Project name: salmonella_wo_donor

Status: done

Started: 2026-03-07 00:20:21
Settings
Chain sequence(s) A: TVCRNSNGTATDIFYDLSDVFTSGNNQPGQVVTLPEKSGWVGVNATCPAGTTVNYTYRSYVSELPVQSTEGNFKYLKLNDYLLGAMSITDSVAGVFYPPRNYILMGVDYNVSQQKPFGVQDSKLVFKLKVIRPFINMVTIPRQTMFTVYVTTSTGDALSTPVYTISYSGKVEVPQNCEVNAGQVVEFDFGDIGASLFSQAGAGNRPQGVTPQTKTIAIKCTNAAAQAYLSMRLEAEKASGQAMVSDNPDLGFVVANSNGTPLTPNNLSSKIPFHLDDNAAARVGIRAWPISVTGIKPAEGPFTARGYLRVDYD
input PDB
Selected Chain(s) A
Distance of aggregation 5 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                                          (00:03:42)
[INFO]       Auto_mut: Residue number 95 from chain A and a score of 1.739 (valine) selected for   
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 92 from chain A and a score of 1.739 (valine) selected for   
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 107 from chain A and a score of 1.719 (valine) selected for  
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 295 from chain A and a score of 1.690 (isoleucine) selected  
                       for automated muatation                                                     (00:03:45)
[INFO]       Auto_mut: Residue number 184 from chain A and a score of 1.633 (valine) selected for  
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Residue number 104 from chain A and a score of 1.338 (leucine) selected for 
                       automated muatation                                                         (00:03:45)
[INFO]       Auto_mut: Mutating residue number 95 from chain A (valine) into glutamic acid         (00:03:45)
[INFO]       Auto_mut: Mutating residue number 95 from chain A (valine) into aspartic acid         (00:03:45)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (valine) into glutamic acid         (00:03:45)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (valine) into lysine                (00:06:08)
[INFO]       Auto_mut: Mutating residue number 95 from chain A (valine) into lysine                (00:06:14)
[INFO]       Auto_mut: Mutating residue number 95 from chain A (valine) into arginine              (00:06:30)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (valine) into aspartic acid         (00:09:10)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (valine) into glutamic acid        (00:09:27)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (valine) into aspartic acid        (00:09:41)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (valine) into arginine              (00:11:36)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (valine) into lysine               (00:11:41)
[INFO]       Auto_mut: Mutating residue number 107 from chain A (valine) into arginine             (00:12:03)
[INFO]       Auto_mut: Mutating residue number 295 from chain A (isoleucine) into glutamic acid    (00:13:50)
[INFO]       Auto_mut: Mutating residue number 295 from chain A (isoleucine) into aspartic acid    (00:14:06)
[INFO]       Auto_mut: Mutating residue number 184 from chain A (valine) into glutamic acid        (00:14:21)
[INFO]       Auto_mut: Mutating residue number 295 from chain A (isoleucine) into lysine           (00:16:03)
[INFO]       Auto_mut: Mutating residue number 295 from chain A (isoleucine) into arginine         (00:16:13)
[INFO]       Auto_mut: Mutating residue number 184 from chain A (valine) into lysine               (00:16:44)
[INFO]       Auto_mut: Mutating residue number 184 from chain A (valine) into aspartic acid        (00:18:25)
[INFO]       Auto_mut: Mutating residue number 104 from chain A (leucine) into glutamic acid       (00:18:26)
[INFO]       Auto_mut: Mutating residue number 104 from chain A (leucine) into aspartic acid       (00:19:13)
[INFO]       Auto_mut: Mutating residue number 184 from chain A (valine) into arginine             (00:20:31)
[INFO]       Auto_mut: Mutating residue number 104 from chain A (leucine) into lysine              (00:20:34)
[INFO]       Auto_mut: Mutating residue number 104 from chain A (leucine) into arginine            (00:21:15)
