Project name: 1fon_v3best

Status: done

Started: 2025-02-17 23:37:54
Settings
Chain sequence(s) A: SRPGLPVELLQVPSPSMGRDIKVQFQSGGNNSPAVYLLDGLRAQDDYNGWDINTPAFEWYYQSGLSIVMPVGGQSSFYSDWLKPACGKAGCQTYKWETFLTSELPQWLSANRAVKPTGSAAIGLSMAGSSAMILAAYHPQQFIYAGSLSALLDPSQGDGPAFIDKAMGDAGGYKAADMWGPSSDPAWERNDPTQQIPKLVANNTRLWVYCGNGTPNELGGANAPAEALENYVRSSNLKFQDAYNAAGGHNATFDFPPNGTHSWEYWGAQLNAMKGDLQSSLGAG
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                                          (00:03:49)
[INFO]       Auto_mut: Residue number 53 from chain A and a score of 1.512 (isoleucine) selected   
                       for automated muatation                                                     (00:03:50)
[INFO]       Auto_mut: Residue number 256 from chain A and a score of 1.262 (phenylalanine)        
                       selected for automated muatation                                            (00:03:50)
[INFO]       Auto_mut: Residue number 254 from chain A and a score of 0.676 (phenylalanine)        
                       selected for automated muatation                                            (00:03:50)
[INFO]       Auto_mut: Residue number 210 from chain A and a score of 0.565 (tyrosine) selected    
                       for automated muatation                                                     (00:03:50)
[INFO]       Auto_mut: Residue number 257 from chain A and a score of 0.246 (proline) selected for 
                       automated muatation                                                         (00:03:50)
[INFO]       Auto_mut: Residue number 152 from chain A and a score of 0.227 (leucine) selected for 
                       automated muatation                                                         (00:03:50)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into glutamic acid     (00:03:50)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into aspartic acid     (00:03:50)
[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 (00:03:50)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into arginine          (00:05:17)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into lysine        (00:05:20)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (isoleucine) into lysine            (00:05:24)
[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 (00:06:53)
[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 (00:06:54)
[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 (00:07:13)
[INFO]       Auto_mut: Mutating residue number 256 from chain A (phenylalanine) into arginine      (00:08:25)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into lysine        (00:08:32)
[INFO]       Auto_mut: Mutating residue number 254 from chain A (phenylalanine) into arginine      (00:08:50)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (tyrosine) into glutamic acid      (00:09:58)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (tyrosine) into aspartic acid      (00:10:03)
[INFO]       Auto_mut: Mutating residue number 257 from chain A (proline) into glutamic acid       (00:10:26)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (tyrosine) into arginine           (00:11:45)
[INFO]       Auto_mut: Mutating residue number 210 from chain A (tyrosine) into lysine             (00:11:47)
[INFO]       Auto_mut: Mutating residue number 257 from chain A (proline) into lysine              (00:11:54)
[INFO]       Auto_mut: Mutating residue number 257 from chain A (proline) into aspartic acid       (00:13:56)
[INFO]       Auto_mut: Mutating residue number 152 from chain A (leucine) into glutamic acid       (00:14:18)
[INFO]       Auto_mut: Mutating residue number 152 from chain A (leucine) into aspartic acid       (00:14:29)
[INFO]       Auto_mut: Mutating residue number 257 from chain A (proline) into arginine            (00:15:28)
[INFO]       Auto_mut: Mutating residue number 152 from chain A (leucine) into lysine              (00:16:01)
[INFO]       Auto_mut: Mutating residue number 152 from chain A (leucine) into arginine            (00:16:10)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.8119 kcal/mol, Difference in average    
                       score from the base case: -0.0399                                           (00:18:01)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.2415 kcal/mol, Difference in average score from the   
                       base case: -0.0256                                                          (00:18:01)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.2308 kcal/mol, Difference in average    
                       score from the base case: -0.0364                                           (00:18:01)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.8016 kcal/mol, Difference in average score  
                       from the base case: -0.0099                                                 (00:18:01)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.3993 kcal/mol, Difference in average   
