Project name: 1f0n_stab

Status: done

Started: 2025-02-06 08:48:09
Settings
Chain sequence(s) A: SRPGLPVEYLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDYNGWDINTPAFEWYYQSGLSIVMPVGGQSSFYSDWYSPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGDGPAFLDKAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNSAGGNTPAAKAFENFVRSSNLKFQDAYNAAGGHNAVFNFPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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                                          (00:03:39)
[INFO]       Auto_mut: Residue number 53 from chain A and a score of 1.519 (isoleucine) selected   
                       for automated muatation                                                     (00:03:41)
[INFO]       Auto_mut: Residue number 256 from chain A and a score of 1.339 (phenylalanine)        
                       selected for automated muatation                                            (00:03:41)
[INFO]       Auto_mut: Residue number 254 from chain A and a score of 1.074 (phenylalanine)        
                       selected for automated muatation                                            (00:03:41)
[INFO]       Auto_mut: Residue number 83 from chain A and a score of 0.945 (tyrosine) selected for 
                       automated muatation                                                         (00:03:41)
[INFO]       Auto_mut: Residue number 253 from chain A and a score of 0.689 (valine) selected for  
                       automated muatation                                                         (00:03:41)
[INFO]       Auto_mut: Residue number 255 from chain A and a score of 0.668 (asparagine) selected  
                       for automated muatation                                                     (00:03:41)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into glutamic acid     (00:03:41)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into aspartic acid     (00:03:41)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 256 from chain A (phenylalanine) into glutamic acid (00:03:41)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into arginine          (00:05:03)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into lysine        (00:05:08)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into lysine            (00:05:10)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 256 from chain A (phenylalanine) into aspartic acid (00:06:37)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 254 from chain A (phenylalanine) into glutamic acid (00:06:49)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 254 from chain A (phenylalanine) into aspartic acid (00:06:53)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into arginine      (00:08:04)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into lysine        (00:08:23)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into arginine      (00:08:24)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (tyrosine) into glutamic acid       (00:09:30)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (tyrosine) into aspartic acid       (00:09:51)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into glutamic acid        (00:09:55)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (tyrosine) into lysine              (00:10:58)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (tyrosine) into arginine            (00:11:12)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into lysine               (00:11:17)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into aspartic acid        (00:12:36)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into glutamic acid    (00:12:46)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into aspartic acid    (00:12:59)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (valine) into arginine             (00:13:54)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into lysine           (00:14:08)
[INFO]       Auto_mut: Mutating residue number 255 from chain A (asparagine) into arginine         (00:14:26)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.6856 kcal/mol, Difference in average    
                       score from the base case: -0.0271                                           (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.9756 kcal/mol, Difference in average score from the   
                       base case: -0.0309                                                          (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.1975 kcal/mol, Difference in average    
                       score from the base case: -0.0329                                           (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.8693 kcal/mol, Difference in average score  
