Project name: YfjR_mut1

Status: done

Started: 2025-08-08 08:51:36
Settings
Chain sequence(s) A: MTQAERRHDRLAVRLSLIISRLVAGETLSVRKLAAEFGVSVRTLRRDFRERLMYLDLEYQSGYCRLRTAGSEMQMVPDVLIFAHRSGLAGLFPGLDRRLVNALLMCDESPCVIAPANPVPSPSGALSFWRLIQAITGRRRVTLIAEGRRCERLAPCRLLIHQQTWYLVAEHEGHIAVFTLDEIHLIQPLQETFRRNDSLCRLVEDPVFIQALPHFRFIQHSRKTRVPADSPPE
B: MTQAERRHDRLAVRLSLIISRLVAGETLSVRKLAAEFGVSVRTLRRDFRERLMYLDLEYQSGYCRLRTAGSEMQMVPDVLIFAHRSGLAGLFPGLDRRLVNALLMCDESPCVIAPANPVPSPSGALSFWRLIQAITGRRRVTLIAEGRRCERLAPCRLLIHQQTWYLVAEHEGHIAVFTLDEIHLIQPLQETFRRNDSLCRLVEDPVFIQALPHFRFIQHSRKTRVPADSPPE
input PDB
Selected Chain(s) A,B
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 all chain(s) selected           (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:07:05)
[INFO]       Auto_mut: Residue number 217 from chain B and a score of 1.022 (phenylalanine)        
                       selected for automated muatation                                            (00:07:09)
[INFO]       Auto_mut: Residue number 119 from chain B and a score of 0.872 (valine) selected for  
                       automated muatation                                                         (00:07:09)
[INFO]       Auto_mut: Residue number 217 from chain A and a score of 0.851 (phenylalanine)        
                       selected for automated muatation                                            (00:07:09)
[INFO]       Auto_mut: Residue number 119 from chain A and a score of 0.841 (valine) selected for  
                       automated muatation                                                         (00:07:09)
[INFO]       Auto_mut: Residue number 207 from chain B and a score of 0.816 (valine) selected for  
                       automated muatation                                                         (00:07:09)
[INFO]       Auto_mut: Residue number 207 from chain A and a score of 0.816 (valine) selected for  
                       automated muatation                                                         (00:07:09)
[INFO]       Auto_mut: Mutating residue number 119 from chain B (valine) into glutamic acid        (00:07:09)
[INFO]       Auto_mut: Mutating residue number 217 from chain B (phenylalanine) into glutamic acid 
                       Mutating residue number 217 from chain B (phenylalanine) into glutamic acid (00:07:09)
[INFO]       Auto_mut: Mutating residue number 217 from chain B (phenylalanine) into aspartic acid 
                       Mutating residue number 217 from chain B (phenylalanine) into aspartic acid (00:07:09)
[INFO]       Auto_mut: Mutating residue number 217 from chain B (phenylalanine) into lysine        (00:10:19)
[INFO]       Auto_mut: Mutating residue number 119 from chain B (valine) into lysine               (00:10:32)
[INFO]       Auto_mut: Mutating residue number 217 from chain B (phenylalanine) into arginine      (00:10:41)
[INFO]       Auto_mut: Mutating residue number 119 from chain B (valine) into aspartic acid        (00:13:43)
[INFO]       Auto_mut: Mutating residue number 217 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 217 from chain A (phenylalanine) into glutamic acid (00:14:08)
[INFO]       Auto_mut: Mutating residue number 217 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 217 from chain A (phenylalanine) into aspartic acid (00:14:17)
[INFO]       Auto_mut: Mutating residue number 119 from chain B (valine) into arginine             (00:16:58)
[INFO]       Auto_mut: Mutating residue number 217 from chain A (phenylalanine) into arginine      (00:17:29)
[INFO]       Auto_mut: Mutating residue number 217 from chain A (phenylalanine) into lysine        (00:17:35)
[INFO]       Auto_mut: Mutating residue number 119 from chain A (valine) into glutamic acid        (00:20:29)
[INFO]       Auto_mut: Mutating residue number 119 from chain A (valine) into aspartic acid        (00:20:57)
