Project name: efa116aac8ded03

Status: done

Started: 2025-03-06 09:07:11
Settings
Chain sequence(s) A: ATFDVVNQCTFTVWAGASPGGGKQLDQGQTWTITVAPGSTKARIWGRTGCNFDANGQGKCQTGDCNGLLQCQGYGSPPNTLAEFSLNQPNNLDYVDISLVDGFNIPMDFSPAAAGVCKDIRCATDITAQCPAELQAPGGCNNPCTVYKTNEYCCTNGQGTCGPTALSKFFKDRCPDAYSYPQDDPTSLFTCPAGTNYKVVFCPNLDA
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:01:42)
[INFO]       Auto_mut: Residue number 11 from chain A and a score of 0.284 (phenylalanine)         
                       selected for automated muatation                                            (00:01:43)
[INFO]       Auto_mut: Residue number 190 from chain A and a score of 0.251 (threonine) selected   
                       for automated muatation                                                     (00:01:43)
[INFO]       Auto_mut: Residue number 94 from chain A and a score of 0.222 (tyrosine) selected for 
                       automated muatation                                                         (00:01:43)
[INFO]       Auto_mut: Residue number 188 from chain A and a score of 0.218 (leucine) selected for 
                       automated muatation                                                         (00:01:43)
[INFO]       Auto_mut: Residue number 146 from chain A and a score of 0.200 (valine) selected for  
                       automated muatation                                                         (00:01:43)
[INFO]       Auto_mut: Residue number 100 from chain A and a score of 0.117 (valine) selected for  
                       automated muatation                                                         (00:01:43)
[INFO]       Auto_mut: Mutating residue number 190 from chain A (threonine) into glutamic acid     (00:01:43)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 11 from chain A (phenylalanine) into glutamic acid  (00:01:43)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 11 from chain A (phenylalanine) into aspartic acid  (00:01:43)
[INFO]       Auto_mut: Mutating residue number 190 from chain A (threonine) into lysine            (00:02:38)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (phenylalanine) into lysine         (00:02:39)
[INFO]       Auto_mut: Mutating residue number 11 from chain A (phenylalanine) into arginine       (00:02:40)
[INFO]       Auto_mut: Mutating residue number 190 from chain A (threonine) into aspartic acid     (00:03:20)
[INFO]       Auto_mut: Mutating residue number 94 from chain A (tyrosine) into glutamic acid       (00:03:28)
[INFO]       Auto_mut: Mutating residue number 94 from chain A (tyrosine) into aspartic acid       (00:03:33)
[INFO]       Auto_mut: Mutating residue number 190 from chain A (threonine) into arginine          (00:03:58)
[INFO]       Auto_mut: Mutating residue number 94 from chain A (tyrosine) into lysine              (00:04:10)
[INFO]       Auto_mut: Mutating residue number 94 from chain A (tyrosine) into arginine            (00:04:13)
[INFO]       Auto_mut: Mutating residue number 188 from chain A (leucine) into glutamic acid       (00:04:40)
[INFO]       Auto_mut: Mutating residue number 188 from chain A (leucine) into aspartic acid       (00:04:55)
[INFO]       Auto_mut: Mutating residue number 146 from chain A (valine) into glutamic acid        (00:04:58)
[INFO]       Auto_mut: Mutating residue number 188 from chain A (leucine) into lysine              (00:05:23)
[INFO]       Auto_mut: Mutating residue number 188 from chain A (leucine) into arginine            (00:05:36)
[INFO]       Auto_mut: Mutating residue number 146 from chain A (valine) into lysine               (00:05:47)
[INFO]       Auto_mut: Mutating residue number 146 from chain A (valine) into aspartic acid        (00:06:22)
[INFO]       Auto_mut: Mutating residue number 100 from chain A (valine) into glutamic acid        (00:06:23)
[INFO]       Auto_mut: Mutating residue number 100 from chain A (valine) into aspartic acid        (00:06:51)
[INFO]       Auto_mut: Mutating residue number 100 from chain A (valine) into lysine               (00:07:04)
[INFO]       Auto_mut: Mutating residue number 146 from chain A (valine) into arginine             (00:07:05)
[INFO]       Auto_mut: Mutating residue number 100 from chain A (valine) into arginine             (00:07:31)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 2.3276 kcal/mol, Difference in average    
                       score from the base case: -0.0375                                           (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (phenylalanine) into      
                       lysine: Energy difference: 1.6143 kcal/mol, Difference in average score     
                       from the base case: -0.0249                                                 (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 2.5104 kcal/mol, Difference in average    
