Project name: 123

Status: done

Started: 2024-06-17 12:34:04
Settings
Chain sequence(s) A: STKYPIVLVHGLAGFNEIVGFPYFYGIADALRQDGHQVFTASLSAFNSNEVRGKQLWQFVQTLLQETQAKKVNFIGHSQGPLACRYVAANYPDSVASVTSINGVNHGSEIADLYRRIMRKDSIPEYIVEKVLNAFGTIISTFSGHDPQDAIAALESLTTEQVTEFNNKYPQALPKTPGGEGDEIVNGVHYYCFGSYIQGLIAGEKGNLLDPTHAAMRVLNTFFTEKQNDGLVGRSSMRLGKLIKDDYAQDHIDMVNQVAGLVGYNEDIVAIYTQHAKYLASKQL
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                                          (00:04:26)
[INFO]       Auto_mut: Residue number 212 from chain A and a score of 2.136 (leucine) selected for 
                       automated muatation                                                         (00:04:28)
[INFO]       Auto_mut: Residue number 211 from chain A and a score of 2.103 (leucine) selected for 
                       automated muatation                                                         (00:04:28)
[INFO]       Auto_mut: Residue number 203 from chain A and a score of 1.725 (leucine) selected for 
                       automated muatation                                                         (00:04:28)
[INFO]       Auto_mut: Residue number 204 from chain A and a score of 1.686 (isoleucine) selected  
                       for automated muatation                                                     (00:04:28)
[INFO]       Auto_mut: Residue number 47 from chain A and a score of 1.306 (phenylalanine)         
                       selected for automated muatation                                            (00:04:28)
[INFO]       Auto_mut: Residue number 205 from chain A and a score of 0.959 (alanine) selected for 
                       automated muatation                                                         (00:04:28)
[INFO]       Auto_mut: Mutating residue number 212 from chain A (leucine) into glutamic acid       (00:04:28)
[INFO]       Auto_mut: Mutating residue number 212 from chain A (leucine) into aspartic acid       (00:04:28)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into glutamic acid       (00:04:28)
[INFO]       Auto_mut: Mutating residue number 212 from chain A (leucine) into arginine            (00:06:43)
[INFO]       Auto_mut: Mutating residue number 212 from chain A (leucine) into lysine              (00:06:45)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into lysine              (00:06:47)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into aspartic acid       (00:09:08)
[INFO]       Auto_mut: Mutating residue number 203 from chain A (leucine) into glutamic acid       (00:09:11)
[INFO]       Auto_mut: Mutating residue number 203 from chain A (leucine) into aspartic acid       (00:09:12)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (leucine) into arginine            (00:11:24)
[INFO]       Auto_mut: Mutating residue number 203 from chain A (leucine) into lysine              (00:11:24)
[INFO]       Auto_mut: Mutating residue number 203 from chain A (leucine) into arginine            (00:11:25)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into glutamic acid    (00:13:35)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into aspartic acid    (00:13:46)
[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  (00:13:49)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into lysine           (00:15:57)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into arginine         (00:16:03)
[INFO]       Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into lysine         (00:16:04)
[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  (00:18:11)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (alanine) into glutamic acid       (00:18:15)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (alanine) into aspartic acid       (00:18:29)
[INFO]       Auto_mut: Mutating residue number 47 from chain A (phenylalanine) into arginine       (00:20:25)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (alanine) into lysine              (00:20:31)
[INFO]       Auto_mut: Mutating residue number 205 from chain A (alanine) into arginine            (00:20:42)
[INFO]       Auto_mut: Effect of mutation residue number 212 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.6714 kcal/mol, Difference in average score from  
                       the base case: -0.0426                                                      (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 212 from chain A (leucine) into lysine:   
                       Energy difference: 0.1146 kcal/mol, Difference in average score from the    
                       base case: -0.0399                                                          (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 212 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.6418 kcal/mol, Difference in average score from  
                       the base case: -0.0423                                                      (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 212 from chain A (leucine) into arginine: 