[INFO]       Auto_mut: Mutating residue number 207 from chain B (valine) into glutamic acid        (00:21:11)
[INFO]       Auto_mut: Mutating residue number 119 from chain A (valine) into lysine               (00:23:53)
[INFO]       Auto_mut: Mutating residue number 119 from chain A (valine) into arginine             (00:24:17)
[INFO]       Auto_mut: Mutating residue number 207 from chain B (valine) into lysine               (00:24:24)
[INFO]       Auto_mut: Mutating residue number 207 from chain B (valine) into aspartic acid        (00:27:17)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (valine) into glutamic acid        (00:27:42)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (valine) into aspartic acid        (00:27:47)
[INFO]       Auto_mut: Mutating residue number 207 from chain B (valine) into arginine             (00:30:32)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (valine) into arginine             (00:30:59)
[INFO]       Auto_mut: Mutating residue number 207 from chain A (valine) into lysine               (00:31:01)
[INFO]       Auto_mut: Effect of mutation residue number 217 from chain B (phenylalanine) into     
                       glutamic acid: Energy difference: -0.4372 kcal/mol, Difference in average   
                       score from the base case: -0.0245                                           (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 217 from chain B (phenylalanine) into     
                       lysine: Energy difference: -0.7227 kcal/mol, Difference in average score    
                       from the base case: -0.0281                                                 (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 217 from chain B (phenylalanine) into     
                       aspartic acid: Energy difference: -0.4343 kcal/mol, Difference in average   
                       score from the base case: -0.0309                                           (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 217 from chain B (phenylalanine) into     
                       arginine: Energy difference: -0.7640 kcal/mol, Difference in average score  
                       from the base case: -0.0288                                                 (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain B (valine) into glutamic   
                       acid: Energy difference: -0.3483 kcal/mol, Difference in average score from 
                       the base case: -0.0204                                                      (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain B (valine) into lysine:    
                       Energy difference: -0.8318 kcal/mol, Difference in average score from the   
                       base case: -0.0259                                                          (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain B (valine) into aspartic   
                       acid: Energy difference: 0.0670 kcal/mol, Difference in average score from  
                       the base case: -0.0263                                                      (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain B (valine) into arginine:  
                       Energy difference: -1.6524 kcal/mol, Difference in average score from the   
                       base case: -0.0234                                                          (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 217 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: -0.5373 kcal/mol, Difference in average   
                       score from the base case: -0.0306                                           (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 217 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.8058 kcal/mol, Difference in average score    
