Complet list of 1lir hssp file
Complete list of 1lir.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1LIR
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 2014-05-03
HEADER NEUROTOXIN 02-APR-98 1LIR
COMPND MOL_ID: 1; MOLECULE: LQ2; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: LEIURUS QUINQUESTRIATUS HEBRAEUS; ORGA
AUTHOR J.G.RENISIO,Z.LU,E.BLANC,W.JIN,J.H.LEWIS,O.BORNET,H.DARBON
DBREF 1LIR A 2 37 UNP P45628 SCKD_LEIQH 2 37
SEQLENGTH 37
NCHAIN 1 chain(s) in 1LIR data set
NALIGN 25
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 : KAX12_LEIQH 1.00 1.00 2 37 24 59 36 0 0 59 P45628 Potassium channel toxin alpha-KTx 1.2 OS=Leiurus quinquestriatus hebraeus PE=1 SV=2
2 : KAX11_LEIQH 0.78 0.97 2 37 24 59 36 0 0 59 P13487 Potassium channel toxin alpha-KTx 1.1 OS=Leiurus quinquestriatus hebraeus PE=1 SV=4
3 : KAX1C_LEIQH 0.75 0.94 2 37 24 59 36 0 0 59 P59943 Potassium channel toxin alpha-KTx 1.12 OS=Leiurus quinquestriatus hebraeus PE=3 SV=1
4 : KAX1D_LEIQH 0.72 0.92 2 37 2 37 36 0 0 37 P59944 Potassium channel toxin alpha-KTx 1.13 OS=Leiurus quinquestriatus hebraeus PE=1 SV=1
5 : KAX16_MESMA 0.69 0.86 2 37 23 58 36 0 0 58 Q9NII5 Potassium channel toxin alpha-KTx 1.6 OS=Mesobuthus martensii PE=1 SV=1
6 : Q1EFP8_MESMA 0.69 0.86 2 37 23 58 36 0 0 58 Q1EFP8 Potassium channel toxin BmKTX2' OS=Mesobuthus martensii PE=3 SV=1
7 : KAX1X_MESMA 0.67 0.83 2 37 23 58 36 0 0 58 H2ER22 Potassium channel toxin alpha-KTx Kcug1a OS=Mesobuthus martensii PE=2 SV=1
8 : V9LLY8_MESMA 0.61 0.78 2 37 22 57 36 0 0 57 V9LLY8 Toxin BmTX4 OS=Mesobuthus martensii PE=3 SV=1
9 : KAX13_MESTA 0.60 0.77 2 36 2 36 35 0 0 37 P24663 Potassium channel toxin alpha-KTx 1.3 OS=Mesobuthus tamulus PE=1 SV=2
10 : A0RZD1_MESMA 0.58 0.78 2 37 22 57 36 0 0 57 A0RZD1 Potassium-channel toxin protein OS=Mesobuthus martensii GN=TX1 PE=3 SV=1
11 : KAX15_MESMA 0.58 0.78 2 37 22 57 36 0 0 57 Q9NII6 Potassium channel toxin alpha-KTx 1.5 OS=Mesobuthus martensii PE=1 SV=1
12 : KAX1E_MESMA 0.58 0.81 2 37 24 59 36 0 0 59 H2ETQ6 Potassium channel toxin alpha-KTx 1.14 OS=Mesobuthus martensii PE=2 SV=1
13 : KAX1F_MESMA 0.58 0.78 2 37 22 57 36 0 0 57 H2ER23 Potassium channel toxin alpha-KTx 1.15 OS=Mesobuthus martensii PE=2 SV=1
14 : KAX14_CENLM 0.57 0.74 2 36 2 36 35 0 0 37 P0C167 Potassium channel toxin alpha-KTx 1.4 OS=Centruroides limbatus PE=1 SV=1
15 : I6NWV2_HETLA 0.52 0.67 5 37 27 59 33 0 0 61 I6NWV2 Kv1.3 potassium channel blocker (Precursor) OS=Heterometrus laoticus GN=Tx3 PE=3 SV=1
16 : KAX1B_CENNO 0.51 0.69 2 36 2 36 35 0 0 37 P0C182 Potassium channel toxin alpha-KTx 1.11 OS=Centruroides noxius PE=1 SV=1
17 : KAX19_CENLM 0.50 0.68 2 35 2 35 34 0 0 36 P59848 Potassium channel toxin alpha-KTx 1.9 (Fragment) OS=Centruroides limbatus PE=1 SV=1
18 : KA232_VAEMS 0.47 0.68 3 36 2 34 34 1 1 35 P0DJ32 Potassium channel toxin alpha-KTx 23.2 OS=Vaejovis mexicanus smithi PE=1 SV=1