                       Energy difference: 0.0281 kcal/mol, Difference in average score from the    
                       base case: -0.0455                                                          (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.6537 kcal/mol, Difference in average score from  
                       the base case: -0.0476                                                      (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into lysine:   
                       Energy difference: 0.2847 kcal/mol, Difference in average score from the    
                       base case: -0.0422                                                          (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.1967 kcal/mol, Difference in average score from  
                       the base case: -0.0496                                                      (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (leucine) into arginine: 
                       Energy difference: 0.0327 kcal/mol, Difference in average score from the    
                       base case: -0.0402                                                          (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 203 from chain A (leucine) into glutamic  
                       acid: Energy difference: -0.2490 kcal/mol, Difference in average score from 
                       the base case: -0.0460                                                      (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 203 from chain A (leucine) into lysine:   
                       Energy difference: 0.3433 kcal/mol, Difference in average score from the    
                       base case: -0.0445                                                          (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 203 from chain A (leucine) into aspartic  
                       acid: Energy difference: -0.2716 kcal/mol, Difference in average score from 
                       the base case: -0.0483                                                      (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 203 from chain A (leucine) into arginine: 
                       Energy difference: 0.2821 kcal/mol, Difference in average score from the    
                       base case: -0.0461                                                          (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.6919 kcal/mol, Difference in average    
                       score from the base case: -0.0444                                           (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.4237 kcal/mol, Difference in average score     
                       from the base case: -0.0339                                                 (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.5531 kcal/mol, Difference in average    
                       score from the base case: -0.0445                                           (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.7417 kcal/mol, Difference in average score   
                       from the base case: -0.0394                                                 (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 1.4161 kcal/mol, Difference in average    
                       score from the base case: -0.0604                                           (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into      
                       lysine: Energy difference: 0.7772 kcal/mol, Difference in average score     
                       from the base case: -0.0601                                                 (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 1.3704 kcal/mol, Difference in average    
                       score from the base case: -0.0593                                           (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 47 from chain A (phenylalanine) into      
                       arginine: Energy difference: 0.4582 kcal/mol, Difference in average score   
                       from the base case: -0.0411                                                 (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (alanine) into glutamic  
                       acid: Energy difference: -0.4016 kcal/mol, Difference in average score from 
                       the base case: -0.0312                                                      (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (alanine) into lysine:   
                       Energy difference: -0.4254 kcal/mol, Difference in average score from the   
                       base case: -0.0318                                                          (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (alanine) into aspartic  
                       acid: Energy difference: 0.0215 kcal/mol, Difference in average score from  
                       the base case: -0.0311                                                      (00:23:04)
[INFO]       Auto_mut: Effect of mutation residue number 205 from chain A (alanine) into arginine: 
