Project name: MUT_L395-660TSA1

Status: done

Started: 2025-02-10 19:31:09
Settings
Chain sequence(s) A: MALTEELNTINSVLSTWVQLDASFSESSIPTAGLVGFLSNTTSSGDTWIDGYRSMNATVTKAAKVENGFKFTGPGSRATWPVNSRWDIKQYGFVDYNFTIVAMATIHQVPSESTPLLGASLRGNKRTKLIGLSYGAGGKWETVYDGTKTRQGGTWEPGREYQVALMLQDGNKGFVYVDGRLVGNPAMLPTPEERWTEFSHFYFGGDEGDSGSDATLTDVFLYNRPLSRGELKMIKEVED
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                                          (00:03:12)
[INFO]       Auto_mut: Residue number 18 from chain A and a score of 1.510 (valine) selected for   
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Residue number 17 from chain A and a score of 0.931 (tryptophan) selected   
                       for automated muatation                                                     (00:03:13)
[INFO]       Auto_mut: Residue number 14 from chain A and a score of 0.927 (leucine) selected for  
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Residue number 3 from chain A and a score of 0.818 (leucine) selected for   
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.817 omitted from automated   
                       muatation (excluded by the user).                                           (00:03:13)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 0.545 (alanine) selected for   
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Residue number 187 from chain A and a score of 0.531 (methionine) selected  
                       for automated muatation                                                     (00:03:13)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (valine) into glutamic acid         (00:03:13)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (tryptophan) into glutamic acid     (00:03:13)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (valine) into aspartic acid         (00:03:13)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (valine) into lysine                (00:04:35)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (valine) into arginine              (00:04:36)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (tryptophan) into lysine            (00:04:49)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (tryptophan) into aspartic acid     (00:06:05)
[INFO]       Auto_mut: Mutating residue number 14 from chain A (leucine) into glutamic acid        (00:06:12)
[INFO]       Auto_mut: Mutating residue number 14 from chain A (leucine) into aspartic acid        (00:06:41)
[INFO]       Auto_mut: Mutating residue number 17 from chain A (tryptophan) into arginine          (00:07:32)
[INFO]       Auto_mut: Mutating residue number 14 from chain A (leucine) into lysine               (00:07:36)
[INFO]       Auto_mut: Mutating residue number 14 from chain A (leucine) into arginine             (00:08:09)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into glutamic acid         (00:09:07)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into aspartic acid         (00:09:14)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (alanine) into glutamic acid         (00:09:40)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into lysine                (00:10:29)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into arginine              (00:10:37)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (alanine) into lysine                (00:11:05)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (alanine) into aspartic acid         (00:11:56)
[INFO]       Auto_mut: Mutating residue number 187 from chain A (methionine) into glutamic acid    (00:12:07)
[INFO]       Auto_mut: Mutating residue number 187 from chain A (methionine) into aspartic acid    (00:12:33)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (alanine) into arginine              (00:13:21)
[INFO]       Auto_mut: Mutating residue number 187 from chain A (methionine) into lysine           (00:13:35)
[INFO]       Auto_mut: Mutating residue number 187 from chain A (methionine) into arginine         (00:13:58)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.1972 kcal/mol, Difference in average score from 
                       the base case: -0.0540                                                      (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (valine) into lysine:     
                       Energy difference: -0.4183 kcal/mol, Difference in average score from the   
                       base case: -0.0533                                                          (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.2031 kcal/mol, Difference in average score from  
                       the base case: -0.0518                                                      (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (valine) into arginine:   
                       Energy difference: -0.6353 kcal/mol, Difference in average score from the   
                       base case: -0.0602                                                          (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (tryptophan) into         
