The University of Texas Medical Branch
Department of Biochemistry and Molecular Biology Sealy Center for Structural Biology Computational Biology



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                SDAP - Structural Database of Allergenic Proteins
Go to: SDAP All allergens       Go to: SDAP Food allergens
Send a comment to Werner Braun      Submit new allergen information to SDAP
  
Alphabetical listing of allergens: A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Access to SDAP is available free of charge for Academic and non-profit use.
Licenses for commercial use can be obtained by contacting W. Braun (webraun@utmb.edu).
Secure access to SDAP is available from https://fermi.utmb.edu/SDAP
Allergen Info Description
Allergen ID 5
Allergen Scientific Name Amb a 6
Allergen Species - Systematic Name Ambrosia artemisiifolia
Allergen Species - Common Name short ragweed
Allergen Common source weed
Allergen Common name Asterales
Allergen Keywords Ra6: Nonspecific lipid-transfer protein
Allergen IUIS (Yes=1, No=0) 1
ID Allergen Name
Amb a 6 - References
ID Reference
Pubmed ID: 6863927
Roebber M, Hussain R, Klapper DG, Marsh DG, Isolation and properties of a new short ragweed pollen allergen, Ra6. J Immunol. 1983 Aug;131(2):706-11.
Pubmed ID: 9714407
Hiller KM, Lubahn BC, Klapper DG, Cloning and expression of ragweed allergen Amb a 6. Scand J Immunol. 1998 Jul;48(1):26-36.
Amb a 6 - Protein Sequences
Source Link to source
SwissProt O04004
Amb a 6 - Theoretical Model Structure
Model ID PDB file PDB Snapshot PDB Snapshot 90 PDB Snapshot 180 PDB Snapshot 270 3D PDB View
22 GetModel Model Pic Model Pic Model Pic Model Pic Click here
Amb a 6 - Sequence Search
Sequence Header Sequence
Amb a 6
SDAP Sequence ID: 22
SDAP Allergen ID: 5
MDCIRILWSVAVGLLLVSWRPTMFAASPTCDTVQNILAPCAGFLTGQEPSKACCTGVNNLNNSRKTKADRVAVCNCIKELTKSIAYDPKRMPLLSTKCGVKPDFPAVDKNLDCSKLPV
View 3D Structure Click here to view 3D model structure of allergen
Fasta Search in SDAP
Blast Swissprot database search at NCBI
Blast PDB database search at NCBI
Blast NR database search at NCBI
Expasy Blast Search
Amb a 6 - Statistics from Alphafold ( SI is sequence id, Best template format: PDB_ChainID)
Allergen Name pLDDT Score pTM Score Best PDB template %Seq ID Align length Seq length Query Range Sequence Range E-Value Bit Score Download Model
Amb a 6 82.35 0.65 1AFH_A 35.165 91 118 29 - 116 3 - 92 0.000000000000291 61.6 Download (SI: 22)
Amb a 6 - Alphafold Theoretical Model Structure
Model Structure
22_relaxed_rank_1_model_4.pdb


Coverage Plddt
Amb a 6 - Protein Sequence Properties!
Protein Sequence Protease cleavage sites PeptideCutter at ExPASy
O04004 Click here to process the data
Amb a 6 - PFAM Information
SeqID Aller ID AlnS AlnE EnvS EnvE PFAM ID Family Type Clan Description
22 5 21 104 10 107 PF14368 LTP_2 Family CL0482 Probable lipid transfer
Where: AlnS= Alignment start position, AlnE= Alignment end position, EnvS= Envelope start position, EnvE= Envelope end position.

Welcome

Predicted B-Cell epitope using BCEP method for Amb a 6

Probe radius : 1.400

POLAR area/energy = 2391.33

APOLAR area/energy = 5819.75

Total area/energy = 8211.07

Number of surface atoms = 572

Number of buried atoms = 316

Residues Predicted with high probability (in top five patches) are: 19,20,21,22,23,61,101,102,103,99,92,96,105,45,46,86,87,88 , and medium probability (next top five patches) are : 88,89,90,42,47,18,112,114,115,116,117,58,59,62,63,64,81,106,108 . Predicted residues are shown in red and green color stick representation.

Original PDB file 4637.test.pdb
Original PDB file with surface residue only. All amino acid residue are replaced by their CB atom, in case of GLY CA atom is used. Solvent accessible surface area of each residue is stored in last column of the PDB file. 14637.test.txt
Patch drawn around the residues by patch analysis are stored in this file
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Sum(Pint*Area), Col 4: Sum(Psur*Area), Col 5: Total Residue, Col 6: Interface score, Col 7: Surface Score, Col 8: Max Interface Score, Col 9: Minimum Interface Score
4637.test.tmppat
Residues predicted by patch analysis are stored in this file.
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Res Number Col 4: Neigbouring Res Name, Col 5: Sum(Pint*Area). Col 6: Sum(PSur*Area), Col 7: Sum(Area), Col 8: Similar no of residue in patch (e.g CYS, CYS = 2)
4637.test.res
All residues scored by patch analysis are stored in this file.
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Sum(Pint*Area)/sum(Area), Col 4: Sum(Psur*Area)/sum(Area), Col 5: Total Residue
4637.test.resALL

[For BCEP predicted results, please cite our websites http://fermi.utmb.edu/ http://curie.utmb.edu/ for your future publications (Negi et al., Bioinformatics, 23, 3397-3399, 2007 , Negi et al., J. Mol. Model., 13, 1157-1167, 2007; Negi et al., J. Mol. Model., 12, 921-929, 2006)]



List of B-cell epitopes predicted by BepiPred method using a window size of 9 amino acids
Peptides predicted from BepiPred method can be used to search related peptides in SDAP using PD search and Cross-React method.
Please note: BepiPred Epitopes are predicted using BepiPred webserver implemented in IEDB Analysis Resource at http://tools.iedb.org/main/bcell/
Cleck here for epitopes predicted by BepiPred method

Amb a 6 - Epitope Information from published data
No. Position Epitope Sequence Epitope Type View epitope Search epitope in SDAP PD search in SDAP Cross-React search
No epitope information found!
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