Project name: ag1

Status: done

Started: 2025-02-06 02:08:10
Settings
Chain sequence(s) A: SRPGLPVEYLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDYNGWDINTPAFEWYYQSGLSIVMPVGGQSSFYSDWYSPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGMGPSLIGLAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANIPAEFLENFVRSSNLKFQDAYNAAGGHNAVFNFPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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                                          (00:01:54)
[INFO]       Auto_mut: Residue number 228 from chain A and a score of 2.183 (phenylalanine)        
                       selected for automated muatation                                            (00:01:56)
[INFO]       Auto_mut: Residue number 224 from chain A and a score of 1.888 (isoleucine) selected  
                       for automated muatation                                                     (00:01:56)
[INFO]       Auto_mut: Residue number 229 from chain A and a score of 1.690 (leucine) selected for 
                       automated muatation                                                         (00:01:56)
[INFO]       Auto_mut: Residue number 53 from chain A and a score of 1.241 (isoleucine) selected   
                       for automated muatation                                                     (00:01:56)
[INFO]       Auto_mut: Residue number 225 from chain A and a score of 1.000 (proline) selected for 
                       automated muatation                                                         (00:01:56)
[INFO]       Auto_mut: Residue number 232 from chain A and a score of 0.997 (phenylalanine)        
                       selected for automated muatation                                            (00:01:56)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into glutamic acid    (00:01:56)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 228 from chain A (phenylalanine) into aspartic acid (00:01:56)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 228 from chain A (phenylalanine) into glutamic acid (00:01:56)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into arginine      (00:02:51)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into lysine           (00:02:52)
[INFO]       Auto_mut: Mutating residue number 228 from chain A (phenylalanine) into lysine        (00:02:53)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into aspartic acid    (00:03:51)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into glutamic acid       (00:03:57)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into aspartic acid       (00:04:08)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (isoleucine) into arginine         (00:04:47)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into lysine              (00:04:57)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into arginine            (00:05:05)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into glutamic acid     (00:05:51)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into aspartic acid     (00:06:06)
[INFO]       Auto_mut: Mutating residue number 225 from chain A (proline) into glutamic acid       (00:06:13)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into lysine            (00:06:54)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into arginine          (00:07:03)
[INFO]       Auto_mut: Mutating residue number 225 from chain A (proline) into lysine              (00:07:10)
[INFO]       Auto_mut: Mutating residue number 225 from chain A (proline) into aspartic acid       (00:08:10)
[INFO]       Auto_mut: Mutating residue number 232 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 232 from chain A (phenylalanine) into glutamic acid (00:08:28)
[INFO]       Auto_mut: Mutating residue number 232 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 232 from chain A (phenylalanine) into aspartic acid (00:08:34)
[INFO]       Auto_mut: Mutating residue number 225 from chain A (proline) into arginine            (00:09:05)
[INFO]       Auto_mut: Mutating residue number 232 from chain A (phenylalanine) into arginine      (00:09:33)
[INFO]       Auto_mut: Mutating residue number 232 from chain A (phenylalanine) into lysine        (00:09:36)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.4278 kcal/mol, Difference in average    
                       score from the base case: -0.0543                                           (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.1895 kcal/mol, Difference in average score    
                       from the base case: -0.0532                                                 (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.7699 kcal/mol, Difference in average    
                       score from the base case: -0.0515                                           (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 228 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.0519 kcal/mol, Difference in average score   
