Project name: 123

Status: done

Started: 2024-07-04 11:53:14
Settings
Chain sequence(s) A: MSTTYPIVLVHGLSGFGDIVGYPYFYGIADALEKDGHKVFTASLSAFNSNEVRGEQLWEFVQKVLKETKAKEVNLIGHSQGPLACRYVAAKHAKSIASVTSVNGVNHGSEIADLVRRIMRKDSVPEYIADAVMKAIGTIISTFSGNRGNPQDAVAALEALTTENVTEFNKKYPQGLPAVRGGEGKEIVNGVHYYSFGSYIQGLIAGEKGNLLDPTHAAMRILSAFFSERENDGLVGRTSMRLGKLIKDDYAEDHLDMVNQVAGLVGRGEDIIAIYTNHANFLASKKL
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                                          (00:05:05)
[INFO]       Auto_mut: Residue number 204 from chain A and a score of 1.923 (isoleucine) selected  
                       for automated muatation                                                     (00:05:07)
[INFO]       Auto_mut: Residue number 212 from chain A and a score of 1.914 (leucine) selected for 
                       automated muatation                                                         (00:05:07)
[INFO]       Auto_mut: Residue number 47 from chain A and a score of 1.508 (phenylalanine)         
                       selected for automated muatation                                            (00:05:07)
[INFO]       Auto_mut: Residue number 211 from chain A and a score of 1.446 (leucine) selected for 
                       automated muatation                                                         (00:05:07)
[INFO]       Auto_mut: Residue number 203 from chain A and a score of 1.349 (leucine) selected for 
                       automated muatation                                                         (00:05:07)
[INFO]       Auto_mut: Residue number 19 from chain A and a score of 0.942 (isoleucine) selected   
                       for automated muatation                                                     (00:05:07)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into glutamic acid    (00:05:07)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into aspartic acid    (00:05:07)
[INFO]       Auto_mut: Mutating residue number 212 from chain A (leucine) into glutamic acid       (00:05:07)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into lysine           (00:07:15)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into arginine         (00:07:20)
[INFO]       Auto_mut: Mutating residue number 212 from chain A (leucine) into lysine              (00:07:23)
[INFO]       Auto_mut: Mutating residue number 212 from chain A (leucine) into aspartic acid       (00:09:29)
[INFO]       Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 47 from chain A (phenylalanine) into glutamic acid  (00:09:36)
[INFO]       Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 47 from chain A (phenylalanine) into aspartic acid  (00:09:44)
[INFO]       Auto_mut: Mutating residue number 212 from chain A (leucine) into arginine            (00:11:44)
[INFO]       Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into arginine       (00:11:59)
[INFO]       Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into lysine         (00:11:59)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into glutamic acid       (00:14:09)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into aspartic acid       (00:14:20)
[INFO]       Auto_mut: Mutating residue number 203 from chain A (leucine) into glutamic acid       (00:14:22)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into lysine              (00:16:22)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into arginine            (00:16:33)
[INFO]       Auto_mut: Mutating residue number 203 from chain A (leucine) into lysine              (00:16:48)
[INFO]       Auto_mut: Mutating residue number 203 from chain A (leucine) into aspartic acid       (00:18:50)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into glutamic acid     (00:18:55)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into aspartic acid     (00:19:13)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into lysine            (00:21:10)
[INFO]       Auto_mut: Mutating residue number 203 from chain A (leucine) into arginine            (00:21:12)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (isoleucine) into arginine          (00:21:26)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.4929 kcal/mol, Difference in average   
                       score from the base case: -0.0426                                           (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.1939 kcal/mol, Difference in average score    
                       from the base case: -0.0400                                                 (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.6749 kcal/mol, Difference in average   
                       score from the base case: -0.0405                                           (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.1715 kcal/mol, Difference in average score  
                       from the base case: -0.0165                                                 (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 212 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.5311 kcal/mol, Difference in average score from  