                       score from the base case: -0.0351                                           (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 11 from chain A (phenylalanine) into      
                       arginine: Energy difference: 1.8645 kcal/mol, Difference in average score   
                       from the base case: -0.0295                                                 (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 190 from chain A (threonine) into         
                       glutamic acid: Energy difference: 0.4193 kcal/mol, Difference in average    
                       score from the base case: -0.0157                                           (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 190 from chain A (threonine) into lysine: 
                       Energy difference: -0.6548 kcal/mol, Difference in average score from the   
                       base case: -0.0150                                                          (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 190 from chain A (threonine) into         
                       aspartic acid: Energy difference: 1.8092 kcal/mol, Difference in average    
                       score from the base case: -0.0224                                           (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 190 from chain A (threonine) into         
                       arginine: Energy difference: -0.1524 kcal/mol, Difference in average score  
                       from the base case: -0.0288                                                 (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 1.6980 kcal/mol, Difference in average score from  
                       the base case: -0.0198                                                      (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.4214 kcal/mol, Difference in average score from the    
                       base case: -0.0153                                                          (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 2.6864 kcal/mol, Difference in average score from  
                       the base case: -0.0095                                                      (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.5078 kcal/mol, Difference in average score from the    
                       base case: -0.0259                                                          (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 188 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.8234 kcal/mol, Difference in average score from  
                       the base case: -0.0262                                                      (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 188 from chain A (leucine) into lysine:   
                       Energy difference: 0.1362 kcal/mol, Difference in average score from the    
                       base case: -0.0156                                                          (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 188 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.3310 kcal/mol, Difference in average score from  
                       the base case: -0.0273                                                      (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 188 from chain A (leucine) into arginine: 
                       Energy difference: -0.8740 kcal/mol, Difference in average score from the   
                       base case: -0.0364                                                          (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 146 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.5162 kcal/mol, Difference in average score from  
                       the base case: -0.0271                                                      (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 146 from chain A (valine) into lysine:    
                       Energy difference: -0.2681 kcal/mol, Difference in average score from the   
                       base case: -0.0179                                                          (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 146 from chain A (valine) into aspartic   
                       acid: Energy difference: 1.2183 kcal/mol, Difference in average score from  
                       the base case: -0.0203                                                      (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 146 from chain A (valine) into arginine:  
                       Energy difference: -0.4902 kcal/mol, Difference in average score from the   
                       base case: -0.0119                                                          (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 100 from chain A (valine) into glutamic   
                       acid: Energy difference: 1.5482 kcal/mol, Difference in average score from  
