Complet list of 1vib hssp file
Complete list of 1vib.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1VIB
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 NEUROTOXIN 25-NOV-96 1VIB
COMPND MOL_ID: 1; MOLECULE: NEUROTOXIN B-IV; CHAIN: A
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: CEREBRATULUS LACTEUS; ORGANISM_COMMON:
AUTHOR K.J.BARNHAM,T.R.DYKE,W.R.KEM,R.S.NORTON
DBREF 1VIB A 1 55 UNP P01525 NXB4_CERLA 1 55
SEQLENGTH 55
NCHAIN 1 chain(s) in 1VIB data set
NALIGN 2
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 : NXB4_CERLA 1VIB 0.98 0.98 1 55 1 55 55 0 0 55 P01525 Neurotoxin B-IV OS=Cerebratulus lacteus PE=1 SV=1
2 : NXB2_CERLA 0.73 0.91 1 55 1 55 55 0 0 55 P01526 Neurotoxin B-II OS=Cerebratulus lacteus PE=1 SV=1
## ALIGNMENTS 1 - 2
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A A 0 0 136 3 0 AA
2 2 A S + 0 0 107 3 0 SS
3 3 A A + 0 0 65 3 70 AS
4 4 A T + 0 0 101 3 0 TT
5 5 A W + 0 0 168 3 0 WW
6 6 A G S > S+ 0 0 18 3 0 GG
7 7 A A T 4 S+ 0 0 93 3 51 AG
8 8 A A T 4 S+ 0 0 70 3 70 AS
9 9 A Y T >4 S+ 0 0 51 3 0 YY
10 10 A X T >X + 0 0 58 2 0 PP
11 11 A A H 3> S+ 0 0 66 3 0 AA
12 12 A a H <4 S+ 0 0 41 3 0 CC
13 13 A E H X> S+ 0 0 5 3 0 EE
14 14 A N H >X S+ 0 0 73 3 0 NN
15 15 A N H 3X S+ 0 0 75 3 0 NN
16 16 A b H <> S+ 0 0 21 3 0 CC
17 17 A R H X S+ 0 0 148 3 0 KK
19 19 A K H >X S+ 0 0 101 3 70 KQ
20 20 A Y H 3X S+ 0 0 43 3 0 YY
21 21 A D H << S+ 0 0 79 3 0 DD
22 22 A L H << S+ 0 0 104 3 128 LD
23 23 A c H < S+ 0 0 22 3 0 CC
24 24 A I < + 0 0 30 3 0 II
25 25 A R > + 0 0 88 3 45 RK
26 26 A d T 5 + 0 0 10 3 0 CC
27 27 A Q T > 5S- 0 0 123 3 0 QQ
28 28 A G G > 5S+ 0 0 63 3 0 GG
29 29 A K G 3 5S+ 0 0 168 3 0 KK
30 30 A W G X> + 0 0 127 3 0 KK
34 34 A R H 3X + 0 0 144 3 0 RR
35 35 A G H 3> S+ 0 0 67 3 0 GG
36 36 A K H <> S+ 0 0 120 3 0 KK
37 37 A d H X S+ 0 0 0 3 0 CC
38 38 A A H >X S+ 0 0 36 3 0 AA
39 39 A A H 3X S+ 0 0 45 3 0 AA
40 40 A H H 3< S+ 0 0 82 3 0 HH
41 41 A c H XX S+ 0 0 0 3 0 CC
42 42 A I H 3X S+ 0 0 65 3 96 IA
43 43 A I H 3X S+ 0 0 77 3 25 IV
44 44 A Q H X> S+ 0 0 48 3 0 QQ
45 45 A K H 3X S+ 0 0 22 3 83 KT
46 46 A N H 3< S+ 0 0 68 3 83 NT
47 47 A N H X< S+ 0 0 106 3 77 NS
48 48 A b H >X>S+ 0 0 2 3 0 CC
49 49 A K T 3<5S+ 0 0 76 3 70 KN
50 50 A G T <45S+ 0 0 66 3 51 GD
51 51 A K T <45S+ 0 0 147 3 0 KK
52 52 A a T <5S+ 0 0 11 3 0 CC
53 53 A K < - 0 0 72 3 0 KK
54 54 A K 0 0 117 3 0 KK
55 55 A E 0 0 145 3 70 EH
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 67 0 33 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.29
4 4 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 100 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 33 67 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.48
8 8 A 0 0 0 0 0 0 0 0 67 0 33 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.29
9 9 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
10 10 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
11 11 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
12 12 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
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 3 0 0 0.000 0 1.00
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 3 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 3 0 0 0.000 0 1.00
16 16 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
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 3 0 0 0.000 0 1.00
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 33 0 0 0 3 0 0 0.637 21 0.29
20 20 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
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 3 0 0 0.000 0 1.00
22 22 A 0 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 3 0 0 0.637 21 -0.29
23 23 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
24 24 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
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 33 0 0 0 0 3 0 0 0.637 21 0.55
26 26 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
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 3 0 0 0.000 0 1.00
28 28 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
29 29 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
31 31 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
32 32 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
33 33 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
34 34 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 3 0 0 0.000 0 1.00
35 35 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
36 36 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
37 37 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
38 38 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
39 39 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
40 40 A 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 3 0 0 0.000 0 1.00
41 41 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
42 42 A 0 0 67 0 0 0 0 0 33 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.03
43 43 A 33 0 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.74
44 44 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 3 0 0 0.000 0 1.00
45 45 A 0 0 0 0 0 0 0 0 0 0 0 33 0 0 0 67 0 0 0 0 3 0 0 0.637 21 0.16
46 46 A 0 0 0 0 0 0 0 0 0 0 0 33 0 0 0 0 0 0 67 0 3 0 0 0.637 21 0.16
47 47 A 0 0 0 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 67 0 3 0 0 0.637 21 0.23
48 48 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
49 49 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 0 0 33 0 3 0 0 0.637 21 0.29
50 50 A 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 0 0 0 0 33 3 0 0 0.637 21 0.48
51 51 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
52 52 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
53 53 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
54 54 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 3 0 0 0.000 0 1.00
55 55 A 0 0 0 0 0 0 0 0 0 0 0 0 0 33 0 0 0 67 0 0 3 0 0 0.637 21 0.29
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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