                       the base case: -0.0377                                                      (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 212 from chain A (leucine) into lysine:   
                       Energy difference: 0.1022 kcal/mol, Difference in average score from the    
                       base case: -0.0363                                                          (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 212 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.0088 kcal/mol, Difference in average score from  
                       the base case: -0.0360                                                      (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 212 from chain A (leucine) into arginine: 
                       Energy difference: 0.1805 kcal/mol, Difference in average score from the    
                       base case: -0.0143                                                          (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: -0.2713 kcal/mol, Difference in average   
                       score from the base case: -0.0649                                           (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into      
                       lysine: Energy difference: -0.0830 kcal/mol, Difference in average score    
                       from the base case: -0.0536                                                 (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 0.2109 kcal/mol, Difference in average    
                       score from the base case: -0.0600                                           (00:23:57)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into      
                       arginine: Energy difference: 0.3944 kcal/mol, Difference in average score   
                       from the base case: -0.0362                                                 (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.1006 kcal/mol, Difference in average score from 
                       the base case: -0.0404                                                      (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into lysine:   
                       Energy difference: -0.0757 kcal/mol, Difference in average score from the   
                       base case: -0.0386                                                          (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.1794 kcal/mol, Difference in average score from  
                       the base case: -0.0395                                                      (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into arginine: 
                       Energy difference: -0.0649 kcal/mol, Difference in average score from the   
                       base case: -0.0341                                                          (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 203 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.5480 kcal/mol, Difference in average score from  
                       the base case: -0.0380                                                      (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 203 from chain A (leucine) into lysine:   
                       Energy difference: -0.4175 kcal/mol, Difference in average score from the   
                       base case: -0.0346                                                          (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 203 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.7190 kcal/mol, Difference in average score from  
                       the base case: -0.0318                                                      (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 203 from chain A (leucine) into arginine: 
                       Energy difference: -0.8960 kcal/mol, Difference in average score from the   
                       base case: -0.0357                                                          (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.2347 kcal/mol, Difference in average    
                       score from the base case: -0.0516                                           (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.4992 kcal/mol, Difference in average score from the   
                       base case: -0.0506                                                          (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.7476 kcal/mol, Difference in average    
                       score from the base case: -0.0527                                           (00:23:58)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.4422 kcal/mol, Difference in average score  
                       from the base case: -0.0522                                                 (00:23:58)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:05)
Show buried residues
Minimal score value
-4.0972
Maximal score value
1.9231
Average score
-0.7321