                       from the base case: -0.0256                                                 (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 217 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: -0.5895 kcal/mol, Difference in average   
                       score from the base case: -0.0298                                           (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 217 from chain A (phenylalanine) into     
                       arginine: Energy difference: -1.2657 kcal/mol, Difference in average score  
                       from the base case: -0.0289                                                 (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.5545 kcal/mol, Difference in average score from 
                       the base case: -0.0235                                                      (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain A (valine) into lysine:    
                       Energy difference: -0.8310 kcal/mol, Difference in average score from the   
                       base case: -0.0258                                                          (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.0192 kcal/mol, Difference in average score from  
                       the base case: -0.0275                                                      (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 119 from chain A (valine) into arginine:  
                       Energy difference: -1.5979 kcal/mol, Difference in average score from the   
                       base case: -0.0238                                                          (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain B (valine) into glutamic   
                       acid: Energy difference: -0.1526 kcal/mol, Difference in average score from 
                       the base case: -0.0196                                                      (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain B (valine) into lysine:    
                       Energy difference: -0.6561 kcal/mol, Difference in average score from the   
                       base case: -0.0140                                                          (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain B (valine) into aspartic   
                       acid: Energy difference: 0.2040 kcal/mol, Difference in average score from  
                       the base case: -0.0184                                                      (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain B (valine) into arginine:  
                       Energy difference: -1.1244 kcal/mol, Difference in average score from the   
                       base case: -0.0155                                                          (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1515 kcal/mol, Difference in average score from 
                       the base case: -0.0188                                                      (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (valine) into lysine:    
                       Energy difference: -0.6617 kcal/mol, Difference in average score from the   
                       base case: -0.0139                                                          (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.2056 kcal/mol, Difference in average score from  
                       the base case: -0.0182                                                      (00:34:29)
[INFO]       Auto_mut: Effect of mutation residue number 207 from chain A (valine) into arginine:  
                       Energy difference: -1.1315 kcal/mol, Difference in average score from the   
                       base case: -0.0153                                                          (00:34:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:34:36)
Show buried residues
Minimal score value
-4.2604
Maximal score value
1.022
Average score
-0.9683