                       score from the base case: -0.0434                                           (00:18:01)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.1180 kcal/mol, Difference in average score    
                       from the base case: -0.0417                                                 (00:18:01)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -0.7896 kcal/mol, Difference in average   
                       score from the base case: -0.0370                                           (00:18:01)
[INFO]       Auto_mut: Effect of mutation residue number 256 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.4082 kcal/mol, Difference in average score   
                       from the base case: -0.0551                                                 (00:18:01)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 2.7233 kcal/mol, Difference in average    
                       score from the base case: -0.0209                                           (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       lysine: Energy difference: 2.5150 kcal/mol, Difference in average score     
                       from the base case: -0.0226                                                 (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 3.3265 kcal/mol, Difference in average    
                       score from the base case: -0.0349                                           (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 254 from chain A (phenylalanine) into     
                       arginine: Energy difference: 2.1457 kcal/mol, Difference in average score   
                       from the base case: -0.0284                                                 (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: -11.9310 kcal/mol, Difference in average score     
                       from the base case: -0.0150                                                 (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (tyrosine) into lysine:  
                       Energy difference: -13.9588 kcal/mol, Difference in average score from the  
                       base case: -0.0150                                                          (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: -15.2947 kcal/mol, Difference in average score     
                       from the base case: -0.0148                                                 (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 210 from chain A (tyrosine) into          
                       arginine: Energy difference: -14.1970 kcal/mol, Difference in average score 
                       from the base case: -0.0140                                                 (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 257 from chain A (proline) into glutamic  
                       acid: Energy difference: 2.4302 kcal/mol, Difference in average score from  
                       the base case: -0.0308                                                      (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 257 from chain A (proline) into lysine:   
                       Energy difference: 1.5578 kcal/mol, Difference in average score from the    
                       base case: -0.0184                                                          (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 257 from chain A (proline) into aspartic  
                       acid: Energy difference: 1.6611 kcal/mol, Difference in average score from  
                       the base case: -0.0238                                                      (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 257 from chain A (proline) into arginine: 
                       Energy difference: 1.6103 kcal/mol, Difference in average score from the    
                       base case: -0.0307                                                          (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 152 from chain A (leucine) into glutamic  
                       acid: Energy difference: 2.9029 kcal/mol, Difference in average score from  
                       the base case: -0.0102                                                      (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 152 from chain A (leucine) into lysine:   
                       Energy difference: 2.1308 kcal/mol, Difference in average score from the    
                       base case: -0.0106                                                          (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 152 from chain A (leucine) into aspartic  
                       acid: Energy difference: 3.5083 kcal/mol, Difference in average score from  
                       the base case: -0.0109                                                      (00:18:02)
[INFO]       Auto_mut: Effect of mutation residue number 152 from chain A (leucine) into arginine: 
                       Energy difference: 0.6837 kcal/mol, Difference in average score from the    