Total score value
-210.1091
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 0.4823
2 S A -0.6678
3 T A -0.7068
4 T A -0.6303
5 Y A -0.8848
6 P A 0.0000
7 I A 0.0000
8 V A 0.0000
9 L A 0.0000
10 V A 0.0000
11 H A 0.0000
12 G A 0.0000
13 L A 0.7155
14 S A 0.1404
15 G A -0.2914
16 F A 0.0000
17 G A -0.5844
18 D A -1.0847
19 I A 0.9419
20 V A 0.3664
21 G A -0.3093
22 Y A 0.0053
23 P A -0.3452
24 Y A 0.1691
25 F A 0.0000
26 Y A 0.1875
27 G A -0.3617
28 I A 0.0000
29 A A -1.6934
30 D A -2.9274
31 A A -2.1578
32 L A 0.0000
33 E A -4.0972
34 K A -3.8632
35 D A -3.1851
36 G A -2.5416
37 H A 0.0000
38 K A -2.1912
39 V A -1.0676
40 F A 0.0059
41 T A 0.2041
42 A A 0.0000
43 S A -0.0832
44 L A 0.0000
45 S A 0.4611
46 A A 0.9213
47 F A 1.5081
48 N A 0.2397
49 S A -0.2733
50 N A 0.0000
51 E A -0.7583
52 V A -0.1741
53 R A 0.0000
54 G A 0.0000
55 E A -1.9095
56 Q A -1.5624
57 L A 0.0000
58 W A -1.7435
59 E A -2.7064
60 F A -1.4787
61 V A 0.0000
62 Q A -2.7789
63 K A -3.2173
64 V A 0.0000
65 L A -3.0656
66 K A -4.0275
67 E A -3.7505
68 T A -2.8846
69 K A -3.2852
70 A A -2.2541
71 K A -3.1478
72 E A -1.8216
73 V A 0.0000
74 N A 0.0000
75 L A 0.0000
76 I A 0.0000
77 G A 0.0000
78 H A 0.0000
79 S A 0.0000
80 Q A 0.0000
81 G A 0.0000
82 P A 0.0000
83 L A 0.0000
84 A A 0.0000
85 C A 0.0000
86 R A 0.0000
87 Y A -0.6187
88 V A 0.0000
89 A A 0.0000
90 A A -1.1306
91 K A -1.3232
92 H A -1.4904
93 A A -1.7313
94 K A -2.5984
95 S A 0.0000
96 I A 0.0000
97 A A 0.0000
98 S A 0.0000
99 V A 0.0000
100 T A 0.0000
101 S A 0.0000
102 V A 0.0000
103 N A 0.0000
104 G A 0.0000
105 V A 0.0000
106 N A 0.0000
107 H A -0.7481
108 G A 0.0000
109 S A 0.0000
110 E A -0.5662
111 I A 0.0000
112 A A 0.0000
113 D A -1.1662
114 L A -0.6955
115 V A 0.0000
116 R A -1.9049
117 R A -2.7363
118 I A 0.0000
119 M A -2.1053
120 R A -3.5987
121 K A -3.7192
122 D A -3.5131
123 S A -2.0190
124 V A -0.9943
125 P A -0.8325
126 E A -1.5375
127 Y A -0.0125
128 I A -0.1691
129 A A -1.3464
130 D A -2.0989
131 A A -0.9230
132 V A 0.0000
133 M A -1.2361
134 K A -1.9480
135 A A 0.0000
136 I A -0.5026
137 G A 0.0000
138 T A -0.6547
139 I A 0.0208
140 I A -0.4606
141 S A -1.0241
142 T A -0.2264
143 F A 0.2692
144 S A -0.2429
145 G A -1.0731
146 N A -2.3781
147 R A -2.9329
148 G A -2.5124
149 N A -2.5796
150 P A -2.0410
151 Q A -2.2314
152 D A -2.4977
153 A A -0.9077
154 V A -0.4312
155 A A -0.0152
156 A A 0.1984
157 L A -0.3237
158 E A -1.2798
159 A A 0.0000
160 L A 0.0000
161 T A 0.0000
162 T A -1.7007
163 E A -2.7088
164 N A -2.1666
165 V A 0.0000
166 T A -2.4548
167 E A -3.4025
168 F A 0.0000
169 N A -2.4218
170 K A -3.2636
171 K A -3.0208
172 Y A -1.7022
173 P A -1.4056
174 Q A -1.0145
175 G A 0.0000
176 L A -0.8138
177 P A -1.0389
178 A A -0.0975
179 V A 0.5169
180 R A -1.2882
181 G A -1.0494
182 G A -0.9819
183 E A -2.2566
184 G A -1.6065
185 K A -2.0198
186 E A -1.0939
187 I A 0.0860
188 V A 0.0000
189 N A -1.5218
190 G A -1.0343
191 V A 0.0000
192 H A -0.4065
193 Y A 0.0000
194 Y A 0.0000
195 S A 0.0000
196 F A 0.0000
197 G A 0.0000
198 S A 0.0000
199 Y A -0.5900
200 I A -0.6433
201 Q A -0.4661
202 G A 0.2548
203 L A 1.3485
204 I A 1.9231
205 A A 0.1863
206 G A -1.2806
207 E A -1.8904
208 K A -2.4181
209 G A -0.7918
210 N A 0.0000
211 L A 1.4464
212 L A 1.9140
213 D A 0.0000
214 P A 0.6334
215 T A 0.0000
216 H A 0.0000
217 A A 0.0768
218 A A 0.0000
219 M A 0.0000
220 R A -1.1726
221 I A -0.1926
222 L A 0.0000
223 S A -0.7207
224 A A -0.3677
225 F A 0.0174
226 F A 0.0000
227 S A -0.9544
228 E A -1.5758
229 R A -2.3920
230 E A -1.9677
231 N A 0.0000
232 D A 0.0000
233 G A 0.0000
234 L A -0.0168
235 V A 0.0000
236 G A 0.0000
237 R A -1.0255
238 T A -1.0501
239 S A 0.0000
240 M A 0.0000
241 R A -1.0698
242 L A 0.0000
243 G A 0.0000
244 K A -1.7501
245 L A -0.8872
246 I A -0.0981
247 K A -0.9518
248 D A 0.0000
249 D A -1.1501
250 Y A -0.5274
251 A A -0.5456
252 E A 0.0000
253 D A 0.0000
254 H A 0.0000
255 L A 0.2409
256 D A 0.0000
257 M A 0.0000
258 V A 0.0000
259 N A -0.1204
260 Q A 0.0000
261 V A 0.5710
262 A A 0.2528
263 G A -0.1915
264 L A 0.0052
265 V A 0.0000
266 G A 0.0000
267 R A -3.2930
268 G A -3.0104
269 E A -3.0502
270 D A -2.2353
271 I A 0.0000
272 I A -0.2296
273 A A -0.5137
274 I A -0.4755
275 Y A 0.0000
276 T A -1.0010
277 N A -1.1993
278 H A 0.0000
279 A A 0.0000
280 N A -0.7763
281 F A -0.4063
282 L A 0.0000
283 A A -0.8029
284 S A -0.8592
285 K A -1.6823
286 K A -2.0135
287 L A 0.0000
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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
IK19A -0.4992 -0.0506 View CSV PDB
FE47A -0.2713 -0.0649 View CSV PDB
LR203A -0.896 -0.0357 View CSV PDB
IR19A -0.4422 -0.0522 View CSV PDB
ID204A -0.6749 -0.0405 View CSV PDB
IE204A -0.4929 -0.0426 View CSV PDB
LK203A -0.4175 -0.0346 View CSV PDB
FK47A -0.083 -0.0536 View CSV PDB
LE211A -0.1006 -0.0404 View CSV PDB
LK211A -0.0757 -0.0386 View CSV PDB
LK212A 0.1022 -0.0363 View CSV PDB
LR212A 0.1805 -0.0143 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018