Total score value
-451.2089
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 M A 0.0544
2 T A -1.1743
3 Q A -2.3786
4 A A -2.6512
5 E A -3.2069
6 R A -4.1693
7 R A -4.2604
8 H A -3.5434
9 D A -3.2913
10 R A -3.3652
11 L A -1.8028
12 A A 0.0000
13 V A -0.3623
14 R A 0.0000
15 L A 0.0000
16 S A 0.0000
17 L A 0.6743
18 I A 0.0000
19 I A 0.0000
20 S A -0.1050
21 R A -0.9182
22 L A 0.0000
23 V A -0.2425
24 A A -0.8301
25 G A -1.4490
26 E A -2.1487
27 T A -1.2864
28 L A 0.0000
29 S A -1.2478
30 V A 0.0000
31 R A -2.8879
32 K A -2.6869
33 L A 0.0000
34 A A 0.0000
35 A A -1.3570
36 E A -1.5427
37 F A -0.6139
38 G A -0.5363
39 V A -0.3570
40 S A -1.0734
41 V A -1.8400
42 R A -2.7587
43 T A -1.9367
44 L A 0.0000
45 R A -3.5592
46 R A -3.3927
47 D A 0.0000
48 F A 0.0000
49 R A -2.5516
50 E A -1.6469
51 R A -0.9943
52 L A 0.0000
53 M A 0.2207
54 Y A 0.5459
55 L A 0.0000
56 D A -1.5624
57 L A -1.1443
58 E A -0.8181
59 Y A 0.0036
60 Q A -0.7657
61 S A -0.3396
62 G A -0.5670
63 Y A -0.0634
64 C A 0.0000
65 R A -1.8797
66 L A -1.3807
67 R A -1.6957
68 T A -0.9510
69 A A -0.6146
70 G A -0.4357
71 S A -1.1203
72 E A -1.7462
73 M A -0.1412
74 Q A -0.8440
75 M A 0.3146
76 V A 0.3494
77 P A -0.9419
78 D A -1.6408
79 V A 0.0000
80 L A 0.0000
81 I A -0.1281
82 F A 0.0000
83 A A 0.0000
84 H A -1.4126
85 R A -1.2744
86 S A 0.0000
87 G A -0.5639
88 L A 0.0000
89 A A -0.6988
90 G A -0.4018
91 L A 0.0000
92 F A 0.0000
93 P A 0.0000
94 G A -0.9159
95 L A -1.1311
96 D A -2.0240
97 R A -2.4314
98 R A -2.7976
99 L A 0.0000
100 V A 0.0000
101 N A -1.5434
102 A A 0.0000
103 L A 0.0000
104 L A -0.4847
105 M A 0.4310
106 C A 0.0000
107 D A -2.0092
108 E A -1.7976
109 S A -1.1231
110 P A 0.0000
111 C A 0.0000
112 V A -0.2994
113 I A 0.0000
114 A A 0.0000
115 P A -0.4429
116 A A 0.0000
117 N A -1.0688
118 P A -0.4538
119 V A 0.8406
120 P A -0.0353
121 S A -0.1519
122 P A -0.0504
123 S A -0.4204
124 G A 0.0000
125 A A 0.0618
126 L A 0.5171
127 S A 0.0000
128 F A 0.0000
129 W A -0.2456
130 R A -0.4887
131 L A 0.0000
132 I A 0.0000
133 Q A -1.1958
134 A A 0.0000
135 I A 0.0000
136 T A -1.2701
137 G A -1.3319
138 R A -2.6299
139 R A -2.8135
140 R A -2.6794
141 V A 0.0000
142 T A 0.0000
143 L A 0.0000
144 I A -1.7150
145 A A 0.0000
146 E A -3.1316
147 G A -2.3910
148 R A -3.3490
149 R A -3.1636
150 C A 0.0000
151 E A -3.5668
152 R A -3.4360
153 L A 0.0000
154 A A 0.0000
155 P A 0.0000
156 C A 0.0000
157 R A -0.3215
158 L A 0.0000
159 L A 0.0000
160 I A 0.0000
161 H A 0.0000
162 Q A -2.0526
163 Q A -1.2857
164 T A -0.9490
165 W A 0.0000
166 Y A 0.0000
167 L A 0.0000
168 V A 0.0000
169 A A 0.0000
170 E A -1.4182
171 H A -2.2477
172 E A -2.9309
173 G A -1.8462
174 H A -1.6807
175 I A -0.6076
176 A A -0.5849
177 V A 0.0000
178 F A 0.0000
179 T A -0.6960
180 L A 0.0000
181 D A -2.2904
182 E A -2.0147
183 I A 0.0000
184 H A -1.5030
185 L A -0.4409
186 I A 0.0000
187 Q A -1.0723
188 P A -1.4786
189 L A -1.6901
190 Q A -1.8630
191 E A -1.9743
192 T A -2.2125
193 F A -2.2546
194 R A -3.2604
195 R A -3.3466
196 N A -2.7378
197 D A -2.3968
198 S A -1.5268
199 L A 0.0000
200 C A -2.0353
201 R A -2.7187
202 L A -1.2087
203 V A 0.0000
204 E A -2.4196
205 D A -1.6115
206 P A -0.5052
207 V A 0.8156
208 F A 0.0000
209 I A 0.0000
210 Q A -1.0561
211 A A -0.4494
212 L A 0.0000
213 P A -0.7348
214 H A -0.6302
215 F A -0.2062
216 R A -0.5042
217 F A 0.8511
218 I A -0.0602
219 Q A -1.2856
220 H A -1.8209
221 S A -1.5537
222 R A -2.9770
223 K A -3.2542
224 T A -2.1879
225 R A -2.0991
226 V A -0.0252
227 P A -0.4552
228 A A -0.8550
229 D A -1.7754
230 S A -1.5920
231 P A -1.4563
232 P A -1.6110
233 E A -2.0441
1 M B -0.0374
2 T B -1.2824
3 Q B -2.4826
4 A B -2.6739
5 E B -3.3460
6 R B -4.1477
7 R B -4.1533
8 H B -3.4286
9 D B -2.9157
10 R B -2.9248
11 L B -1.6068
12 A B 0.0000
13 V B -0.2697
14 R B 0.0000
15 L B 0.0000
16 S B 0.0000
17 L B 0.5884
18 I B 0.0000
