Complet list of 1yz2 hssp file
Complete list of 1yz2.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1YZ2
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 2014-05-14
HEADER TOXIN 26-FEB-05 1YZ2
COMPND MOL_ID: 1; MOLECULE: DELTA-CONOTOXIN AM 2766; CHAIN: A
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: CONUS AMADIS; ORGANISM_TAXID: 198732;
AUTHOR S.P.SARMA,G.S.KUMAR,S.SUDARSLAL,P.IENGAR,S.K.SIKDAR, K.S.KRISHNAN,P.BA
DBREF 1YZ2 A 1 26 UNP P60179 CXD6_CONAA 1 26
SEQLENGTH 26
NCHAIN 1 chain(s) in 1YZ2 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 : CO66_CONAA 1YZ2 1.00 1.00 1 26 1 26 26 0 0 26 P60179 Delta-conotoxin Am2766 OS=Conus amadis PE=1 SV=1
2 : W4VSL1_CONVC 0.60 0.88 1 25 52 76 25 0 0 77 W4VSL1 O1_Vc6.41 prepropeptide OS=Conus victoriae PE=3 SV=1
3 : CO6B_CONTE 0.56 0.76 1 24 2 26 25 1 1 27 P24159 Delta-conotoxin TxVIB OS=Conus textile PE=1 SV=1
4 : CO7_CONTE 1F3K 0.56 0.80 1 25 52 76 25 0 0 77 P56714 Omega-conotoxin TxVII OS=Conus textile PE=1 SV=2
5 : O1613_CONTE 0.56 0.76 1 24 53 77 25 1 1 78 Q9U656 Conotoxin TxMKLT1-0111 OS=Conus textile PE=2 SV=1
6 : U6BZU5_CONMR 0.56 0.72 1 25 52 76 25 0 0 76 U6BZU5 Mr_precursor_089 OS=Conus marmoreus PE=3 SV=1
7 : CO16B_CONVC 0.54 0.69 1 25 52 77 26 1 1 77 P69759 Conotoxin Vc6b OS=Conus victoriae PE=1 SV=1
8 : W4VSL2_CONVC 0.54 0.69 1 25 52 77 26 1 1 77 W4VSL2 O1_Vc6.36 prepropeptide OS=Conus victoriae PE=3 SV=1
## ALIGNMENTS 1 - 8
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A a 0 0 112 9 0 CCCCCCCC
2 2 A K - 0 0 52 9 68 KRKKKIHH
3 3 A Q > - 0 0 147 9 59 QLQQQDEK
4 4 A A T 3 S+ 0 0 57 9 63 AGSASGEE
5 5 A G T 3 S+ 0 0 67 9 26 GAGDGGGG
6 6 A E S < S- 0 0 82 9 23 EEEEEEQQ
7 7 A S + 0 0 96 9 82 SSMPMMLL
8 8 A b - 0 0 25 9 0 CCCCCCCC
9 9 A D - 0 0 69 9 22 DDNDNDDD
10 10 A I S S+ 0 0 80 9 67 IVVVLPPP
11 11 A F S S+ 0 0 173 9 19 FILFLFFF
12 12 A S S S- 0 0 46 9 81 SSDSDSLL
13 13 A Q - 0 0 88 9 52 QQQLQSQQ
14 14 A N + 0 0 33 9 24 NNNDNDNN
15 15 A c > - 0 0 7 9 0 CCCCCCCC
16 16 A a T 3 S+ 0 0 79 9 0 CCCCCCCC
17 17 A V T 3 S+ 0 0 132 9 96 VQDTDSLL
18 18 A G S < S- 0 0 17 9 0 GGGGGGgg
19 19 A T + 0 0 118 9 96 TTYIYWnn
20 20 A d + 0 0 0 9 0 CCcCcCCC
21 21 A A S S- 0 0 57 9 48 AVvLvIVV
22 22 A F S S+ 0 0 160 9 37 FFFGFFFF
23 23 A I S S- 0 0 109 9 41 IFVVVFVV
24 24 A d + 0 0 1 9 0 CCCCCCCC
25 25 A I 0 0 105 7 29 IL M III
26 26 A E 0 0 57 2 0 E
## 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 0 100 0 0 0 0 0 0 0 9 0 0 0.000 0 1.00
2 2 A 0 0 11 0 0 0 0 0 0 0 0 0 0 22 11 56 0 0 0 0 9 0 0 1.149 38 0.31
3 3 A 0 11 0 0 0 0 0 0 0 0 0 0 0 0 0 11 56 11 0 11 9 0 0 1.303 43 0.41
4 4 A 0 0 0 0 0 0 0 22 33 0 22 0 0 0 0 0 0 22 0 0 9 0 0 1.369 45 0.37
5 5 A 0 0 0 0 0 0 0 78 11 0 0 0 0 0 0 0 0 0 0 11 9 0 0 0.684 22 0.74
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 78 0 0 9 0 0 0.530 17 0.77
7 7 A 0 22 0 33 0 0 0 0 0 11 33 0 0 0 0 0 0 0 0 0 9 0 0 1.311 43 0.18
8 8 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
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 78 9 0 0 0.530 17 0.78
10 10 A 33 11 22 0 0 0 0 0 0 33 0 0 0 0 0 0 0 0 0 0 9 0 0 1.311 43 0.32
11 11 A 0 22 11 0 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.849 28 0.80
12 12 A 0 22 0 0 0 0 0 0 0 0 56 0 0 0 0 0 0 0 0 22 9 0 0 0.995 33 0.18
13 13 A 0 11 0 0 0 0 0 0 0 0 11 0 0 0 0 0 78 0 0 0 9 0 0 0.684 22 0.48
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 78 22 9 0 0 0.530 17 0.76
15 15 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
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 22 22 0 0 0 0 0 0 0 0 11 11 0 0 0 0 11 0 0 22 9 0 0 1.735 57 0.03
18 18 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 9 0 2 0.000 0 1.00
19 19 A 0 0 11 0 0 11 22 0 0 0 0 33 0 0 0 0 0 0 22 0 9 0 0 1.523 50 0.03
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 9 0 2 0.000 0 1.00
21 21 A 56 11 11 0 0 0 0 0 22 0 0 0 0 0 0 0 0 0 0 0 9 0 0 1.149 38 0.51
22 22 A 0 0 0 0 89 0 0 11 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.349 11 0.63
23 23 A 56 0 22 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0.995 33 0.59
24 24 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
25 25 A 0 14 71 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0.796 26 0.70
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 2 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
3 21 22 1 cIv
5 21 73 1 cIv
7 19 70 1 gWn
8 19 70 1 gWn
//