Project name: 4AJY_L153P [mutate: LP153V]

Status: done

Started: 2020-09-18 14:53:50
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIA
input PDB
Selected Chain(s) V
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues LP153V
Energy difference between WT (input) and mutated protein (by FoldX) -0.157023 kcal/mol
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 V 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]       FoldX:    Building mutant model                                                       (00:01:59)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:02:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:55)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:25:42)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:25:42)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:25:43)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:25:44)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:25:44)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:25:45)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:25:47)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:25:48)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:25:49)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:25:50)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:25:50)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:25:51)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:25:52)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:25:56)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:25:56)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:25:56)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:57)
Show buried residues
Minimal score value
-4.1808
Maximal score value
1.8197
Average score
-0.8025
Total score value
-118.7639
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
60 R V -1.7899
61 P V -0.8569
62 V V 0.8552
63 L V 0.0000
64 R V -1.0764
65 S V 0.0000
66 V V -0.2682
67 N V -1.0505
68 S V -1.3862
69 R V -2.3840
70 E V -1.7018
71 P V -1.1561
72 S V 0.0000
73 Q V -0.9603
74 V V 0.0000
75 I V -0.6808
76 F V 0.0000
77 C V 0.0000
78 N V 0.0000
79 R V -2.3334
80 S V 0.0000
81 P V -0.7274
82 R V -0.2716
83 V V 0.7433
84 V V 0.0000
85 L V 0.2266
86 P V 0.0000
87 V V 0.0000
88 W V -0.2707
89 L V 0.0000
90 N V -1.2688
91 F V -1.1427
92 D V -2.4886
93 G V -1.9525
94 E V -2.7812
95 P V -1.6176
96 Q V -0.9573
97 P V -0.2171
98 Y V 0.2875
99 P V -0.0111
100 T V 0.1610
101 L V 0.0000
102 P V -0.3116
103 P V -0.7772
104 G V -1.2417
105 T V -0.9928
106 G V -1.4648
107 R V -1.5540
108 R V -2.1453
109 I V -1.2456
110 H V -1.2866
111 S V 0.0000
112 Y V -0.6733
113 R V -0.6301
114 G V -0.0425
115 H V 0.0000
116 L V 0.6711
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V 0.0000
121 D V 0.0000
122 A V -0.0652
123 G V -0.3876
124 T V -0.7061
125 H V -0.8268
126 D V 0.0000
127 G V -0.3546
128 L V 0.0000
129 L V -0.2472
130 V V 0.0000
131 N V -1.0624
132 Q V -1.5007
133 T V -0.8627
134 E V -0.5981
135 L V 0.1849
136 F V 0.0000
137 V V 1.2599
138 P V 0.0000
139 S V 0.5594
140 L V 0.6273
141 N V 0.0244
142 V V 0.5601
143 D V -1.4647
144 G V -1.3281
145 Q V -1.2387
146 P V -0.5699
147 I V 0.6918
148 F V 0.4851
149 A V 0.0000
150 N V -0.9049
151 I V 0.0000
152 T V -0.8988
153 P V -0.1221 mutated: LP153V
154 P V 0.6377
155 V V 1.8197
156 Y V 0.6551
157 T V 0.2384
158 L V 0.6490
159 K V -1.1202
160 E V -1.3458
161 R V -0.7445
162 C V -0.1118
163 L V 0.0000
164 Q V 0.0000
165 V V 0.8672
166 V V 0.8291
167 R V -0.1993
168 S V 0.5131
169 L V 1.3861
170 V V -0.4311
171 K V -2.1651
172 P V -2.5907
173 E V -3.4167
174 N V -3.1105
175 Y V 0.0000
176 R V -3.5327
177 R V -3.2525
178 L V -1.7122
179 D V -1.8946
180 I V -0.1124
181 V V 0.7769
182 R V -1.5909
183 S V -0.9012
184 L V -1.0475
185 Y V 0.0000
186 E V -3.4497
187 D V -2.8854
188 L V 0.0000
189 E V -3.3808
190 D V -3.4846
191 H V -2.9026
192 P V -1.9334
193 N V -2.1483
194 V V -1.8169
195 Q V -3.0216
196 K V -3.2969
197 D V -2.7504
198 L V 0.0000
199 E V -4.1016
200 R V -4.1808
201 L V -2.5110
202 T V -1.9447
203 Q V -2.5858
204 E V -2.9483
205 R V -1.5502
206 I V 0.7955
207 A V -0.2414
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.8025 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
input -0.8025 View CSV PDB
model_4 -0.8212 View CSV PDB
model_6 -0.853 View CSV PDB
model_5 -0.8594 View CSV PDB
model_0 -0.8624 View CSV PDB
model_8 -0.8749 View CSV PDB
model_1 -0.9004 View CSV PDB
model_3 -0.9342 View CSV PDB
model_2 -0.9669 View CSV PDB
model_7 -1.0035 View CSV PDB
model_10 -1.0189 View CSV PDB
model_9 -1.0761 View CSV PDB
model_11 -1.1227 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018