[INFO]       Auto_mut: Effect of mutation residue number 95 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.6220 kcal/mol, Difference in average score from 
                       the base case: -0.0142                                                      (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 95 from chain A (valine) into lysine:     
                       Energy difference: -0.8236 kcal/mol, Difference in average score from the   
                       base case: -0.0140                                                          (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 95 from chain A (valine) into aspartic    
                       acid: Energy difference: -0.0973 kcal/mol, Difference in average score from 
                       the base case: -0.0141                                                      (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 95 from chain A (valine) into arginine:   
                       Energy difference: -1.3287 kcal/mol, Difference in average score from the   
                       base case: -0.0141                                                          (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.1066 kcal/mol, Difference in average score from  
                       the base case: -0.0146                                                      (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (valine) into lysine:     
                       Energy difference: -0.4516 kcal/mol, Difference in average score from the   
                       base case: -0.0132                                                          (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (valine) into aspartic    
                       acid: Energy difference: 1.1619 kcal/mol, Difference in average score from  
                       the base case: -0.0143                                                      (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (valine) into arginine:   
                       Energy difference: -0.5029 kcal/mol, Difference in average score from the   
                       base case: -0.0139                                                          (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.2135 kcal/mol, Difference in average score from  
                       the base case: -0.0158                                                      (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (valine) into lysine:    
                       Energy difference: -0.0313 kcal/mol, Difference in average score from the   
                       base case: -0.0156                                                          (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.7236 kcal/mol, Difference in average score from  
                       the base case: -0.0155                                                      (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain A (valine) into arginine:  
                       Energy difference: 0.0972 kcal/mol, Difference in average score from the    
                       base case: -0.0162                                                          (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 295 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.6508 kcal/mol, Difference in average   
                       score from the base case: -0.0141                                           (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 295 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.8672 kcal/mol, Difference in average score    
                       from the base case: -0.0132                                                 (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 295 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.5046 kcal/mol, Difference in average   
                       score from the base case: -0.0155                                           (00:23:22)
[INFO]       Auto_mut: Effect of mutation residue number 295 from chain A (isoleucine) into        