19 : KAX43_TITDI 0.47 0.64 2 37 2 37 36 0 0 37 P59925 Potassium channel toxin alpha-KTx 4.3 OS=Tityus discrepans PE=1 SV=1
20 : KA165_LEIQH 0.46 0.66 2 36 2 36 35 0 0 36 P45660 Potassium channel toxin alpha-KTx 16.5 OS=Leiurus quinquestriatus hebraeus PE=1 SV=1
21 : KA15S_CHATC 0.44 0.78 3 37 27 62 36 1 1 62 P0DJO5 Potassium channel toxin alpha-KTx Ctri9577 OS=Chaerilus tricostatus PE=2 SV=1
22 : KAX24_CENNO 0.44 0.75 2 37 2 37 36 0 0 38 Q9TXD1 Potassium channel toxin alpha-KTx 2.4 OS=Centruroides noxius PE=1 SV=1
23 : KAX28_CENEL 0.44 0.64 3 37 3 38 36 1 1 39 P0C161 Potassium channel toxin alpha-KTx 2.8 OS=Centruroides elegans PE=1 SV=1
24 : KAX21_CENNO 0.43 0.68 2 37 2 38 37 1 1 39 P08815 Potassium channel toxin alpha-KTx 2.1 OS=Centruroides noxius PE=1 SV=3
25 : KAX29_CENEL 0.43 0.65 2 37 2 38 37 1 1 39 P0C162 Potassium channel toxin alpha-KTx 2.9 OS=Centruroides elegans PE=1 SV=1
## ALIGNMENTS 1 - 25
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A X 0 0 57 0 0
2 2 A F - 0 0 87 22 18 FFFFFFFFFFFFFF FF FL I II
3 3 A T - 0 0 36 25 52 TTTTTTTTTTTTTI IIAIITIIII
4 4 A Q S S+ 0 0 183 25 39 QNDNNNNDDDDDDD DDANDNNNNN
5 5 A E - 0 0 62 26 40 EVVVVVVVVVVVVVIVVIVVQEVVV
6 6 A S - 0 0 76 26 62 SSSSSSSKDKKRKSSDKSKRPKKKK
7 7 A a - 0 0 7 26 0 CCCCCCCCCCCCCCCCCCCCCCCCC
8 8 A T S S+ 0 0 118 26 53 TTTTSSSTSTTSTSTTTVTYTFTTT
9 9 A A > - 0 0 42 26 64 ATTTAAAAVGGAAVGVTGGDSASSS
10 10 A S H > S+ 0 0 45 26 32 SSSSSSSSSSSSSSSSSSSSNTPPP
11 11 A N H > S+ 0 0 107 26 46 NKKKSSSKKKKSKKKKKKKRnSKKK
12 12 A Q H >> S+ 0 0 76 26 35 QEEEQQQQEQQKQEQEEEQQrQQQQ
13 13 A b H 3X S+ 0 0 0 26 0 CCCCCCCCCCCCCCCCCCCCCCCCC
14 14 A W H 3X S+ 0 0 74 26 30 WWWWWWWWWWWWWWYWWLLWRWLSL
15 15 A S H X S+ 0 0 0 26 0 CCCCCCCCCCCCCCCCCCCCCCCCC
18 18 A K H 3X S+ 0 0 108 26 35 KQQEKKEKKKKKNKKKKKKKIKKKK
19 19 A R H 3< S+ 0 0 171 26 70 RRRKKKKQDQQKQARAAAAKKKDED
20 20 A L H <4 S- 0 0 55 26 59 LLLLLLLMLMMLMAKAAQAVVALLL
21 21 A H H < S- 0 0 75 25 72 HHHYFFFFFFFFFVTFT.VTHIYYY
22 22 A N S < S+ 0 0 119 26 34 NNNNGGGGGGGGGGGGGGGGKGGGG
23 23 A T - 0 0 13 26 77 TTTTTTTKVKKTKTCVKCKSISPSP
24 24 A N S S+ 0 0 87 26 92 NSSSYYYPDPPYPDPDAKATNLHSH
25 25 A R + 0 0 166 26 80 RRIRRRRNRNNKNRNRASAQSQAAA
26 26 A G E -A 35 0A 2 26 10 GGGGGGGGGGGGGGAGGGGGGSggg
27 27 A K E -A 34 0A 55 26 0 KKKKKKKKKKKKKKKKKKKKKKkkk
28 28 A a E +A 33 0A 39 26 0 CCCCCCCCCCCCCCCCCCCCCCCCC
29 29 A M E > -A 32 0A 96 26 15 MMMMMMMMMMMKMMMMMMMQMMMMM
30 30 A N T 3 S- 0 0 132 26 16 NNNNNNNNGNNNNGNGNNNNNNNNN
31 31 A K T 3 S+ 0 0 137 26 64 KKKKSSSGKGGSGKKKKKGKSGGGG
32 32 A K E < -A 29 0A 70 26 14 KKKKKKKKKKKKKKSKKKKQKKKKK
33 33 A b E -A 28 0A 0 26 0 CCCCCCCCCCCCCCCCCCCCCCCCC
34 34 A R E -A 27 0A 80 26 36 RRRRRRRRRRRRRRKKKKKRVKKKK
35 35 A c E -A 26 0A 0 26 0 CCCCCCCCCCCCCCCCCCCCCCCCC
36 36 A Y 0 0 117 25 9 YYYYYYYYYYYYYYYY YYYHYYYY
