Complet list of 2bbg hssp file
Complete list of 2bbg.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2BBG
THRESHOLD according to: t(L)=(290.15 * L ** -0.562) + 5
REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).
CONTACT Maintained at http://www.cmbi.ru.nl/ by Maarten L. Hekkelman
DATE file generated on 2014-05-16
HEADER ALLERGEN 24-APR-98 2BBG
COMPND MOL_ID: 1; MOLECULE: POLLEN ALLERGEN 5; CHAIN: A
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: AMBROSIA TRIFIDA; ORGANISM_COMMON: GIA
AUTHOR G.L.WARREN,C.J.TUNER,G.A.PETSKO,A.T.BRUNGER
DBREF 2BBG A 1 40 UNP P10414 MPAT5_AMBTR 34 73
SEQLENGTH 40
NCHAIN 1 chain(s) in 2BBG data set
NALIGN 3
NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein
NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken
NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry
NOTATION : %IDE: percentage of residue identity of the alignment
NOTATION : %SIM (%WSIM): (weighted) similarity of the alignment
NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence
NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein
NOTATION : LALI: length of the alignment excluding insertions and deletions
NOTATION : NGAP: number of insertions and deletions in the alignment
NOTATION : LGAP: total length of all insertions and deletions
NOTATION : LSEQ2: length of the entire sequence of the aligned protein
NOTATION : ACCNUM: SwissProt accession number
NOTATION : PROTEIN: one-line description of aligned protein
NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary
NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983)
NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments
NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of insertion in this sequence
NOTATION : dots (....) in the alignend sequence indicate points of deletion in this sequence
NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their
NOTATION : acid/amide form in proportion to their database frequencies
NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence)
NOTATION : NDEL: number of sequences with a deletion in the test protein at this position
NOTATION : NINS: number of sequences with an insertion in the test protein at this position
NOTATION : ENTROPY: entropy measure of sequence variability at this position
NOTATION : RELENT: relative entropy, i.e. entropy normalized to the range 0-100
NOTATION : WEIGHT: conservation weight
## PROTEINS : identifier and alignment statistics
NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN
1 : MPAT5_AMBTR 3BBG 1.00 1.00 1 40 34 73 40 0 0 73 P10414 Pollen allergen Amb t 5 OS=Ambrosia trifida PE=1 SV=2
2 : MPAA5_AMBEL 0.48 0.61 11 39 11 43 33 1 4 45 P02878 Pollen allergen Amb a 5 OS=Ambrosia artemisiifolia var. elatior PE=1 SV=1
3 : MPA5B_AMBPS 0.44 0.56 5 38 26 64 39 2 5 77 P43175 Pollen allergen Amb p 5b OS=Ambrosia psilostachya PE=1 SV=1
## ALIGNMENTS 1 - 3
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A D 0 0 170 2 0 D
2 2 A D + 0 0 139 2 0 D
3 3 A G - 0 0 44 2 0 G
4 4 A L - 0 0 128 2 0 L
5 5 A a - 0 0 39 3 0 C C
6 6 A Y E -A 18 0A 76 3 0 Y Y
7 7 A E E +A 17 0A 141 3 80 E A
8 8 A G S S- 0 0 37 3 53 G A
9 9 A T S > S+ 0 0 88 3 73 T G
10 10 A N T 3 S+ 0 0 128 3 80 N s
11 11 A b T 3 S- 0 0 32 4 0 CCc
12 12 A G S < S+ 0 0 60 4 0 GGG
13 13 A K > + 0 0 2 4 72 KEE
14 14 A V T 3 S+ 0 0 105 4 103 VKK
15 15 A G T 3 S+ 0 0 69 4 109 GRR
16 16 A K S < S- 0 0 90 4 99 KAG
17 17 A Y E -AB 7 29A 74 4 0 YYY
18 18 A c E -AB 6 28A 0 4 0 CCC
19 19 A d E + B 0 27A 9 4 30 CCS
20 20 A S - 0 0 20 4 0 SSS
21 21 A P S S+ 0 0 86 4 84 PDD
22 22 A I S S- 0 0 126 4 103 IPP
23 23 A G S S+ 0 0 47 4 0 GGG
24 24 A K S S+ 0 0 135 4 42 KRR
25 25 A Y S S- 0 0 148 4 0 YYY
26 26 A b + 0 0 57 4 0 CCC
27 27 A V E -B 19 0A 43 4 84 Vpp
28 28 A c E +B 18 0A 33 4 0 Ccc
29 29 A Y E -B 17 0A 68 4 0 YYY
30 30 A D S S+ 0 0 101 4 30 DEE
31 31 A S S >> S- 0 0 42 4 0 SSS
32 32 A K H 3> S+ 0 0 98 4 68 KSR
33 33 A A H 3> S+ 0 0 59 4 89 AEK
34 34 A I H <4>S+ 0 0 39 4 0 III
35 35 A a H X5S+ 0 0 0 4 0 CCC
36 36 A N H X5S+ 0 0 80 4 82 NSA
37 37 A K H ><5S+ 0 0 134 4 0 KKK
38 38 A N H 345S+ 0 0 66 4 38 NKN
39 39 A d H 3<< 0 0 34 3 0 CC
40 40 A T << 0 0 135 2 0 T
## SEQUENCE PROFILE AND ENTROPY
SeqNo PDBNo V L I M F W Y G A P S T C H R K Q E N D NOCC NDEL NINS ENTROPY RELENT WEIGHT
1 1 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 2 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 2 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
4 4 A 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 0 67 0 0 3 0 0 0.637 21 0.20
8 8 A 0 0 0 0 0 0 0 67 33 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.47
9 9 A 0 0 0 0 0 0 0 33 0 0 0 67 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.27
10 10 A 0 0 0 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 67 0 3 0 1 0.637 21 0.20
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 50 0 0 4 0 0 0.693 23 0.27
14 14 A 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 4 0 0 0.693 23 -0.03
15 15 A 0 0 0 0 0 0 0 50 0 0 0 0 0 0 50 0 0 0 0 0 4 0 0 0.693 23 -0.09
16 16 A 0 0 0 0 0 0 0 25 25 0 0 0 0 0 0 50 0 0 0 0 4 0 0 1.040 34 0.01
17 17 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 0 0 0 25 0 75 0 0 0 0 0 0 0 4 0 0 0.562 18 0.70
20 20 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 50 4 0 0 0.693 23 0.15
22 22 A 0 0 50 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 4 0 0 0.693 23 -0.03
23 23 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 0 0 0 0 4 0 0 0.693 23 0.58
25 25 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
27 27 A 50 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 4 0 2 0.693 23 0.15
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
29 29 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 50 4 0 0 0.693 23 0.70
31 31 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
32 32 A 0 0 0 0 0 0 0 0 0 0 25 0 0 0 25 50 0 0 0 0 4 0 0 1.040 34 0.32
33 33 A 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 25 0 25 0 0 4 0 0 1.040 34 0.10
34 34 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
35 35 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
36 36 A 0 0 0 0 0 0 0 0 25 0 25 0 0 0 0 0 0 0 50 0 4 0 0 1.040 34 0.17
37 37 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 4 0 0 0.000 0 1.00
38 38 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 75 0 4 0 0 0.562 18 0.62
39 39 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
40 40 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
2 18 28 4 pWQVVc
3 7 32 1 sIc
3 24 50 4 pWQVVc
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