                       arginine: Energy difference: -3.4423 kcal/mol, Difference in average score  
                       from the base case: -0.0146                                                 (00:23:23)
[INFO]       Auto_mut: Effect of mutation residue number 184 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.4386 kcal/mol, Difference in average score from 
                       the base case: -0.0145                                                      (00:23:23)
[INFO]       Auto_mut: Effect of mutation residue number 184 from chain A (valine) into lysine:    
                       Energy difference: -0.4242 kcal/mol, Difference in average score from the   
                       base case: -0.0142                                                          (00:23:23)
[INFO]       Auto_mut: Effect of mutation residue number 184 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.3595 kcal/mol, Difference in average score from  
                       the base case: -0.0144                                                      (00:23:23)
[INFO]       Auto_mut: Effect of mutation residue number 184 from chain A (valine) into arginine:  
                       Energy difference: -0.5733 kcal/mol, Difference in average score from the   
                       base case: -0.0146                                                          (00:23:23)
[INFO]       Auto_mut: Effect of mutation residue number 104 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.2507 kcal/mol, Difference in average score from  
                       the base case: -0.0102                                                      (00:23:23)
[INFO]       Auto_mut: Effect of mutation residue number 104 from chain A (leucine) into lysine:   
                       Energy difference: 0.1037 kcal/mol, Difference in average score from the    
                       base case: -0.0102                                                          (00:23:23)
[INFO]       Auto_mut: Effect of mutation residue number 104 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.6814 kcal/mol, Difference in average score from  
                       the base case: -0.0091                                                      (00:23:23)
[INFO]       Auto_mut: Effect of mutation residue number 104 from chain A (leucine) into arginine: 
                       Energy difference: -0.5550 kcal/mol, Difference in average score from the   
                       base case: -0.0088                                                          (00:23:23)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:31)
Show buried residues
Minimal score value
-2.1659
Maximal score value
1.7391
Average score
-0.2766
Total score value
-86.5679
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 T A 0.0560
2 V A 0.4388
3 C A 0.0000
4 R A -1.8441
5 N A 0.0000
6 S A -0.3173
7 N A -1.3337
8 G A -0.4903
9 T A -0.1133
10 A A -0.0036
11 T A -0.3428
12 D A -1.7554
13 I A 0.0862
14 F A 1.0894
15 Y A 0.0000
16 D A -1.7894
17 L A 0.0000
18 S A -0.5205
19 D A -1.7520
20 V A -0.0355
21 F A 0.0000
22 T A -0.0920
23 S A -0.2458
24 G A -0.5259
25 N A -0.2646
26 N A 0.0000
27 Q A -1.2438
28 P A -0.4512
29 G A -0.5764
30 Q A -0.5406
31 V A 0.4510
32 V A 0.3093
33 T A -0.0572
34 L A 0.0000
35 P A -0.5876
36 E A -2.0309
37 K A -1.2684
38 S A -0.5843
39 G A -0.2857
40 W A 1.1361
41 V A 0.3256
42 G A -0.4313
43 V A 0.0000
44 N A -0.7039
45 A A 0.0000
46 T A -0.0388
47 C A 0.0000
48 P A -0.1154
49 A A -0.0488
50 G A -0.4558
51 T A 0.0000
52 T A 0.0061
53 V A 0.3525
54 N A -0.1778
55 Y A 0.7291
56 T A 0.0000
57 Y A 0.3659
58 R A 0.0000
59 S A 0.0000
60 Y A 0.0000
61 V A 0.6149
62 S A -0.2576
63 E A -1.7948
64 L A -0.1945
65 P A -0.0192
66 V A 0.8019
67 Q A -0.9701
68 S A -0.2782
69 T A -0.2851
70 E A -0.9262
71 G A -0.8430
72 N A -1.3155
73 F A -0.0765
74 K A -0.3805
75 Y A 0.0000
76 L A 0.0000
77 K A -0.8370
78 L A 0.0000
79 N A -0.6653
80 D A -1.8512
81 Y A 0.0000
82 L A 0.0000
83 L A 0.0000
84 G A 0.0000
85 A A 0.0000
86 M A 0.0000
87 S A 0.0000
88 I A 0.0000
89 T A 0.2292