                       from the base case: -0.0094                                                 (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.1521 kcal/mol, Difference in average   
                       score from the base case: -0.0287                                           (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.1196 kcal/mol, Difference in average score    
                       from the base case: -0.0294                                                 (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -0.8790 kcal/mol, Difference in average   
                       score from the base case: -0.0230                                           (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.1074 kcal/mol, Difference in average score  
                       from the base case: -0.0366                                                 (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 2.6222 kcal/mol, Difference in average    
                       score from the base case: -0.0102                                           (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       lysine: Energy difference: 2.4799 kcal/mol, Difference in average score     
                       from the base case: -0.0105                                                 (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 3.0837 kcal/mol, Difference in average    
                       score from the base case: -0.0233                                           (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       arginine: Energy difference: 2.1298 kcal/mol, Difference in average score   
                       from the base case: -0.0147                                                 (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 1.3946 kcal/mol, Difference in average score from  
                       the base case: -0.0295                                                      (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.6464 kcal/mol, Difference in average score from the    
                       base case: -0.0233                                                          (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.1835 kcal/mol, Difference in average score from  
                       the base case: -0.0334                                                      (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.4274 kcal/mol, Difference in average score from the    
                       base case: -0.0241                                                          (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.2250 kcal/mol, Difference in average score from  
                       the base case: -0.0244                                                      (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into lysine:    
                       Energy difference: -0.1651 kcal/mol, Difference in average score from the   
                       base case: -0.0093                                                          (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.4213 kcal/mol, Difference in average score from  
                       the base case: -0.0223                                                      (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (valine) into arginine:  
                       Energy difference: -0.2145 kcal/mol, Difference in average score from the   
                       base case: -0.0163                                                          (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       glutamic acid: Energy difference: 0.2430 kcal/mol, Difference in average    
                       score from the base case: -0.0045                                           (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       lysine: Energy difference: -0.4202 kcal/mol, Difference in average score    
                       from the base case: -0.0070                                                 (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       aspartic acid: Energy difference: 0.1327 kcal/mol, Difference in average    
                       score from the base case: -0.0015                                           (00:15:55)
[INFO]       Auto_mut: Effect of mutation residue number 255 from chain A (asparagine) into        
                       arginine: Energy difference: 0.0822 kcal/mol, Difference in average score   
                       from the base case: -0.0138                                                 (00:15:55)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:01)
