127 T A -1.3726
128 V A 0.0000
129 G A -2.0789
130 E A -1.6953
131 N A -0.8743
132 K A -1.3085
133 E A -1.6222
134 L A 0.6967
135 L A 0.6802
136 A A -0.4383
137 K A -1.3744
138 P A -1.6551
139 D A 0.0000
140 K A -1.2533
141 G A -1.1114
142 F A 0.0000
143 G A -1.7551
144 R A -3.0050
145 I A -2.4470
146 E A -3.4116
147 D A -3.2907
148 F A -2.2285
149 D A -2.5993
150 F A 0.0000
151 E A -2.2819
152 S A -1.6990
153 V A -1.8917
154 R A -2.4061
155 T A -2.0634
156 Q A -2.7781
157 E A -3.6097
158 G A -2.7671
159 L A 0.0000
160 D A -3.5649
161 R A -3.4419
162 F A -2.2591
163 A A -2.5087
164 A A -2.2689
165 R A -2.5959
166 A A 0.0000
167 K A -3.2204
168 N A -2.3815
169 R A -2.4344
170 S A -2.8901
171 K A -2.5522
172 E A -2.5653
173 A A -1.9914
174 Y A -1.8712
175 Y A 0.0000
176 E A -3.7387
177 E A -3.6356
178 S A -2.6849
179 L A 0.0000
180 R A -4.1875
181 R A -4.0250
182 L A 0.0000
183 Q A 0.0000
184 D A -3.8467
185 N A -2.7821
186 F A 0.0000
187 I A 0.0000
188 R A -3.1945
189 S A -2.2304
190 V A 0.0000
191 E A -3.1373
192 G A -2.1074
193 T A -1.6694
194 F A -1.8037
195 N A -2.9274
196 S A -2.6554
197 D A -3.3022
198 A A 0.0000
199 D A -3.8490
200 D A -2.9685
201 V A 0.0000
202 V A 0.0000
203 E A -3.8135
204 K A -2.8183
205 L A 0.0000
206 R A -3.7005
207 N A -2.6648
208 L A 0.0000
209 P A -1.2706
210 A A -2.5152
211 D A -1.6688
212 D A 0.0000
213 F A 0.0000
214 Y A 0.0000
215 E A 0.0000
216 L A 0.0000
217 F A 0.0000
218 S A 0.0000
219 I A 0.0000
220 Y A -0.9515
221 D A -1.4622
222 E A 0.0000
223 I A 0.0000
224 S A 0.0000
225 F A -1.3125
226 E A -2.4660
227 N A -1.6519
228 F A 0.0000
229 D A -3.1044
230 S A -2.5688
231 E A -2.7252
232 N A -2.0758
233 A A -0.9480
234 L A 0.5873
235 G A 0.1836
236 M A 0.5478
237 A A -0.0267
238 S A 0.0000
239 E A -1.9485
240 S A -1.3655
241 I A -1.1046
242 L A 0.0000
243 E A -2.2173
244 R A -1.6463
245 V A 0.0000
246 R A -0.9891
247 M A -0.0837
248 Y A 0.0000
249 V A 0.0000
250 N A -0.6747
251 A A -1.1353
252 Y A -0.7547
253 F A -0.2215
254 D A -1.9564
255 G A -2.1823
256 K A -2.7077
257 S A -2.1814
258 D A -2.3937
259 M A 0.0000
260 S A -1.2485
261 L A -1.1478
262 K A -1.7122
263 G A -0.5127
264 F A 1.0952
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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
LR134A -0.4748 -0.0579 View CSV PDB
LK234A -0.6711 -0.0361 View CSV PDB
LR234A -0.509 -0.0384 View CSV PDB
ME236A -0.9121 -0.0267 View CSV PDB
MD236A -0.7623 -0.0276 View CSV PDB
FR264A 0.0173 -0.0248 View CSV PDB
LK134A 0.2662 -0.0394 View CSV PDB
FK264A 0.1628 -0.0236 View CSV PDB
LR135A 0.2736 -0.0317 View CSV PDB
LK135A 0.3423 -0.0246 View CSV PDB
YR42A 0.3799 -0.0245 View CSV PDB
YK42A 0.3943 -0.0192 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018