Complet list of 1emx hssp file
Complete list of 1emx.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1EMX
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 2014-04-28
HEADER TOXIN 20-MAR-00 1EMX
COMPND MOL_ID: 1; MOLECULE: HETEROPODATOXIN 2; CHAIN: A; SYNONYM: HPTX2; ENGI
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: HETEROPODA VENATORIA; ORGANISM_COMMON:
AUTHOR C.BERNARD,C.LEGROS,G.FERRAT,U.BISHOFF,A.MARQUARDT,O.PONGS, H.DARBON
DBREF 1EMX A 1 30 UNP P58426 TXHP2_HETVE 1 30
SEQLENGTH 30
NCHAIN 1 chain(s) in 1EMX data set
NALIGN 8
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 : TXHP2_HETVE 1EMX 1.00 1.00 1 30 1 30 30 0 0 30 P58426 Kappa-sparatoxin-Hv1b OS=Heteropoda venatoria PE=1 SV=1
2 : TXU2_HETVE 0.93 0.96 1 27 1 27 27 0 0 30 P61792 Kappa-sparatoxin-Hv1d OS=Heteropoda venatoria PE=1 SV=1
3 : TXJ1_HETVE 0.85 0.93 1 27 1 27 27 0 0 29 P61791 Kappa-sparatoxin-Hv1e OS=Heteropoda venatoria PE=1 SV=1
4 : TXHP3_HETVE 0.62 0.90 2 30 1 29 29 0 0 31 P58427 Kappa-sparatoxin-Hv1c OS=Heteropoda venatoria PE=1 SV=1
5 : TXPR2_THRPR 0.60 0.68 3 27 2 26 25 0 0 30 P83476 Beta/omega-theraphotoxin-Tp2a OS=Thrixopelma pruriens PE=1 SV=1
6 : JZT45_CHIGU 0.56 0.67 3 29 55 81 27 0 0 83 P0C5X7 Kappa-theraphotoxin-Cj2a OS=Chilobrachys guangxiensis PE=1 SV=2
7 : JZT46_CHIGU 0.56 0.67 3 29 55 81 27 0 0 83 B1P1B6 Kappa-theraphotoxin-Cj2b OS=Chilobrachys guangxiensis PE=2 SV=1
8 : TX3_THEBL 0.50 0.56 1 28 1 32 32 2 4 35 P83747 Kappa-theraphotoxin-Tb1c OS=Theraphosa blondi PE=1 SV=1
## ALIGNMENTS 1 - 8
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A D 0 0 205 5 0 DDD D
2 2 A D + 0 0 132 6 15 DDDE D
3 3 A a - 0 0 34 9 0 CCCCCCCC
4 4 A G - 0 0 3 9 82 GGGGQQQL
5 5 A K > - 0 0 124 9 68 KGTTKKKG
6 6 A L T 3 S- 0 0 73 9 52 LLLLWWWM
7 7 A F T 3 S+ 0 0 100 9 43 FFFFMMMF
8 8 A S X - 0 0 33 9 52 SSSSWWWS
9 9 A G T 3 - 0 0 33 9 59 GGGGTTTS
10 10 A b T 3 - 0 0 56 9 0 CCCCCCCC
11 11 A D < - 0 0 85 9 25 DDDSDDDD
12 12 A T S > S+ 0 0 138 9 62 TSTTSSSP
13 13 A N T 3 S+ 0 0 164 9 63 NNSHEEEN
14 14 A A T 3 S+ 0 0 35 9 88 AAKARRRn
15 15 A D < - 0 0 94 9 56 DDDDKKKk
16 16 A c - 0 0 8 9 0 CCCCCCCC
17 17 A a > - 0 0 46 9 0 CCCCCCCC
18 18 A E T 3 S+ 0 0 171 9 28 EEEEEEEP
19 19 A G T 3 S+ 0 0 51 9 22 GGGGGGGN
20 20 A Y B < S-A 28 0A 60 9 59 YYYFMYYR
21 21 A V - 0 0 33 9 7 VVVIVVVV
22 22 A b + 0 0 76 9 0 CCCCCCCC
23 23 A R S S- 0 0 158 9 59 RRHKREEr
24 24 A L S S+ 0 0 121 9 32 LLLLLLLq
25 25 A W S S- 0 0 116 9 0 WWWWWWWW
26 26 A c + 0 0 3 9 0 CCCCCCCC
27 27 A K - 0 0 17 9 13 KKKRKKKK
28 28 A L B S-A 20 0A 97 6 43 L Y YYY
29 29 A D 0 0 125 5 53 D E NN
30 30 A W 0 0 207 3 6 W R
## 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 5 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 17 0 83 6 0 0 0.451 15 0.84
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
4 4 A 0 11 0 0 0 0 0 56 0 0 0 0 0 0 0 0 33 0 0 0 9 0 0 0.937 31 0.17
5 5 A 0 0 0 0 0 0 0 22 0 0 0 22 0 0 0 56 0 0 0 0 9 0 0 0.995 33 0.32
6 6 A 0 56 0 11 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.937 31 0.48
7 7 A 0 0 0 33 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.637 21 0.57
8 8 A 0 0 0 0 0 33 0 0 0 0 67 0 0 0 0 0 0 0 0 0 9 0 0 0.637 21 0.48
9 9 A 0 0 0 0 0 0 0 56 0 0 11 33 0 0 0 0 0 0 0 0 9 0 0 0.937 31 0.41
10 10 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 0 89 9 0 0 0.349 11 0.75
12 12 A 0 0 0 0 0 0 0 0 0 11 44 44 0 0 0 0 0 0 0 0 9 0 0 0.965 32 0.38
13 13 A 0 0 0 0 0 0 0 0 0 0 11 0 0 11 0 0 0 33 44 0 9 0 0 1.215 40 0.36
14 14 A 0 0 0 0 0 0 0 0 44 0 0 0 0 0 33 11 0 0 11 0 9 0 1 1.215 40 0.12
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 44 0 0 0 56 9 0 0 0.687 22 0.43
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 0 11 0 0 0 0 0 0 0 89 0 0 9 0 0 0.349 11 0.72
19 19 A 0 0 0 0 0 0 0 89 0 0 0 0 0 0 0 0 0 0 11 0 9 0 0 0.349 11 0.78
20 20 A 0 0 0 11 11 0 67 0 0 0 0 0 0 0 11 0 0 0 0 0 9 0 0 1.003 33 0.41
21 21 A 89 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.349 11 0.92
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 0 11 56 11 0 22 0 0 9 0 1 1.149 38 0.41
24 24 A 0 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0 9 0 0 0.349 11 0.68
25 25 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 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 9 0 0 0.000 0 1.00
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 89 0 0 0 0 9 0 0 0.349 11 0.86
28 28 A 0 33 0 0 0 0 67 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.637 21 0.57
29 29 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 40 40 5 0 0 1.055 35 0.46
30 30 A 0 0 0 0 0 67 0 0 0 0 0 0 0 0 33 0 0 0 0 0 3 0 0 0.637 21 0.93
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
8 15 15 1 nDk
8 24 25 3 rVRDq
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