                       glutamic acid: Energy difference: 2.3542 kcal/mol, Difference in average    
                       score from the base case: -0.0047                                           (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (tryptophan) into lysine: 
                       Energy difference: 1.4574 kcal/mol, Difference in average score from the    
                       base case: -0.0063                                                          (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (tryptophan) into         
                       aspartic acid: Energy difference: 3.6683 kcal/mol, Difference in average    
                       score from the base case: 0.0023                                            (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 17 from chain A (tryptophan) into         
                       arginine: Energy difference: 1.4306 kcal/mol, Difference in average score   
                       from the base case: -0.0036                                                 (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 14 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.8687 kcal/mol, Difference in average score from  
                       the base case: -0.0281                                                      (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 14 from chain A (leucine) into lysine:    
                       Energy difference: 0.5976 kcal/mol, Difference in average score from the    
                       base case: -0.0307                                                          (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 14 from chain A (leucine) into aspartic   
                       acid: Energy difference: 1.5526 kcal/mol, Difference in average score from  
                       the base case: -0.0265                                                      (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 14 from chain A (leucine) into arginine:  
                       Energy difference: 0.5397 kcal/mol, Difference in average score from the    
                       base case: -0.0386                                                          (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into glutamic    
                       acid: Energy difference: -0.3007 kcal/mol, Difference in average score from 
                       the base case: -0.0379                                                      (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into lysine:     
                       Energy difference: -0.0369 kcal/mol, Difference in average score from the   
                       base case: -0.0357                                                          (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into aspartic    
                       acid: Energy difference: -0.9177 kcal/mol, Difference in average score from 
                       the base case: -0.0379                                                      (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into arginine:   
                       Energy difference: -0.0831 kcal/mol, Difference in average score from the   
                       base case: -0.0519                                                          (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (alanine) into glutamic    
                       acid: Energy difference: -0.8653 kcal/mol, Difference in average score from 
                       the base case: -0.0149                                                      (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (alanine) into lysine:     
                       Energy difference: -0.0419 kcal/mol, Difference in average score from the   
                       base case: -0.0138                                                          (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (alanine) into aspartic    
                       acid: Energy difference: -2.0543 kcal/mol, Difference in average score from 
                       the base case: -0.0268                                                      (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (alanine) into arginine:   
                       Energy difference: -0.2025 kcal/mol, Difference in average score from the   
                       base case: 0.0002                                                           (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 187 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.2647 kcal/mol, Difference in average    
                       score from the base case: -0.0301                                           (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 187 from chain A (methionine) into        
                       lysine: Energy difference: -0.1042 kcal/mol, Difference in average score    
                       from the base case: -0.0334                                                 (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 187 from chain A (methionine) into        
