Complet list of 1omb hssp file
Complete list of 1omb.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1OMB
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 2014-05-05
HEADER TOXIN 09-SEP-93 1OMB
COMPND MOL_ID: 1; MOLECULE: OMEGA-AGA-IVB; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: AGELENOPSIS APERTA; ORGANISM_TAXID: 69
AUTHOR H.YU,M.K.ROSEN,S.L.SCHREIBER
DBREF 1OMB A 1 48 UNP P37045 TOG4B_AGEAP 36 83
SEQLENGTH 34
NCHAIN 1 chain(s) in 1OMB data set
NALIGN 5
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 : TOG4B_AGEAP 1OMA 1.00 1.00 1 34 39 72 34 0 0 83 P37045 Omega-agatoxin-Aa4b OS=Agelenopsis aperta PE=1 SV=2
2 : TOG4A_AGEAP 1OAV 0.76 0.85 1 33 4 36 33 0 0 48 P30288 Omega-agatoxin-Aa4a OS=Agelenopsis aperta PE=1 SV=1
3 : TXC5_PHORI 0.53 0.63 4 33 4 31 30 1 2 34 P84000 U10-ctenitoxin-Pr1a (Fragment) OS=Phoneutria reidyi PE=1 SV=1
4 : TXG01_LYCSI 0.50 0.57 4 33 38 67 30 0 0 82 B6DD52 U16-lycotoxin-Ls1a OS=Lycosa singoriensis PE=2 SV=1
5 : TXG02_LYCSI 0.50 0.57 4 33 38 67 30 0 0 82 B6DD53 U16-lycotoxin-Ls1b OS=Lycosa singoriensis PE=2 SV=1
## ALIGNMENTS 1 - 5
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 4 A a 0 0 108 3 0 CC
2 5 A I B +a 16 0A 21 3 0 II
3 6 A A + 0 0 86 3 0 AA
4 7 A E S > S- 0 0 145 6 60 EKDKK
5 8 A D T 3 S- 0 0 141 6 49 DDAEE
6 9 A Y T 3 S+ 0 0 142 6 0 YYYYY
7 10 A G < - 0 0 7 6 81 GGKQQ
8 11 A K B +B 32 0B 143 6 73 KRSWW
9 12 A b - 0 0 13 6 0 CCCCC
10 13 A T > - 0 0 90 5 84 TK.DD
11 14 A W T 3 S+ 0 0 210 5 0 WW.WW
12 15 A G T 3 S+ 0 0 89 6 58 GGDNN
13 16 A G S < S- 0 0 46 6 65 GGSTT
14 17 A T S S- 0 0 80 6 101 TTLRR
15 18 A K - 0 0 143 6 65 KPKPP
16 19 A c B > -a 2 0A 9 6 0 CCCCC
17 20 A a T 3 S+ 0 0 48 6 0 CCCCC
18 21 A R T 3 S- 0 0 226 6 81 RRNDD
19 22 A G < + 0 0 46 6 54 GGNNN
20 23 A R - 0 0 125 6 80 RRRII
21 24 A P - 0 0 105 6 74 PGTSS
22 25 A b E -C 33 0B 27 6 0 CCCCC
23 26 A R E -C 32 0B 174 6 80 RIMII
24 27 A d - 0 0 31 6 0 CCCCC
25 28 A S - 0 0 63 6 0 SSSSS
26 29 A M S S+ 0 0 189 6 93 MIMWW
27 30 A I S S- 0 0 119 6 19 IMIII
28 31 A G S S+ 0 0 59 6 0 GGGGG
29 32 A T S S+ 0 0 85 6 0 TTTTT
30 33 A N S S- 0 0 87 6 0 NNNNN
31 34 A d - 0 0 11 6 0 CCCCC
32 35 A E E -BC 8 23B 72 6 36 EETEE
33 36 A c E C 0 22B 4 6 0 CCCCC
34 37 A T 0 0 76 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 4 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
2 5 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
3 6 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
4 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 33 0 17 6 0 0 1.011 33 0.39
5 8 A 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 33 0 50 6 0 0 1.011 33 0.50
6 9 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
7 10 A 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 17 33 0 0 0 6 0 0 1.011 33 0.18
8 11 A 0 0 0 0 0 33 0 0 0 0 17 0 0 0 17 33 0 0 0 0 6 0 0 1.330 44 0.27
9 12 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 1 0 0.000 0 1.00
10 13 A 0 0 0 0 0 0 0 0 0 0 0 40 0 0 0 20 0 0 0 40 5 0 0 1.055 35 0.15
11 14 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0.000 0 1.00
12 15 A 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 33 17 6 0 0 1.011 33 0.41
13 16 A 0 0 0 0 0 0 0 50 0 0 17 33 0 0 0 0 0 0 0 0 6 0 0 1.011 33 0.35
14 17 A 0 17 0 0 0 0 0 0 0 0 0 50 0 0 33 0 0 0 0 0 6 0 0 1.011 33 -0.01
15 18 A 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0 50 0 0 0 0 6 0 0 0.693 23 0.35
16 19 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
17 20 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
18 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 17 33 6 0 0 1.011 33 0.18
19 22 A 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 50 0 6 0 0 0.693 23 0.46
20 23 A 0 0 33 0 0 0 0 0 0 0 0 0 0 0 67 0 0 0 0 0 6 0 0 0.637 21 0.19
21 24 A 0 0 0 0 0 0 0 17 0 33 33 17 0 0 0 0 0 0 0 0 6 0 0 1.330 44 0.26
22 25 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
23 26 A 0 0 50 17 0 0 0 0 0 0 0 0 0 0 33 0 0 0 0 0 6 0 0 1.011 33 0.19
24 27 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
25 28 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
26 29 A 0 0 17 50 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1.011 33 0.07
27 30 A 0 0 83 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.451 15 0.80
28 31 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
29 32 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
30 33 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 6 0 0 0.000 0 1.00
31 34 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
32 35 A 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 83 0 0 6 0 0 0.451 15 0.64
33 36 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
34 37 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
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