                       Energy difference: -0.4529 kcal/mol, Difference in average score from the   
                       base case: -0.0325                                                          (00:23:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:13)
Show buried residues
Minimal score value
-3.4798
Maximal score value
2.1362
Average score
-0.6969
Total score value
-197.9263
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
2 S A -1.6461
3 T A -1.8039
4 K A -2.4644
5 Y A -1.6179
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 0.7872
14 A A 0.1144
15 G A -0.4309
16 F A 0.0000
17 N A -1.5526
18 E A -1.6660
19 I A 0.4751
20 V A -0.0045
21 G A -0.6898
22 F A -0.2283
23 P A -0.5601
24 Y A 0.0076
25 F A 0.0000
26 Y A 0.1295
27 G A -0.4699
28 I A 0.0000
29 A A -1.5079
30 D A -2.6410
31 A A -1.8963
32 L A 0.0000
33 R A -3.4599
34 Q A -2.9811
35 D A -2.6132
36 G A -2.0555
37 H A 0.0000
38 Q A -2.0810
39 V A 0.0000
40 F A -0.1073
41 T A 0.1513
42 A A 0.0000
43 S A -0.1290
44 L A 0.0000
45 S A 0.3917
46 A A 0.0000
47 F A 1.3062
48 N A -0.3397
49 S A -0.3667
50 N A 0.0000
51 E A -0.7753
52 V A -0.2369
53 R A 0.0000
54 G A 0.0000
55 K A -2.0188
56 Q A -1.4579
57 L A 0.0000
58 W A -1.1861
59 Q A -1.7929
60 F A -0.7111
61 V A 0.0000
62 Q A -1.8477
63 T A -1.4374
64 L A 0.0000
65 L A -2.1635
66 Q A -2.8670
67 E A -2.8312
68 T A -2.2063
69 Q A -2.5280
70 A A -2.2285
71 K A -2.9152
72 K A -2.0696
73 V A 0.0000
74 N A 0.0000
75 F 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 0.0000
88 V A 0.0000
89 A A 0.0000
90 A A -0.8724
91 N A -0.8658
92 Y A -0.7167
93 P A -1.3805
94 D A -2.4707
95 S A 0.0000
96 V 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 I 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 -0.9239
108 G A 0.0000
109 S A 0.0000
110 E A -0.7641
111 I A 0.0000
112 A A 0.0000
113 D A -1.7625
114 L A -0.9778
115 Y A 0.0000
116 R A -2.8377
117 R A -2.9686
118 I A 0.0000
119 M A -2.0281
120 R A -3.4798
121 K A -3.3818
122 D A -2.8282
123 S A -1.7169
124 I A -1.0502
125 P A -0.8614
126 E A -1.6152
127 Y A -0.2213
128 I A -0.4892
129 V A -1.3877
130 E A -2.5462
131 K A -2.1513
132 V A 0.0000
133 L A -1.7099
134 N A -2.2240
135 A A 0.0000
136 F A 0.0000
137 G A -1.2064
138 T A -0.3153
139 I A 0.1641
140 I A -0.1004
141 S A -0.5215
142 T A -0.0708
143 F A 0.4538
144 S A -0.0791
145 G A -0.5661
146 H A -1.3122
149 D A -2.7230
150 P A -1.8490
151 Q A -2.0853
152 D A -2.5139
153 A A -1.1185
154 I A -0.8739
155 A A -0.4657
156 A A -0.1293
157 L A 0.0000
158 E A -2.1160
159 S A 0.0000
160 L A 0.0000
161 T A 0.0000
162 T A -1.7608
163 E A -2.7728
164 Q A -2.3993
165 V A 0.0000
166 T A -2.3595
167 E A -3.3389
168 F A 0.0000
169 N A -2.2383
170 N A -2.9184
171 K A -2.8507
172 Y A -1.6335
173 P A -1.3541
174 Q A -0.9773
175 A A 0.0000
176 L A -1.3131
177 P A -2.1282
178 K A -2.3776
179 T A -1.4187
180 P A -1.1238
181 G A -1.1696
182 G A -1.5772
183 E A -2.6693
184 G A -2.2566
185 D A -2.3214
186 E A -1.1652
187 I A -0.0980
188 V A -0.5308
189 N A -1.3709
190 G A -1.0616
191 V A 0.0000
192 H A -0.4909
193 Y A 0.0000
194 Y A 0.0000
195 C A 0.0000
196 F A 0.0000
197 G A 0.0000
198 S A 0.0000
199 Y A -0.5729
200 I A -0.2373
201 Q A -0.1768
202 G A 0.4466
203 L A 1.7247
204 I A 1.6857
205 A A 0.9588
206 G A 0.4130
207 E A 0.0000
208 K A -0.6988
209 G A 0.0436
210 N A 0.0000
211 L A 2.1034
212 L A 2.1362
213 D A 0.0000
214 P A 0.6438
215 T A 0.0000
216 H A 0.0000
217 A A 0.5642
218 A A 0.0000
219 M A 0.0000
220 R A 0.1823
221 V A -0.1772
222 L A 0.0000
223 N A -0.5592
224 T A -0.3656
225 F A -0.0983
226 F A 0.0000
227 T A -0.8950
228 E A -1.6435
229 K A -2.2410
230 Q A -1.8139
231 N A 0.0000
232 D A 0.0000
233 G A 0.0000
234 L A 0.0000
235 V A 0.0000
236 G A 0.0000
237 R A -1.0795
238 S A -0.8781
239 S A 0.0000
240 M A 0.0000
241 R A -0.8438
242 L A 0.0000
243 G A 0.0000
244 K A -1.4140
245 L A -0.7528
246 I A -0.1543
247 K A -1.0234
248 D A 0.0000
249 D A -1.2906
250 Y A -0.5695
251 A A -0.2676
252 Q A 0.0000
253 D A 0.0000
254 H A 0.0000
255 I A 0.0000
256 D A 0.0000
257 M A 0.0000
258 V A 0.0000
259 N A -0.1805
260 Q A 0.0000
261 V A 0.5837
262 A A 0.2835
263 G A -0.2394
264 L A 0.5174
265 V A 0.0000
266 G A 0.0000
267 Y A -1.0680
268 N A -2.0591
269 E A -1.8994
270 D A -2.2297
271 I A 0.0000
272 V A -0.6582
273 A A -0.8045
274 I A 0.0000
275 Y A 0.0000
276 T A -1.1896
277 Q A -1.5442
278 H A 0.0000
279 A A 0.0000
280 K A -1.8873
281 Y A -1.0487
282 L A 0.0000
283 A A -1.6804
284 S A -1.4329
285 K A -1.8232
286 Q A -2.1547
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
LD203A -0.2716 -0.0483 View CSV PDB
LE203A -0.249 -0.046 View CSV PDB
AR205A -0.4529 -0.0325 View CSV PDB
AK205A -0.4254 -0.0318 View CSV PDB
LR212A 0.0281 -0.0455 View CSV PDB
LR211A 0.0327 -0.0402 View CSV PDB
LK212A 0.1146 -0.0399 View CSV PDB
LK211A 0.2847 -0.0422 View CSV PDB
FR47A 0.4582 -0.0411 View CSV PDB
IK204A 0.4237 -0.0339 View CSV PDB
FK47A 0.7772 -0.0601 View CSV PDB
IE204A 0.6919 -0.0444 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018