                       the base case: -0.0057                                                      (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 100 from chain A (valine) into lysine:    
                       Energy difference: 0.2460 kcal/mol, Difference in average score from the    
                       base case: -0.0068                                                          (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 100 from chain A (valine) into aspartic   
                       acid: Energy difference: 2.7246 kcal/mol, Difference in average score from  
                       the base case: -0.0029                                                      (00:08:21)
[INFO]       Auto_mut: Effect of mutation residue number 100 from chain A (valine) into arginine:  
                       Energy difference: -2.4223 kcal/mol, Difference in average score from the   
                       base case: -0.0001                                                          (00:08:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:08:28)
Show buried residues
Minimal score value
-3.0105
Maximal score value
0.2845
Average score
-0.7342
Total score value
-151.9834
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 A A -0.6516
2 T A -0.7415
3 F A 0.0000
4 D A -1.1017
5 V A 0.0000
6 V A 0.0000
7 N A 0.0000
8 Q A -1.4175
9 C A 0.0000
10 T A -0.2484
11 F A 0.2845
12 T A -0.5985
13 V A 0.0000
14 W A -0.6846
15 A A 0.0000
16 G A 0.0000
17 A A 0.0000
18 S A -1.0281
19 P A -0.9482
20 G A -1.1316
21 G A -1.1358
22 G A 0.0000
23 K A -1.3027
24 Q A -1.2474
25 L A 0.0000
26 D A -1.8272
27 Q A -1.9833
28 G A -1.6894
29 Q A -1.7343
30 T A -1.1348
31 W A -0.4654
32 T A -0.4972
33 I A 0.0000
34 T A -0.4186
35 V A 0.0000
36 A A -0.3704
37 P A -0.9116
38 G A -1.0198
39 S A -0.8974
40 T A -1.2071
41 K A -1.8168
42 A A 0.0000
43 R A -0.8653
44 I A 0.0000
45 W A 0.0000
46 G A 0.0000
47 R A 0.0000
48 T A -0.8704
49 G A -1.4422
50 C A 0.0000
51 N A -2.3655
52 F A -2.0670
53 D A -2.5365
54 A A -1.4410
55 N A -2.0788
56 G A -2.0484
57 Q A -2.5649
58 G A -2.4373
59 K A -3.0105
60 C A 0.0000
61 Q A -2.1429
62 T A 0.0000
63 G A 0.0000
64 D A -1.2122
65 C A 0.0000
66 N A -1.9760
67 G A 0.0000
68 L A -1.7912
69 L A -1.7092
70 Q A -1.8845
71 C A 0.0000
72 Q A -1.6983
73 G A -0.9807
74 Y A -0.3429
75 G A -0.4379
76 S A -0.5755
77 P A -0.3598
78 P A 0.0000
79 N A 0.0000
80 T A 0.0000
81 L A 0.0000
82 A A 0.0000
83 E A -0.6785
84 F A 0.0000
85 S A -0.7419
86 L A 0.0000
87 N A -1.5732
88 Q A -1.3172
89 P A -1.4307
90 N A -2.0824
91 N A -2.2234
92 L A -1.0407
93 D A 0.0000
94 Y A 0.2224
95 V A 0.0000
96 D A 0.0000
97 I A 0.0000
98 S A 0.0000
99 L A 0.0000
100 V A 0.1172
101 D A -0.2347
102 G A 0.0000
103 F A 0.0000
104 N A 0.0000
105 I A 0.0000
106 P A -0.4327
107 M A 0.0000
108 D A -0.9547
109 F A 0.0000
110 S A -1.3784
111 P A 0.0000
112 A A -0.7145
113 A A -0.0781
114 A A -0.2913
115 G A -0.5118
116 V A 0.0522
117 C A -0.5517
118 K A -1.7842
119 D A -2.4436
120 I A 0.0000
121 R A -1.1567
122 C A 0.0000
123 A A -0.5205
124 T A -0.7455
125 D A -1.3868
126 I A 0.0000
127 T A -1.0764
128 A A -0.9681
129 Q A -1.3272
130 C A 0.0000
131 P A -1.0619
132 A A -1.3337
133 E A -2.0560
134 L A 0.0000
135 Q A -1.9709
136 A A -1.2417
137 P A -1.0635
138 G A -1.1054
139 G A 0.0000
140 C A 0.0000
141 N A -0.6994
142 N A 0.0000
143 P A 0.0000
144 C A -0.3303
145 T A -0.0412
146 V A 0.1998
147 Y A -0.0237
148 K A -1.4544
149 T A -1.3292
150 N A -1.7251
151 E A -2.1813
152 Y A -0.8838
153 C A -0.8933
154 C A 0.0000
155 T A -1.5207
156 N A -1.9778
157 G A -1.5600
158 Q A -1.8289
159 G A -1.3319
160 T A -1.4085
161 C A -1.2856
162 G A -0.7174
163 P A -0.8024
164 T A -0.6136
165 A A -0.2784
166 L A -0.3092
167 S A 0.0000
168 K A -1.7283
169 F A -1.1080
170 F A 0.0000
171 K A -1.7444
172 D A -2.5044
173 R A -1.9831
174 C A 0.0000
175 P A -1.3251
176 D A -1.0126
177 A A 0.0000
178 Y A 0.0000
179 S A 0.0000
180 Y A -0.4356
181 P A -0.4647
182 Q A -0.9796
183 D A 0.0000
184 D A -1.2415
185 P A -0.7600
186 T A -0.5485
187 S A 0.0000
188 L A 0.2177
189 F A 0.1010
190 T A 0.2512
191 C A 0.0000
192 P A -0.6857
193 A A -1.2551
194 G A -1.0561
195 T A 0.0000
196 N A -1.3020
197 Y A 0.0000
198 K A -1.4416
199 V A 0.0000
200 V A -0.5504
201 F A 0.0000
202 C A -0.2416
203 P A 0.0000
204 N A -1.1916
205 L A -0.0169
206 D A -1.4280
207 A A -0.7007
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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
LR188A -0.874 -0.0364 View CSV PDB
TR190A -0.1524 -0.0288 View CSV PDB
TK190A -0.6548 -0.015 View CSV PDB
VK146A -0.2681 -0.0179 View CSV PDB
VR146A -0.4902 -0.0119 View CSV PDB
VR100A -2.4223 -0.0001 View CSV PDB
LK188A 0.1362 -0.0156 View CSV PDB
YR94A 0.5078 -0.0259 View CSV PDB
YK94A 0.4214 -0.0153 View CSV PDB
VK100A 0.246 -0.0068 View CSV PDB
FE11A 2.3276 -0.0375 View CSV PDB
FR11A 1.8645 -0.0295 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018