90 D A 0.0000
91 S A 0.1030
92 V A 1.7386
93 A A 0.3077
94 G A 0.1481
95 V A 1.7391
96 F A 0.0000
97 Y A 0.2548
98 P A 0.0000
99 P A -0.3324
100 R A -1.6977
101 N A -0.8062
102 Y A 0.1963
103 I A 0.0000
104 L A 1.3382
105 M A 0.0000
106 G A 0.2151
107 V A 1.7191
108 D A -0.0198
109 Y A 1.1316
110 N A -0.4931
111 V A 0.0000
112 S A -0.2970
113 Q A -1.4342
114 Q A -1.4599
115 K A -1.7689
116 P A -0.5269
117 F A 0.0000
118 G A -0.4036
119 V A 0.0000
120 Q A -0.7696
121 D A 0.0000
122 S A 0.0000
123 K A -0.9621
124 L A 0.0000
125 V A 0.2373
126 F A 0.0000
127 K A -0.2546
128 L A 0.0000
129 K A -0.1424
130 V A 0.0000
131 I A 0.8578
132 R A -0.1214
133 P A -0.0861
134 F A 0.0000
135 I A 0.0000
136 N A -0.5540
137 M A -0.0054
138 V A 0.0000
139 T A -0.1833
140 I A 0.0000
141 P A -0.5923
142 R A -1.9789
143 Q A -0.7990
144 T A -0.1091
145 M A 0.0000
146 F A 0.0000
147 T A -0.0130
148 V A 0.0000
149 Y A 0.1326
150 V A 0.0000
151 T A 0.0000
152 T A 0.0000
153 S A -0.0941
154 T A -0.1695
155 G A -0.5263
156 D A -0.3342
157 A A 0.0710
158 L A 0.3049
159 S A -0.1559
160 T A -0.0708
161 P A -0.0738
162 V A 0.0000
163 Y A 0.0000
164 T A -0.2093
165 I A 0.0000
166 S A 0.0000
167 Y A 0.0000
168 S A -0.3010
169 G A -0.2605
170 K A -1.0167
171 V A 0.0000
172 E A -1.4901
173 V A 0.0000
174 P A -0.1471
175 Q A -0.3801
176 N A -0.6344
177 C A -0.3226
178 E A -1.5452
179 V A -0.0687
180 N A -0.1168
181 A A -0.0574
182 G A -0.6707
183 Q A -0.9585
184 V A 1.6327
185 V A 0.4197
186 E A -1.6739
187 F A -0.2931
188 D A -1.6689
189 F A -0.1124
190 G A -0.7402
191 D A -1.8173
192 I A -0.0933
193 G A -0.4068
194 A A -0.1128
195 S A -0.1320
196 L A 0.2830
197 F A 0.0000
198 S A -0.4941
199 Q A -1.1651
200 A A -0.2272
201 G A -0.1116
202 A A -0.0244
203 G A -0.3939
204 N A -1.1801
205 R A -1.1721
206 P A 0.0000
207 Q A -1.2830
208 G A -0.6480
209 V A 0.1033
210 T A -0.0441
211 P A -0.1309
212 Q A -0.4515
213 T A -0.3941
214 K A -0.9006
215 T A -0.2457
216 I A 0.0000
217 A A -0.1992
218 I A 0.0000
219 K A -1.6985
220 C A 0.0000
221 T A -0.2853
222 N A -1.2945
223 A A -0.2114
224 A A 0.0679
225 A A -0.1600
226 Q A -1.1891
227 A A 0.0310
228 Y A 1.1958
229 L A 0.0000
230 S A 0.0000
231 M A 0.0000
232 R A 0.0000
233 L A 0.0000
234 E A -0.7539
235 A A 0.0000
236 E A -2.1133
237 K A -1.9458
238 A A -0.2928
239 S A -0.2174
240 G A -0.5803
241 Q A -0.5791
242 A A 0.0000
243 M A 0.0000
244 V A 0.0000
245 S A 0.0000
246 D A -1.8213
247 N A -0.5453
248 P A -0.3413
249 D A -0.3244
250 L A 0.0000
251 G A 0.0000
252 F A 0.2098
253 V A 0.0000
254 V A 0.0000
255 A A 0.0000
256 N A -0.3029
257 S A -0.4971
258 N A -1.3433
259 G A -0.4222
260 T A -0.1253
261 P A -0.1375
262 L A 0.0000
263 T A -0.0939
264 P A 0.0000
265 N A -1.4438
266 N A -0.7273
267 L A 0.2754
268 S A -0.1431
269 S A -0.2108
270 K A -0.7544
271 I A 0.0142
272 P A -0.1829
273 F A -0.0323
274 H A -0.7940
275 L A 0.0000
276 D A -1.1460
277 D A -2.1659
278 N A -1.5941
279 A A -0.2134
280 A A -0.2096
281 A A -0.3268
282 R A -1.8393
283 V A 0.0000
284 G A -0.1299
285 I A 0.0000
286 R A -0.7336
287 A A 0.0000
288 W A 0.1147
289 P A 0.0000
290 I A 0.0000
291 S A 0.0000
292 V A 0.2345
293 T A 0.0020
294 G A 0.2346
295 I A 1.6903
296 K A -1.3063
297 P A 0.0000
298 A A -0.2717
299 E A -1.8943
300 G A -0.8444
301 P A -0.2852
302 F A 0.2399
303 T A -0.0130
304 A A -0.3311
305 R A -1.9272
306 G A -0.5656
307 Y A 1.2606
308 L A 0.4093
309 R A 0.0000
310 V A 0.0000
311 D A 0.0000
312 Y A -0.1112
313 D A -1.7510
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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
IR295A -3.4423 -0.0146 View CSV PDB
VR95A -1.3287 -0.0141 View CSV PDB
VK95A -0.8236 -0.014 View CSV PDB
IK295A -0.8672 -0.0132 View CSV PDB
VR184A -0.5733 -0.0146 View CSV PDB
VR92A -0.5029 -0.0139 View CSV PDB
VE184A -0.4386 -0.0145 View CSV PDB
VK92A -0.4516 -0.0132 View CSV PDB
LR104A -0.555 -0.0088 View CSV PDB
VK107A -0.0313 -0.0156 View CSV PDB
VR107A 0.0972 -0.0162 View CSV PDB
LK104A 0.1037 -0.0102 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018