                       aspartic acid: Energy difference: 0.2802 kcal/mol, Difference in average    
                       score from the base case: -0.0359                                           (00:15:34)
[INFO]       Auto_mut: Effect of mutation residue number 187 from chain A (methionine) into        
                       arginine: Energy difference: -1.8832 kcal/mol, Difference in average score  
                       from the base case: -0.0322                                                 (00:15:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:41)
Show buried residues
Minimal score value
-3.5268
Maximal score value
1.5104
Average score
-0.835
Total score value
-199.5631
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 0.8168
2 A A 0.5448
3 L A 0.8175
4 T A -0.3718
5 E A -1.9405
6 E A -1.6517
7 L A -0.5860
8 N A -1.7660
9 T A -1.0071
10 I A -0.1069
11 N A -1.0505
12 S A -0.3852
13 V A 0.4210
14 L A 0.9273
15 S A 0.5116
16 T A 0.3548
17 W A 0.9315
18 V A 1.5104
19 Q A -0.1603
20 L A -0.0754
21 D A -0.3692
22 A A -0.6326
23 S A -0.9021
24 F A 0.0000
25 S A -1.4570
26 E A -2.1076
27 S A -1.4701
28 S A -1.1286
29 I A 0.0000
30 P A -0.4197
31 T A -0.1954
32 A A -0.2135
33 G A -0.3548
34 L A 0.0000
35 V A -0.0596
36 G A 0.0000
37 F A 0.0000
38 L A 0.0000
39 S A -1.3612
40 N A -2.1142
41 T A -1.7149
42 T A -0.9332
43 S A -0.9381
44 S A -1.0078
45 G A -1.7350
46 D A -1.9813
47 T A -1.2710
48 W A 0.0000
49 I A -0.8351
50 D A 0.0000
51 G A -0.6205
52 Y A 0.0000
53 R A -1.1002
54 S A -0.8056
55 M A -0.7241
56 N A -1.0919
57 A A 0.0000
58 T A -0.6904
59 V A 0.0000
60 T A -1.3720
61 K A -2.3704
62 A A -1.8019
63 A A -1.5544
64 K A -2.8652
65 V A -2.0436
66 E A -2.8445
67 N A -2.4469
68 G A 0.0000
69 F A 0.0000
70 K A -1.6820
71 F A 0.0000
72 T A -1.0319
73 G A -1.0876
74 P A -1.7778
75 G A -1.9072
76 S A 0.0000
77 R A -1.4505
78 A A 0.0000
79 T A -0.5702
80 W A 0.0000
81 P A -0.4459
82 V A 0.0000
83 N A -1.3502
84 S A -1.5569
85 R A -1.9038
86 W A -0.4467
87 D A -1.3139
88 I A 0.0798
89 K A -1.6631
90 Q A -1.1318
91 Y A 0.0000
92 G A -0.4003
93 F A 0.0698
94 V A 0.0000
95 D A 0.0000
96 Y A -0.0096
97 N A -0.8127
98 F A 0.0000
99 T A 0.0000
100 I A 0.0000
101 V A 0.0000
102 A A 0.0000
103 M A -0.5085
104 A A 0.0000
105 T A -1.6329
106 I A 0.0000
107 H A -1.5365
108 Q A -0.9721
109 V A 0.3980
110 P A -0.3888
111 S A -0.9146
112 E A -1.7878
113 S A -1.4281
114 T A 0.0000
115 P A 0.0000
116 L A 0.0000
117 L A 0.0000
118 G A 0.0000
119 A A 0.0000
120 S A 0.0000
121 L A 0.0000
122 R A -2.0941
123 G A -2.2127
124 N A -2.8550
125 K A -3.5268
126 R A -3.3544
127 T A -2.4170
128 K A -1.5516
129 L A 0.0000
130 I A 0.0000
131 G A 0.0000
132 L A 0.0000
133 S A 0.0000
134 Y A 0.0000
135 G A 0.0000
136 A A -0.6436
137 G A -1.2301
138 G A -1.2413
139 K A -2.7744
140 W A 0.0000
141 E A 0.0000
142 T A 0.0000
143 V A 0.0000
144 Y A 0.0000
145 D A -1.3009
146 G A -1.6672
147 T A -1.2592
148 K A -2.1062
149 T A -2.1888
150 R A -3.2893
151 Q A -3.0028
152 G A -2.1080
153 G A -1.5773
154 T A -1.5153
155 W A 0.0000
156 E A -2.2857
157 P A -1.7239
158 G A -2.0072
159 R A -2.3009
160 E A -2.5948
161 Y A 0.0000
162 Q A 0.0000
163 V A 0.0000
164 A A 0.0000
165 L A 0.0000
166 M A 0.0000
167 L A 0.0000
168 Q A -1.3083
169 D A -1.9707
170 G A 0.0000
171 N A -0.8769
172 K A -0.8294
173 G A 0.0000
174 F A -0.0544
175 V A 0.0000
176 Y A -0.4058
177 V A 0.0000
178 D A 0.0000
179 G A 0.0000
180 R A -1.6406
181 L A -0.7249
182 V A 0.0000
183 G A -1.6750
184 N A -1.3650
185 P A -0.4872
186 A A -0.0856
187 M A 0.5309
188 L A 0.0000
189 P A -0.8681
190 T A -1.3274
191 P A -1.4021
192 E A -2.4713
193 E A -2.4908
194 R A -1.2943
195 W A -0.3173
196 T A -0.6436
197 E A -0.7511
198 F A 0.0000
199 S A -0.9561
200 H A -0.4893
201 F A 0.0000
202 Y A 0.0000
203 F A 0.0000
204 G A 0.0000
205 G A 0.0000
206 D A -1.8610
207 E A -2.6811
208 G A -2.4685
209 D A -2.6672
210 S A -2.1218
211 G A -1.5654
212 S A 0.0000
213 D A -0.7834
214 A A 0.0000
215 T A -0.8722
216 L A 0.0000
217 T A -0.9404
218 D A -0.9512
219 V A 0.0000
220 F A 0.0000
221 L A 0.0000
222 Y A 0.0000
223 N A -0.6763
224 R A -0.9537
225 P A -0.9782
226 L A 0.0000
227 S A -1.5141
228 R A -2.5864
229 G A -1.7381
230 E A -1.4526
231 L A 0.0000
232 K A -2.2476
233 M A -1.2608
234 I A 0.0000
235 K A -2.6653
236 E A -2.9950
237 V A -1.8144
238 E A -3.0680
239 D A -3.0045
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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
MR187A -1.8832 -0.0322 View CSV PDB
AD2A -2.0543 -0.0268 View CSV PDB
VR18A -0.6353 -0.0602 View CSV PDB
LD3A -0.9177 -0.0379 View CSV PDB
VK18A -0.4183 -0.0533 View CSV PDB
LE3A -0.3007 -0.0379 View CSV PDB
AE2A -0.8653 -0.0149 View CSV PDB
MK187A -0.1042 -0.0334 View CSV PDB
LR14A 0.5397 -0.0386 View CSV PDB
LK14A 0.5976 -0.0307 View CSV PDB
WK17A 1.4574 -0.0063 View CSV PDB
WR17A 1.4306 -0.0036 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018