Complet list of 1v5a hssp file
Complete list of 1v5a.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1V5A
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 2014-05-11
HEADER TOXIN 21-NOV-03 1V5A
COMPND MOL_ID: 1; MOLECULE: COVALITOXIN-I; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY
AUTHOR T.KOHNO,T.SASAKI,K.SATO
DBREF 1V5A A 1 28 PDB 1V5A 1V5A 1 28
SEQLENGTH 28
NCHAIN 1 chain(s) in 1V5A data set
NALIGN 9
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 : JZT51_CHIGU 0.68 0.79 1 28 38 64 28 1 1 64 B1P1B4 U6-theraphotoxin-Cj1a OS=Chilobrachys guangxiensis PE=2 SV=1
2 : JZ708_CHIGU 0.67 0.81 2 28 2 27 27 1 1 27 P0CH53 Jingzhaotoxin F7-8.06 OS=Chilobrachys guangxiensis PE=1 SV=1
3 : TXH10_HAPSC 1Y29 0.64 0.82 1 28 41 68 28 0 0 68 P68424 Omega-theraphotoxin-Hh1a OS=Haplopelma schmidti PE=1 SV=2
4 : H10A1_HAPHA 0.61 0.82 1 28 38 65 28 0 0 65 D2Y2C4 Hainantoxin-X OS=Haplopelma hainanum PE=2 SV=1
5 : H10A2_HAPHA 0.61 0.82 1 28 38 65 28 0 0 65 D2Y2R1 Hainantoxin-X.2 OS=Haplopelma hainanum PE=3 SV=1
6 : H10A3_HAPHA 0.61 0.82 1 28 38 65 28 0 0 65 D2Y2R3 Hainantoxin-X.3 OS=Haplopelma hainanum PE=3 SV=1
7 : H10B1_HAPHA 0.57 0.79 1 28 44 71 28 0 0 71 D2Y2F2 Hainantoxin-X-2 OS=Haplopelma hainanum PE=2 SV=1
8 : H10C1_HAPHA 0.54 0.75 1 28 38 65 28 0 0 65 D2Y2R4 Hainantoxin-X-3 OS=Haplopelma hainanum PE=3 SV=1
9 : TXFK2_PSACA 0.54 0.75 1 28 38 65 28 0 0 65 P0C202 U2-theraphotoxin-Pc1a OS=Psalmopoeus cambridgei PE=1 SV=1
## ALIGNMENTS 1 - 9
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A R 0 0 228 9 38 R KKKKKKR
2 2 A a - 0 0 47 10 19 CCCCCCGYC
3 3 A L B -a 18 0A 22 10 64 EELLLLLLL
4 4 A P - 0 0 80 10 0 PPPPPPPPP
5 5 A S S S+ 0 0 79 10 64 SSPPPPPPA
6 6 A G S S+ 0 0 63 10 0 GGGGGGGGG
7 7 A K S S- 0 0 100 10 0 KKKKKKKKK
8 8 A A - 0 0 81 10 37 PPPPPPPPT
9 9 A b + 0 0 6 10 0 CCCCCCCCC
10 10 A A + 0 0 92 9 112 .RYYYYYYV
11 11 A G > - 0 0 28 10 82 RPGGGGGER
12 12 A V T 3 S+ 0 0 147 10 76 PLAAAAAAG
13 13 A T T 3 S+ 0 0 136 10 75 LMTTTTTTP
14 14 A Q S < S- 0 0 65 10 68 MRQQQQQQM
15 15 A K S S+ 0 0 189 9 30 R.KKKKKKR
16 16 A I S S- 0 0 60 10 7 IIIIIIIIV
17 17 A P - 0 0 87 10 0 PPPPPPPPP
18 18 A c B -a 3 0A 8 10 0 CCCCCCCCC
19 19 A a S S+ 0 0 84 10 0 CCCCCCCCC
20 20 A G S S- 0 0 48 10 0 GGGGGGGGG
21 21 A S - 0 0 68 10 85 SSVVVVVVS
22 22 A b E +B 27 0B 57 10 0 CCCCCCCCC
23 23 A V E > +B 26 0B 79 10 74 VVSSSSSSS
24 24 A R T 3 S- 0 0 228 10 57 RRHHHHHHQ
25 25 A G T 3 S+ 0 0 38 10 51 GGNNNNNNN
26 26 A K E < S-B 23 0B 113 10 51 KKKNNNNNK
27 27 A c E B 22 0B 0 10 0 CCCCCCCCC
28 28 A S 0 0 83 10 55 AATTTTTTT
## 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 33 67 0 0 0 0 9 0 0 0.637 21 0.62
2 2 A 0 0 0 0 0 0 10 10 0 0 0 0 80 0 0 0 0 0 0 0 10 0 0 0.639 21 0.80
3 3 A 0 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 10 0 0 0.500 16 0.35
4 4 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 0 10 60 30 0 0 0 0 0 0 0 0 0 10 0 0 0.898 29 0.35
6 6 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 10 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 0 10 80 0 10 0 0 0 0 0 0 0 0 10 0 0 0.639 21 0.63
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 10 1 0 0.000 0 1.00
10 10 A 11 0 0 0 0 0 67 0 11 0 0 0 0 0 11 0 0 0 0 0 9 0 0 1.003 33 -0.13
11 11 A 0 0 0 0 0 0 0 60 0 10 0 0 0 0 20 0 0 10 0 0 10 0 0 1.089 36 0.18
12 12 A 10 10 0 0 0 0 0 10 60 10 0 0 0 0 0 0 0 0 0 0 10 0 0 1.228 40 0.23
13 13 A 0 10 0 10 0 0 0 0 0 10 0 70 0 0 0 0 0 0 0 0 10 0 0 0.940 31 0.25
14 14 A 0 0 0 20 0 0 0 0 0 0 0 0 0 0 10 0 70 0 0 0 10 1 0 0.802 26 0.31
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 78 0 0 0 0 9 0 0 0.530 17 0.69
16 16 A 10 0 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.325 10 0.92
17 17 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 10 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 10 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
21 21 A 60 0 0 0 0 0 0 0 0 0 40 0 0 0 0 0 0 0 0 0 10 0 0 0.673 22 0.14
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
23 23 A 30 0 0 0 0 0 0 0 0 0 70 0 0 0 0 0 0 0 0 0 10 0 0 0.611 20 0.25
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 60 30 0 10 0 0 0 10 0 0 0.898 29 0.42
25 25 A 0 0 0 0 0 0 0 30 0 0 0 0 0 0 0 0 0 0 70 0 10 0 0 0.611 20 0.49
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 50 0 10 0 0 0.693 23 0.48
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
28 28 A 0 0 0 0 0 0 0 0 20 0 10 70 0 0 0 0 0 0 0 0 10 0 0 0.802 26 0.44
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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