Project name: VHL_WT

Chain sequence(s)	A: MEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	Yes
pH calculations	Yes
alphaCutter usage	No
Dynamic mode	No
Automated mutations	No

Simulation log

[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:42)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4b3f29de0556df7/tmp/folded.pdb                (00:03:42)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:44)

• Minimal score value: -4.3053
• Maximal score value: 1.8894
• Average score: -1.0385
• Total score value: -166.158

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index	residue name	chain	Aggrescan4D score	mutation
1	M	A	0.1301
2	E	A	-1.7344
3	A	A	-1.2690
4	G	A	-2.1116
5	R	A	-2.9728
6	P	A	-2.0836
7	R	A	-2.7366
8	P	A	-1.8228
9	V	A	-0.4937
10	L	A	0.0000
11	R	A	-1.2129
12	S	A	0.0000
13	V	A	0.7221
14	N	A	-1.0800
15	S	A	-1.3811
16	R	A	-2.3426
17	E	A	-1.7956
18	P	A	-1.2988
19	S	A	0.0000
20	Q	A	-1.1409
21	V	A	0.0000
22	I	A	-0.6109
23	F	A	0.0000
24	C	A	0.0000
25	N	A	0.0000
26	R	A	-2.2098
27	S	A	0.0000
28	P	A	-1.0015
29	R	A	-0.9857
30	V	A	-0.2035
31	V	A	0.0000
32	L	A	0.0281
33	P	A	0.0000
34	V	A	0.0000
35	W	A	-0.4306
36	L	A	0.0000
37	N	A	-1.1992
38	F	A	-0.8006
39	D	A	-2.4619
40	G	A	-2.0322
41	E	A	-2.8383
42	P	A	-1.7250
43	Q	A	-1.1977
44	P	A	-0.5496
45	Y	A	0.1151
46	P	A	-0.1206
47	T	A	0.0529
48	L	A	0.0000
49	P	A	-0.6454
50	P	A	-1.1086
51	G	A	-1.3170
52	T	A	-0.9453
53	G	A	-1.4118
54	R	A	-1.5763
55	R	A	-2.2281
56	I	A	0.0000
57	H	A	-1.5257
58	S	A	0.0000
59	Y	A	-0.7325
60	R	A	-0.8532
61	G	A	0.1148
62	H	A	0.0000
63	L	A	0.0000
64	W	A	0.0000
65	L	A	0.0000
66	F	A	0.0000
67	R	A	0.0000
68	D	A	0.0000
69	A	A	-0.3755
70	G	A	-0.6320
71	T	A	-0.9145
72	H	A	-1.0085
73	D	A	-0.9146
74	G	A	-0.6831
75	L	A	0.0000
76	L	A	-0.9249
77	V	A	0.0000
78	N	A	-1.4920
79	Q	A	-1.8443
80	T	A	-1.6278
81	E	A	-2.0318
82	L	A	-0.4050
83	F	A	0.0000
84	V	A	1.7890
85	P	A	0.0000
86	S	A	0.4228
87	L	A	0.2281
88	N	A	-0.3348
89	V	A	0.4686
90	D	A	-1.5175
91	G	A	-1.3737
92	Q	A	-1.3481
93	P	A	-0.5768
94	I	A	0.4723
95	F	A	0.4821
96	A	A	0.0000
97	N	A	-0.9983
98	I	A	0.0000
99	T	A	-0.7142
100	L	A	0.3651
101	P	A	0.7586
102	V	A	1.8894
103	Y	A	0.5463
104	T	A	0.1192
105	L	A	0.4319
106	K	A	-1.2547
107	E	A	-1.3387
108	R	A	-0.8493
109	C	A	-0.1195
110	L	A	0.0000
111	Q	A	-0.0152
112	V	A	1.4365
113	V	A	0.9946
114	R	A	0.0168
115	S	A	0.7315
116	L	A	1.5609
117	V	A	-0.0760
118	K	A	-2.1396
119	P	A	-2.3901
120	E	A	-3.4415
121	N	A	-3.1444
122	Y	A	0.0000
123	R	A	-3.8199
124	R	A	-3.3929
125	L	A	-1.8533
126	D	A	-1.9342
127	I	A	-0.1863
128	V	A	0.7009
129	R	A	-1.7093
130	S	A	-0.9362
131	L	A	-1.2483
132	Y	A	0.0000
133	E	A	-3.4630
134	D	A	-2.8527
135	L	A	0.0000
136	E	A	-3.2646
137	D	A	-3.3087
138	H	A	-2.6004
139	P	A	-1.9631
140	N	A	-2.3141
141	V	A	-2.0983
142	Q	A	-3.2658
143	K	A	-3.7751
144	D	A	-3.2583
145	L	A	0.0000
146	E	A	-4.2068
147	R	A	-4.3053
148	L	A	-2.9679
149	T	A	-2.6295
150	Q	A	-3.3306
151	E	A	-3.6894
152	R	A	-3.0282
153	I	A	-1.6201
154	A	A	-2.1405
155	H	A	-2.8995
156	Q	A	-3.1928
157	R	A	-2.8714
158	M	A	-1.2355
159	G	A	-2.0364
160	D	A	-2.6635

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is partially or entirely disordered. Average score is recommended for pH analysis.

pH	Average A4D Score	Max A4D Score
4.0	-0.9697	2.5673
4.5	-1.0468	2.5673
5.0	-1.1432	2.5673
5.5	-1.2397	2.5673
6.0	-1.3202	2.5673
6.5	-1.3777	2.5673
7.0	-1.4132	2.5673
7.5	-1.4335	2.5673
8.0	-1.445	2.5672
8.5	-1.4498	2.5669
9.0	-1.4465	2.5659