Show buried residues
Minimal score value
-3.2048
Maximal score value
1.5191
Average score
-0.6045
Total score value
-171.6639
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 -1.1796
3 R A -1.9230
4 P A -1.2558
5 G A -0.9413
6 L A -0.4636
7 P A -0.0598
8 V A 0.2451
9 E A -0.2611
10 Y A 0.0361
11 L A 0.0000
12 Q A -1.4250
13 V A 0.0000
14 P A -1.3081
15 S A 0.0000
16 P A -0.9476
17 S A -0.7110
18 M A 0.0000
19 G A -1.3469
20 R A -1.8788
21 D A -2.1846
22 I A 0.0000
23 K A -1.4105
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.7893
29 G A -1.0968
30 G A -1.5526
31 N A -2.2971
32 N A -2.3737
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 -0.8392
42 L A 0.0000
43 R A -2.7753
44 A A 0.0000
45 Q A -2.8898
46 D A -3.2048
47 D A -2.2784
48 Y A -0.2459
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 D A 0.5260
53 I A 1.5191
54 N A -0.4226
55 T A 0.0000
56 P A -0.5226
57 A A 0.0000
58 F A 0.0000
59 E A -0.6787
60 W A -0.2754
61 Y A 0.0000
62 Y A -0.0474
63 Q A -1.0849
64 S A 0.0000
65 G A -1.0183
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 -1.8448
74 G A -1.2766
75 Q A -1.7461
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 -0.4355
82 W A 0.0000
83 Y A 0.9446
84 S A 0.0217
85 P A -0.2598
86 A A 0.0000
87 C A -0.2464
88 G A -1.1116
89 K A -1.8487
90 A A -0.7887
91 G A -0.4350
92 C A 0.2066
93 Q A -0.4925
94 T A -0.4391
95 Y A 0.0000
96 K A -0.6727
97 W A 0.0000
98 E A 0.0000
99 T A -0.4389
100 F A 0.0000
101 L A 0.0000
102 T A -0.4089
103 S A -0.6512
104 E A -0.8105
105 L A 0.0000
106 P A 0.0000
107 Q A -1.4447
108 W A -0.6075
109 L A 0.0000
110 S A -1.2983
111 A A -0.7504
112 N A -1.0536
113 R A -1.5323
114 A A -1.6645
115 V A 0.0000
116 K A -1.8538
117 P A -1.1861
118 T A -0.9048
119 G A -0.5651
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 0.0000
127 M A 0.0000
128 A A 0.0000
129 G A 0.0000
130 S A -0.0169
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 -0.2010
139 H A -0.5641
140 P A -0.9930
141 Q A -1.4046
142 Q A -0.9579
143 F A 0.0000
144 I A -0.4276
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 0.3003
153 L A 0.0000
154 D A -1.4090
155 P A 0.0000
156 S A -1.7310
157 Q A -2.2476
158 G A -1.9734
159 D A -2.3838
160 G A -1.6898
161 P A 0.0000
162 A A -1.4233
163 F A -1.1174
164 L A 0.0000
165 D A -2.5320
166 K A -2.8211
167 A A 0.0000
168 M A 0.0000
169 G A -2.6786
170 D A -3.1222
171 A A 0.0000
172 G A -1.8325
173 G A -2.1240
174 Y A 0.0000
175 K A -2.5190
176 A A 0.0000
177 A A -0.8802
178 D A -0.5591
179 M A 0.0000
180 W A 0.0000
181 G A -0.5126
182 P A -0.8428
183 S A -1.2395
184 S A -0.8347
185 D A -1.1156
186 P A -1.0770
187 A A 0.0000
188 W A 0.0000
189 E A -1.8748
190 R A -1.3292
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.1818
195 Q A -1.5279
196 Q A 0.0000
197 I A 0.0000
198 P A -0.9680
199 K A -1.2635
200 L A 0.0000
201 V A -1.2634
202 A A -0.8861
203 N A -1.4909
204 N A -1.6967
205 T A 0.0000
206 R A -1.2903
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 -0.7379
214 G A 0.0000
215 T A -1.3275
216 P A -1.6959
217 N A -1.7621
218 S A -1.0440
219 A A -1.1533
220 G A -1.3432
221 G A -1.5199
222 N A -1.8723
223 T A -1.0272
224 P A -0.7268
225 A A -0.4965
226 A A 0.0000
227 K A -1.2386
228 A A -0.3412
229 F A 0.1232
230 E A 0.0000
231 N A -1.0234
232 F A 0.3775
233 V A 0.0000
234 R A 0.0000
235 S A -0.4262
236 S A -0.6254
237 N A 0.0000
238 L A -0.2211
239 K A -2.1555
240 F A 0.0000
241 Q A 0.0000
242 D A -2.5821
243 A A -1.7644
244 Y A 0.0000
245 N A -2.3544
246 A A -1.2579
247 A A -0.9152
248 G A -1.1341
249 G A -1.7468
250 H A -1.6983
251 N A -1.3427
252 A A -0.4774
253 V A 0.6885
254 F A 1.0739
255 N A 0.6677
256 F A 1.3394
257 P A 0.2387
258 P A -0.4256
259 N A -0.8747
260 G A 0.0000
261 T A 0.0000
262 H A -0.7981
263 S A -0.8550
264 W A -0.6545
265 E A -1.6777
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.5151
270 Q A 0.0000
271 L A 0.0000
272 N A -0.7280
273 A A -0.6275
274 M A 0.0000
275 K A -1.2211
276 G A -1.3996
277 D A -1.5619
278 L A 0.0000
279 Q A -1.2077
280 S A -1.0580
281 S A -0.7667
282 L A -0.5017
283 G A -0.7864
284 A A -0.9430
285 G A -0.8972
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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
IK53A -0.9756 -0.0309 View CSV PDB
FD256A -0.879 -0.023 View CSV PDB
FR256A -0.1074 -0.0366 View CSV PDB
IR53A -0.8693 -0.0094 View CSV PDB
VR253A -0.2145 -0.0163 View CSV PDB
NK255A -0.4202 -0.007 View CSV PDB
VK253A -0.1651 -0.0093 View CSV PDB
NR255A 0.0822 -0.0138 View CSV PDB
YR83A 0.4274 -0.0241 View CSV PDB
YK83A 0.6464 -0.0233 View CSV PDB
FD254A 3.0837 -0.0233 View CSV PDB
FR254A 2.1298 -0.0147 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018