Bork Group Sunyaev Lab
PolyPhen report
New Prediction
 
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refSNP Predictions found for proteins:
rs5247 P23946

 
Query
Acc number Position AA1 AA2 Description
P23946 66 H R Chymase precursor (EC 3.4.21.39) (Mast cell protease I). LENGTH: 247 AA

Prediction
This variant is predicted to be probably damaging
Prediction Available data Prediction basis Substitution effect Prediction data
probably
damaging
FT
alignment
structure
sequence annotation 2.2: functional effect, functional site
Disruption of annotated functional site
site type: ACT_SITE
Remarks
Closest contact with ligand: PMS, distance 2.907
Closest contact with functional site: ASP 102A, distance 2.504 �
Closest contact with other chains: CH2 5I, distance 1.471 �

Details
Sequence features of the substitution site
Region Site Feature table Critical sites
N/A ACT_SITE show FT fields for P23946 66, 110, 203
PSIC profile scores for two amino acid variants
Score1 Score2 |Score1-Score2| Observations Diagnostics Multiple alignment around substitution position
+2.811 -0.306 3.117 62 precomputed Sequences:  Flanks:  
Mapping of the substitution site to known protein 3D structures
Database Initial number of structures Number of structures
PQS 501 16

Num ID   Res AA E-value Len Ide Gaps Params Cont PDB TITLE
1 1klt _ 57 H 9.4e-133 226 1.00 Params Het
Site
N/A
2 1nn6 A 60 H 2.0e-130 224 1.00 2   Site HUMAN PRO-CHYMASE
3 1pjp A 57 H 6.1e-132 226 0.99   Chain
Site
COMPLEX WITH SUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYLKETONE
4 3rp2 B 57 H 8.1e-76 223 0.60   Site N/A
5 3rp2 A 57 H 8.1e-76 223 0.60   Site N/A
6 1euf B 57 H 1.4e-64 225 0.56 2   Chain
Site
BOVINE DUODENASE(NEW SERINE PROTEASE), CRYSTAL STRUCTURE
7 1euf A 57 H 1.4e-64 225 0.56 2   Chain
Site
BOVINE DUODENASE(NEW SERINE PROTEASE), CRYSTAL STRUCTURE
8 1iau A 57 H 1.8e-59 228 0.54 7   Chain
Site
HUMAN GRANZYME B IN COMPLEX WITH AC-IEPD-CHO
9 1kyn_2 A 57 H 2.5e-61 225 0.53 3   Het
Site
CATHEPSIN-G
10 1fq3 B 57 H 5.2e-59 228 0.53 7   Site CRYSTAL STRUCTURE OF HUMAN GRANZYME B
11 1fq3 A 57 H 5.2e-59 228 0.53 7   Site CRYSTAL STRUCTURE OF HUMAN GRANZYME B
12 1fi8 B 57 H 3.9e-62 226 0.52 2   Chain
Site
RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]
13 1kyn_1 B 357 H 1.9e-61 226 0.52 3   Het
Site
CATHEPSIN-G
14 1cgh A 57 H 1.9e-61 226 0.52 3   Chain
Site
HUMAN CATHEPSIN G
15 1au8 A 57 H 1.9e-61 226 0.52 3   Chain
Site
HUMAN CATHEPSIN G
16 1fi8 A 57 H 5.6e-61 226 0.52 3   Chain
Site
RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]

Structural parameters
Num ID   Res SecStr Acc Acc Normed dPropens (Phi, Psi) Map Region dVol Normed B-factor
1 1klt _ 57 G 94 0.55 1.03 (-70.6, -3.9) A 20 0.24

Contacts
Num ID   Res Heteroatoms Interchain Critical sites
  1 1klt _ 57 0.000�
  102_ ASP 2.954�
195_ SER 4.357�
  2 1nn6 A 60     104A ASP 2.819�
197A SER 2.689�
  3 1pjp A 57   4I PRO 3.575�
0.000�
102A ASP 2.831�
195A SER 2.747�
  4 3rp2 B 57     102B ASP 2.815�
195B SER 2.843�
  5 3rp2 A 57     102A ASP 2.917�
195A SER 3.073�
  6 1euf B 57   36BA SER 3.263�
36CA GLY 4.172�
102B ASP 2.603�
195B SER 3.173�
  7 1euf A 57   36BB SER 3.263�
36CB GLY 4.172�
102A ASP 2.603�
195A SER 3.173�
  8 1iau A 57   404B PRO 3.324�
405B ASA 4.075�
102A ASP 2.965�
195A SER 3.956�
  9 1kyn_2 A 57 601A KTP 3.286�
  102A ASP 2.619�
195A SER 2.605�
  10 1fq3 B 57     102B ASP 2.620�
195B SER 3.386�
  11 1fq3 A 57     0.000�
195A SER 3.324�
  12 1fi8 B 57   52E LEU 5.178�
83E PRO 3.569�
84E ASP 3.523�
102B ASP 2.579�
195B SER 3.423�
  13 1kyn_1 B 357 701B KTP 3.478�
  402B ASP 2.974�
495B SER 2.782�
  14 1cgh A 57   3S PRO 3.382�
4S PPH 2.837�
102A ASP 2.722�
195A SER 3.075�
  15 1au8 A 57   3S PRO 3.243�
4S KPH 2.797�
102A ASP 2.683�
195A SER 3.075�
  16 1fi8 A 57   52C LEU 5.298�
83C PRO 3.703�
84C ASP 3.481�
102A ASP 2.591�
195A SER 3.421