Complet list of 1pqr hssp file
Complete list of 1pqr.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1PQR
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 2014-05-06
HEADER TOXIN 18-JUN-03 1PQR
COMPND MOL_ID: 1; MOLECULE: ALPHA-A-CONOTOXIN EIVA; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS SEQUENCE OCCURS NATURAL
AUTHOR S.-W.CHI,K.-H.PARK,J.-E.SUK,B.M.OLIVERA,J.M.MCINTOSH,K.- H.HAN
DBREF 1PQR A 1 30 UNP P58782 CXVA_CONER 1 30
SEQLENGTH 30
NCHAIN 1 chain(s) in 1PQR 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 : CA4A_CONER 1PQR 0.83 0.83 1 30 1 30 30 0 0 30 P58782 Alpha-conotoxin EIVA OS=Conus ermineus PE=1 SV=1
2 : CA4B_CONER 0.77 0.77 1 30 1 30 30 0 0 30 P58783 Alpha-conotoxin EIVB OS=Conus ermineus PE=1 SV=1
3 : E2DEK7_CONPU 0.62 0.81 1 26 42 66 26 1 1 68 E2DEK7 Alpha conotoxin A-superfamily protein (Fragment) OS=Conus purpurascens PE=2 SV=1
## ALIGNMENTS 1 - 3
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A G 0 0 140 4 0 GGG
2 2 A a - 0 0 81 4 0 CCC
3 3 A b - 0 0 90 4 0 CCC
4 4 A G - 0 0 8 4 0 GGG
5 5 A P S S+ 0 0 80 4 71 PKS
6 6 A Y S S- 0 0 188 4 0 YYY
7 7 A X S S- 0 0 126 3 0 PPP
8 8 A N S S+ 0 0 143 4 0 NNN
9 9 A A S S- 0 0 98 4 0 AAA
10 10 A A S S+ 0 0 87 4 0 AAA
11 11 A b + 0 0 12 4 0 CCC
12 12 A H > - 0 0 93 4 0 HHH
13 13 A X T 3 S+ 0 0 60 3 0 PPP
14 14 A c T 3 S+ 0 0 26 4 0 CCC
15 15 A G < + 0 0 52 4 39 GGS
16 16 A a S S- 0 0 31 4 0 CCC
17 17 A K S S+ 0 0 190 4 37 KTK
18 18 A V S S+ 0 0 127 3 0 VV.
19 19 A G S S+ 0 0 63 4 34 GGD
20 20 A R - 0 0 88 4 0 RRR
21 21 A X >> - 0 0 48 3 0 PPP
22 22 A X H 3> S+ 0 0 135 3 65 PPS
23 23 A Y H 34 S+ 0 0 128 4 0 YYY
24 24 A c H <4 S+ 0 0 44 4 0 CCC
25 25 A D H < S+ 0 0 107 4 34 DDG
26 26 A R S < S- 0 0 167 4 47 RRQ
27 27 A X + 0 0 153 2 0 PP
28 28 A S - 0 0 121 3 0 SS
29 29 A G 0 0 76 3 0 GG
30 30 A G 0 0 136 3 0 GG
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
2 2 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
3 3 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
4 4 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
5 5 A 0 0 0 0 0 0 0 0 0 50 25 0 0 0 0 25 0 0 0 0 4 0 0 1.040 34 0.29
6 6 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
7 7 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 4 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
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 0 0 0 0 0 0 100 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 0 100 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 4 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 0 75 0 0 25 0 0 0 0 0 0 0 0 0 4 0 0 0.562 18 0.61
16 16 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
17 17 A 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 75 0 0 0 0 4 1 0 0.562 18 0.63
18 18 A 100 0 0 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
19 19 A 0 0 0 0 0 0 0 75 0 0 0 0 0 0 0 0 0 0 0 25 4 0 0 0.562 18 0.65
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 4 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 3 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 0 0 67 33 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.35
23 23 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
24 24 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
25 25 A 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 75 4 0 0 0.562 18 0.65
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 75 0 25 0 0 0 4 0 0 0.562 18 0.52
27 27 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
28 28 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
29 29 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
30 30 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
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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