19 I B 0.0000
20 S B -0.1694
21 R B -0.9979
22 L B 0.0000
23 V B -0.3977
24 A B -0.9439
25 G B -1.4811
26 E B -2.1524
27 T B -1.2096
28 L B 0.0000
29 S B -1.2137
30 V B 0.0000
31 R B -2.9207
32 K B -2.7151
33 L B 0.0000
34 A B 0.0000
35 A B -1.4162
36 E B -1.6030
37 F B 0.0000
38 G B -0.6819
39 V B -0.4526
40 S B -1.1353
41 V B -1.9445
42 R B -2.8415
43 T B -1.9858
44 L B 0.0000
45 R B -3.8201
46 R B -3.3639
47 D B 0.0000
48 F B 0.0000
49 R B -2.5435
50 E B -1.6217
51 R B -1.0461
52 L B 0.0000
53 M B 0.3095
54 Y B 0.6522
55 L B 0.0000
56 D B -1.4213
57 L B -0.9766
58 E B -0.5656
59 Y B 0.3287
60 Q B -0.6164
61 S B -0.2905
62 G B -0.5744
63 Y B 0.0352
64 C B 0.0000
65 R B -1.7105
66 L B -1.2755
67 R B -1.4950
68 T B -0.8085
69 A B -0.6231
70 G B -0.3661
71 S B -1.1084
72 E B -1.7397
73 M B -0.1192
74 Q B -0.7582
75 M B 0.4266
76 V B 0.7528
77 P B -0.7085
78 D B -1.5136
79 V B 0.0000
80 L B 0.0000
81 I B -0.0218
82 F B 0.0000
83 A B 0.0000
84 H B -1.3690
85 R B -1.1920
86 S B 0.0000
87 G B -0.5737
88 L B 0.0000
89 A B -0.6953
90 G B -0.4266
91 L B 0.0000
92 F B 0.0000
93 P B 0.0000
94 G B -0.8602
95 L B -1.0462
96 D B -1.8044
97 R B -2.1285
98 R B -2.6638
99 L B 0.0000
100 V B 0.0000
101 N B -1.4330
102 A B 0.0000
103 L B 0.0000
104 L B -0.5153
105 M B 0.3949
106 C B 0.0000
107 D B -2.2127
108 E B -2.2212
109 S B -1.3248
110 P B 0.0000
111 C B 0.0000
112 V B -0.3113
113 I B 0.0000
114 A B 0.0000
115 P B -0.3752
116 A B 0.0000
117 N B -0.9873
118 P B -0.4080
119 V B 0.8723
120 P B -0.0237
121 S B -0.2554
122 P B -0.0585
123 S B -0.4382
124 G B 0.0000
125 A B 0.0396
126 L B 0.4602
127 S B 0.0000
128 F B 0.0000
129 W B -0.3327
130 R B -0.5772
131 L B 0.0000
132 I B 0.0000
133 Q B -1.4480
134 A B 0.0000
135 I B 0.0000
136 T B -1.3141
137 G B -1.4373
138 R B -2.9268
139 R B -2.7961
140 R B -2.6047
141 V B 0.0000
142 T B -1.7601
143 L B 0.0000
144 I B -1.6057
145 A B 0.0000
146 E B -3.0295
147 G B -2.2070
148 R B -2.9536
149 R B -2.9547
150 C B 0.0000
151 E B -3.4417
152 R B -3.3453
153 L B 0.0000
154 A B 0.0000
155 P B 0.0000
156 C B 0.0000
157 R B -0.3387
158 L B 0.0000
159 L B 0.0000
160 I B 0.0000
161 H B 0.0000
162 Q B -2.0277
163 Q B -1.2258
164 T B -0.9125
165 W B 0.0000
166 Y B 0.0000
167 L B 0.0000
168 V B 0.0000
169 A B 0.0000
170 E B -1.3969
171 H B -2.1898
172 E B -2.9010
173 G B -1.8332
174 H B -1.6634
175 I B -0.5520
176 A B -0.5123
177 V B 0.0000
178 F B 0.0000
179 T B -0.7236
180 L B 0.0000
181 D B -2.3191
182 E B -2.0550
183 I B 0.0000
184 H B -1.5125
185 L B -0.4936
186 I B 0.0000
187 Q B -1.0625
188 P B -1.4370
189 L B -1.5756
190 Q B -1.7996
191 E B -1.8841
192 T B -2.1951
193 F B -2.2669
194 R B -3.4674
195 R B -3.7847
196 N B -3.2265
197 D B -3.3562
198 S B -1.9888
199 L B 0.0000
200 C B -2.3922
201 R B -2.9589
202 L B -1.3424
203 V B 0.0000
204 E B -2.4185
205 D B -1.6133
206 P B -0.5107
207 V B 0.8161
208 F B 0.0000
209 I B 0.0000
210 Q B -1.0580
211 A B -0.4185
212 L B 0.0000
213 P B -0.6934
214 H B -0.5453
215 F B -0.0229
216 R B -0.1513
217 F B 1.0220
218 I B 0.0483
219 Q B -1.1346
220 H B -1.6822
221 S B -1.5249
222 R B -2.9242
223 K B -3.2312
224 T B -2.1706
225 R B -2.0565
226 V B 0.0076
227 P B -0.4324
228 A B -0.8440
229 D B -1.7787
230 S B -1.5786
231 P B -1.4356
232 P B -1.5975
233 E B -2.0415
Download PDB file
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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
FR217A -1.2657 -0.0289 View CSV PDB
VR119B -1.6524 -0.0234 View CSV PDB
VR119A -1.5979 -0.0238 View CSV PDB
FR217B -0.764 -0.0288 View CSV PDB
VK119B -0.8318 -0.0259 View CSV PDB
FK217B -0.7227 -0.0281 View CSV PDB
VK119A -0.831 -0.0258 View CSV PDB
FK217A -0.8058 -0.0256 View CSV PDB
VR207B -1.1244 -0.0155 View CSV PDB
VR207A -1.1315 -0.0153 View CSV PDB
VK207B -0.6561 -0.014 View CSV PDB
VK207A -0.6617 -0.0139 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018