                       from the base case: -0.0527                                                 (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.9673 kcal/mol, Difference in average   
                       score from the base case: -0.0450                                           (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.2969 kcal/mol, Difference in average score    
                       from the base case: -0.0461                                                 (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.5469 kcal/mol, Difference in average    
                       score from the base case: -0.0464                                           (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.2106 kcal/mol, Difference in average score  
                       from the base case: -0.0477                                                 (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.5066 kcal/mol, Difference in average score from  
                       the base case: -0.0269                                                      (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into lysine:   
                       Energy difference: 0.4564 kcal/mol, Difference in average score from the    
                       base case: -0.0250                                                          (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.9426 kcal/mol, Difference in average score from  
                       the base case: -0.0262                                                      (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into arginine: 
                       Energy difference: 0.2089 kcal/mol, Difference in average score from the    
                       base case: -0.0315                                                          (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.7951 kcal/mol, Difference in average    
                       score from the base case: -0.0294                                           (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.0649 kcal/mol, Difference in average score from the   
                       base case: -0.0292                                                          (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.8929 kcal/mol, Difference in average    
                       score from the base case: -0.0340                                           (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       arginine: Energy difference: -1.3997 kcal/mol, Difference in average score  
                       from the base case: -0.0184                                                 (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 225 from chain A (proline) into glutamic  
                       acid: Energy difference: 0.9099 kcal/mol, Difference in average score from  
                       the base case: -0.0174                                                      (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 225 from chain A (proline) into lysine:   
                       Energy difference: 1.4416 kcal/mol, Difference in average score from the    
                       base case: -0.0252                                                          (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 225 from chain A (proline) into aspartic  
                       acid: Energy difference: 1.6984 kcal/mol, Difference in average score from  
                       the base case: -0.0187                                                      (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 225 from chain A (proline) into arginine: 
                       Energy difference: 1.3827 kcal/mol, Difference in average score from the    
                       base case: -0.0266                                                          (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 232 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.2353 kcal/mol, Difference in average    
                       score from the base case: -0.0269                                           (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 232 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.7500 kcal/mol, Difference in average score     
                       from the base case: -0.0272                                                 (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 232 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.5495 kcal/mol, Difference in average    
                       score from the base case: -0.0283                                           (00:11:07)
[INFO]       Auto_mut: Effect of mutation residue number 232 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.3777 kcal/mol, Difference in average score   
                       from the base case: -0.0375                                                 (00:11:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:13)
Show buried residues
Minimal score value
-2.886