                       base case: -0.0060                                                          (00:18:02)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:08)
Show buried residues
Minimal score value
-3.2642
Maximal score value
1.5124
Average score
-0.673
Total score value
-191.1221
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 -1.1910
3 R A -1.9452
4 P A -1.2832
5 G A -0.9756
6 L A -0.5491
7 P A -0.1814
8 V A 0.0343
9 E A -0.3420
10 L A -0.0057
11 L A 0.0000
12 Q A -1.9454
13 V A 0.0000
14 P A -1.8444
15 S A 0.0000
16 P A -1.1394
17 S A -0.8093
18 M A 0.0000
19 G A -1.6721
20 R A -2.5883
21 D A -2.8851
22 I A 0.0000
23 K A -1.6488
24 V A 0.0000
25 Q A 0.0000
26 F A 0.0000
27 Q A 0.0000
28 S A -0.8320
29 G A -1.1401
30 G A -1.5764
31 N A -2.3230
32 N A -2.4489
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 -0.7264
42 L A -1.2069
43 R A -2.6823
44 A A 0.0000
45 Q A -2.9339
46 D A -3.2642
47 D A -2.3846
48 Y A -0.4117
49 N A 0.0000
50 G A 0.0000
51 W A 0.0000
52 D A 0.5179
53 I A 1.5124
54 N A -0.3043
55 T A 0.0000
56 P A -0.5179
57 A A 0.0000
58 F A 0.0000
59 E A -0.7363
60 W A -0.3178
61 Y A 0.0000
62 Y A -0.1800
63 Q A -1.1365
64 S A 0.0000
65 G A -1.0339
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 -1.8605
74 G A -1.2585
75 Q A -1.7045
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 -0.7453
82 W A 0.0000
83 L A -0.0126
84 K A -1.6708
85 P A -1.1263
86 A A 0.0000
87 C A -0.7118
88 G A -1.1898
89 K A -1.9118
90 A A -0.8619
91 G A -0.5742
92 C A 0.0315
93 Q A -0.8394
94 T A -0.8546
95 Y A 0.0000
96 K A -0.8917
97 W A 0.0000
98 E A -0.5600
99 T A -0.5384
100 F A 0.0000
101 L A 0.0000
102 T A -0.4854
103 S A -0.7657
104 E A -1.0131
105 L A 0.0000
106 P A 0.0000
107 Q A -1.6890
108 W A -1.0290
109 L A 0.0000
110 S A -1.5606
111 A A -1.0659
112 N A -1.5490
113 R A -1.7705
114 A A -1.8450
115 V A 0.0000
116 K A -2.0718
117 P A -1.3265
118 T A -0.9756
119 G A -0.6120
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 -0.1088
128 A A 0.0000
129 G A 0.0000
130 S A -0.0046
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 -0.3222
139 H A -0.6091
140 P A -1.0214
141 Q A -1.4029
142 Q A -0.9866
143 F A 0.0000
144 I A -0.4233
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 0.2271
153 L A 0.0000
154 D A -1.4491
155 P A 0.0000
156 S A -1.8348
157 Q A -2.2625
158 G A -1.9645
159 D A -2.3214
160 G A -1.6093
161 P A 0.0000
162 A A -1.2495
163 F A -0.8875
164 I A 0.0000
165 D A -1.9927
166 K A -2.5030
167 A A -1.8872
168 M A 0.0000
169 G A -2.3534
170 D A -2.9491
171 A A 0.0000
172 G A -1.7698
173 G A -1.9958
174 Y A 0.0000
175 K A -2.1818
176 A A 0.0000
177 A A -0.9296
178 D A -1.1108
179 M A 0.0000
180 W A 0.0000
181 G A 0.0000
182 P A -0.7890
183 S A -1.2100
184 S A -0.8508
185 D A -1.2071
186 P A -1.2362
187 A A -0.9939
188 W A 0.0000
189 E A -2.1835
190 R A -1.8652
191 N A 0.0000
192 D A 0.0000
193 P A 0.0000
194 T A -1.2758
195 Q A -1.6697
196 Q A 0.0000
197 I A 0.0000
198 P A -1.0771
199 K A -1.4920
200 L A 0.0000
201 V A -1.3306
202 A A -0.9537
203 N A -1.5307
204 N A -1.7201
205 T A 0.0000
206 R A -1.4632
207 L A 0.0000
208 W A 0.0000
209 V A 0.0000
210 Y A 0.5653
211 C A 0.0000
212 G A 0.0000
213 N A -0.7926
214 G A 0.0000
215 T A -1.1302
216 P A -1.5401
217 N A -2.0916
218 E A -2.1623
219 L A -0.9839
220 G A -1.1073
221 G A -1.0411
222 A A -1.0088
223 N A -1.0946
224 A A -0.6326
225 P A -0.6920
226 A A 0.0000
227 E A -1.1247
228 A A -0.5306
229 L A -0.0299
230 E A 0.0000
231 N A -1.2040
232 Y A 0.0539
233 V A 0.0000
234 R A 0.0000
235 S A -0.4587
236 S A -0.6508
237 N A 0.0000
238 L A -0.0461
239 K A -2.0805
240 F A 0.0000
241 Q A 0.0000
242 D A -2.5422
243 A A -1.7414
244 Y A 0.0000
245 N A -2.3545
246 A A -1.2578
247 A A -0.9151
248 G A -1.1342
249 G A -1.7444
250 H A -1.8209
251 N A -1.5457
252 A A -0.9485
253 T A -0.2610
254 F A 0.6760
255 D A 0.4510
256 F A 1.2624
257 P A 0.2462
258 P A -0.4330
259 N A -0.8012
260 G A 0.0000
261 T A 0.0000
262 H A -0.7032
263 S A -0.5753
264 W A -0.3301
265 E A -1.0615
266 Y A 0.0000
267 W A 0.0000
268 G A 0.0000
269 A A -0.3560
270 Q A 0.0000
271 L A 0.0000
272 N A -0.8025
273 A A -0.6988
274 M A 0.0000
275 K A -1.3239
276 G A -1.5115
277 D A -1.8505
278 L A 0.0000
279 Q A -1.2593
280 S A -1.1160
281 S A -0.8161
282 L A -0.5253
283 G A -0.8012
284 A A -0.9589
285 G A -0.8941
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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
YD210A -15.2947 -0.0148 View CSV PDB
YK210A -13.9588 -0.015 View CSV PDB
FD256A -0.7896 -0.037 View CSV PDB
FE256A -0.3993 -0.0434 View CSV PDB
IK53A -0.2415 -0.0256 View CSV PDB
IR53A -0.8016 -0.0099 View CSV PDB
PR257A 1.6103 -0.0307 View CSV PDB
PD257A 1.6611 -0.0238 View CSV PDB
FR254A 2.1457 -0.0284 View CSV PDB
FD254A 3.3265 -0.0349 View CSV PDB
LR152A 0.6837 -0.006 View CSV PDB
LK152A 2.1308 -0.0106 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018