Maximal score value
2.1833
Average score
-0.4576
Total score value
-129.9651
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 -1.1514
3 R A -1.7566
4 P A -1.1643
5 G A -0.9121
6 L A -0.4419
7 P A -0.0044
8 V A 0.3192
9 E A -0.0027
10 Y A 0.3036
11 L A 0.0000
12 Q A -1.5639
13 V A 0.0000
14 P A -1.4527
15 S A 0.0000
16 P A -0.9222
17 S A -0.7029
18 M A 0.0000
19 G A -1.2819
20 R A -1.7775
21 D A -2.2535
22 I A 0.0000
23 K A -1.3614
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.8102
29 G A -1.0856
30 G A -1.5887
31 N A -2.3131
32 N A -2.3291
33 S A 0.0000
34 P A 0.0000
35 A A 0.0000
36 V A 0.0000
37 Y A 0.0000
38 L A 0.0000
39 L A 0.0000
40 D A 0.0000
41 G A 0.0000
42 L A -1.0888
43 R A -2.5348
44 A A 0.0000
45 Q A -2.4901
46 D A -2.8860
47 D A -1.8438
48 Y A 0.0095
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 D A 0.3737
53 I A 1.2411
54 N A -0.3020
55 T A 0.0000
56 P A -0.7017
57 A A 0.0000
58 F A 0.0000
59 E A -1.1471
60 W A -0.6495
61 Y A 0.0000
62 Y A -0.1788
63 Q A -1.1411
64 S A 0.0000
65 G A -1.0137
66 L A 0.0000
67 S A 0.0000
68 I A 0.0000
69 V A 0.0000
70 M A 0.0000
71 P A 0.0000
72 V A 0.0000
73 G A 0.0000
74 G A 0.0000
75 Q A -1.4310
76 S A 0.0000
77 S A 0.0000
78 F A 0.0000
79 Y A 0.0000
80 S A 0.0000
81 D A -0.6656
82 W A 0.0000
83 Y A 0.9322
84 S A 0.0086
85 P A -0.2799
86 A A 0.0000
87 C A -0.4257
88 G A -1.1437
89 K A -1.8650
90 A A -0.7904
91 G A -0.4416
92 C A 0.1934
93 Q A -0.3531
94 T A -0.4085
95 Y A 0.0000
96 K A -0.8445
97 W A 0.0000
98 E A 0.0000
99 T A -0.4800
100 F A 0.0000
101 L A 0.0000
102 T A -0.3487
103 S A -0.5985
104 E A -0.7199
105 L A 0.0000
106 P A 0.0000
107 Q A -1.5257
108 W A -0.8931
109 L A 0.0000
110 S A -1.4077
111 A A -0.9039
112 N A -1.2919
113 R A -1.7757
114 A A -1.7566
115 V A 0.0000
116 K A -1.6372
117 P A -1.0813
118 T A -0.7234
119 G A -0.3947
120 S A 0.0000
121 A A 0.0000
122 A A 0.0000
123 I A 0.0000
124 G A 0.0000
125 L A 0.0000
126 S A -0.0873
127 M A 0.0000
128 A A 0.0000
129 G A 0.0000
130 S A 0.0000
131 S A 0.0000
132 A A 0.0000
133 M A 0.0000
134 I A 0.0000
135 L A 0.0000
136 A A 0.0000
137 A A 0.0000
138 Y A -0.2447
139 H A -0.5130
140 P A -0.8642
141 Q A -1.2431
142 Q A 0.0000
143 F A 0.0000
144 I A -0.0709
145 Y A 0.0000
146 A A 0.0000
147 G A 0.0000
148 S A 0.0000
149 L A 0.0000
150 S A 0.0000
151 A A 0.0000
152 L A 0.2781
153 L A 0.0000
154 D A -1.0902
155 P A 0.0000
156 S A 0.0000
157 Q A -1.4896
158 G A -0.5799
159 M A 0.4885
160 G A 0.0000
161 P A -0.0198
162 S A 0.3998
163 L A 0.9859
164 I A 0.0000
165 G A 0.0640
166 L A 0.7985
167 A A -0.2534
168 M A 0.0000
169 G A -1.1743
170 D A -2.0550
171 A A 0.0000
172 G A -1.7259
173 G A -1.5431
174 Y A -1.2790
175 K A -1.7716
176 A A -0.7551
177 A A -0.6173
178 D A -0.4183
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.7593
183 S A -0.7873
184 S A -0.6917
185 D A -0.8499
186 P A -0.8790
187 A A -0.5923
188 W A 0.0000
189 E A -1.6382
190 R A -1.2192
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.2926
195 Q A -1.7699
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0034
199 K A -1.2767
200 L A 0.0000
201 V A -1.1521
202 A A -0.8791
203 N A -1.3996
204 N A -1.5629
205 T A 0.0000
206 R A -0.6213
207 L A 0.0000
208 W A 0.0000
209 V A 0.0000
210 Y A 0.0000
211 C A 0.0000
212 G A 0.0000
213 N A -0.6376
214 G A 0.0000
215 T A -0.6332
216 P A -1.3610
217 N A -1.7427
218 E A -1.9278
219 L A -0.6794
220 G A -0.9206
221 G A -0.6925
222 A A -0.5102
223 N A 0.1054
224 I A 1.8881
225 P A 0.9996
226 A A 0.0000
227 E A 0.6066
228 F A 2.1833
229 L A 1.6904
230 E A 0.0000
231 N A -0.3383
232 F A 0.9968
233 V A 0.0000
234 R A -0.4060
235 S A -0.5800
236 S A 0.0000
237 N A 0.0000
238 L A -0.6752
239 K A -2.0884
240 F A 0.0000
241 Q A -1.6756
242 D A -2.6629
243 A A -1.8202
244 Y A 0.0000
245 N A -2.2914
246 A A -1.2523
247 A A -0.9064
248 G A -1.0803
249 G A -1.6746
250 H A -1.6311
251 N A -1.1687
252 A A -0.5361
253 V A 0.2295
254 F A 0.5167
255 N A 0.1062
256 F A 0.1586
257 P A -0.2458
258 P A -0.6145
259 N A -0.9048
260 G A 0.0000
261 T A 0.0000
262 H A -0.0790
263 S A -0.4839
264 W A -0.3121
265 E A -0.8805
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.4332
270 Q A -0.5844
271 L A 0.0000
272 N A -1.0582
273 A A -0.7043
274 M A 0.0000
275 K A -1.1715
276 G A -1.1745
277 D A -0.8907
278 L A 0.0000
279 Q A -1.0122
280 S A -0.8603
281 S A -0.4862
282 L A -0.3348
283 G A -0.7213
284 A A -0.8847
285 G A -0.9020
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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
IE224A -0.9673 -0.045 View CSV PDB
IK224A -0.2969 -0.0461 View CSV PDB
FK228A -0.1895 -0.0532 View CSV PDB
IR53A -1.3997 -0.0184 View CSV PDB
IK53A -0.0649 -0.0292 View CSV PDB
FR228A 0.0519 -0.0527 View CSV PDB
LR229A 0.2089 -0.0315 View CSV PDB
FR232A 0.3777 -0.0375 View CSV PDB
LK229A 0.4564 -0.025 View CSV PDB
FK232A 0.75 -0.0272 View CSV PDB
PR225A 1.3827 -0.0266 View CSV PDB
PE225A 0.9099 -0.0174 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018