37 37 A S 0 0 131 20 54 SSSSSSSS SSSS G T PNNNN
## 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 0 0 0 0 0.000 0 1.00
2 2 A 0 5 14 0 82 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 0 0 0.576 19 0.81
3 3 A 0 0 36 0 0 0 0 0 4 0 0 60 0 0 0 0 0 0 0 0 25 0 0 0.803 26 0.47
4 4 A 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 8 0 44 44 25 0 0 1.053 35 0.60
5 5 A 77 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 4 12 0 0 26 0 0 0.774 25 0.60
6 6 A 0 0 0 0 0 0 0 0 0 4 42 0 0 0 8 38 0 0 0 8 26 0 0 1.251 41 0.38
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 26 0 0 0.000 0 1.00
8 8 A 4 0 0 0 4 0 4 0 0 0 23 65 0 0 0 0 0 0 0 0 26 0 0 0.992 33 0.46
9 9 A 12 0 0 0 0 0 0 19 35 0 15 15 0 0 0 0 0 0 0 4 26 0 0 1.635 54 0.36
10 10 A 0 0 0 0 0 0 0 0 0 12 81 4 0 0 0 0 0 0 4 0 26 0 0 0.672 22 0.67
11 11 A 0 0 0 0 0 0 0 0 0 0 19 0 0 0 4 65 0 0 12 0 26 0 1 0.969 32 0.54
12 12 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 62 31 0 0 26 0 0 0.912 30 0.64
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 26 0 0 0.000 0 1.00
14 14 A 0 15 0 0 0 73 4 0 0 0 4 0 0 0 4 0 0 0 0 0 26 0 0 0.893 29 0.69
15 15 A 0 0 4 0 0 0 0 0 8 42 23 8 0 0 0 12 0 0 0 4 26 0 0 1.597 53 0.29
16 16 A 46 0 8 0 0 0 4 0 8 31 0 0 0 0 0 4 0 0 0 0 26 0 0 1.365 45 0.27
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 26 0 0 0.000 0 1.00
18 18 A 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 77 8 8 4 0 26 0 0 0.847 28 0.64
19 19 A 0 0 0 0 0 0 0 0 19 0 0 0 0 0 19 31 15 4 0 12 26 0 0 1.659 55 0.30
20 20 A 8 50 0 15 0 0 0 0 19 0 0 0 0 0 0 4 4 0 0 0 26 1 0 1.400 46 0.41
21 21 A 8 0 4 0 40 0 16 0 0 0 0 12 0 20 0 0 0 0 0 0 25 0 0 1.567 52 0.27
22 22 A 0 0 0 0 0 0 0 77 0 0 0 0 0 0 0 4 0 0 19 0 26 0 0 0.644 21 0.66
23 23 A 8 0 4 0 0 0 0 0 0 8 12 38 8 0 0 23 0 0 0 0 26 0 0 1.672 55 0.22
24 24 A 0 4 0 0 0 0 15 0 8 19 15 4 0 8 0 4 0 0 12 12 26 0 0 2.162 72 0.07
25 25 A 0 0 4 0 0 0 0 0 19 0 8 0 0 0 38 4 8 0 19 0 26 0 0 1.647 54 0.19
26 26 A 0 0 0 0 0 0 0 92 4 0 4 0 0 0 0 0 0 0 0 0 26 0 3 0.325 10 0.90
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 26 0 0 0.000 0 1.00
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 26 0 0 0.000 0 1.00
29 29 A 0 0 0 92 0 0 0 0 0 0 0 0 0 0 0 4 4 0 0 0 26 0 0 0.325 10 0.84
30 30 A 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 88 0 26 0 0 0.358 11 0.84
31 31 A 0 0 0 0 0 0 0 35 0 0 19 0 0 0 0 46 0 0 0 0 26 0 0 1.041 34 0.36
32 32 A 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 92 4 0 0 0 26 0 0 0.325 10 0.85
33 33 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 26 0 0 0.000 0 1.00
34 34 A 4 0 0 0 0 0 0 0 0 0 0 0 0 0 62 35 0 0 0 0 26 0 0 0.791 26 0.63
35 35 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 26 0 0 0.000 0 1.00
36 36 A 0 0 0 0 0 0 96 0 0 0 0 0 0 4 0 0 0 0 0 0 25 0 0 0.168 5 0.91
37 37 A 0 0 0 0 0 0 0 5 0 5 65 5 0 0 0 0 0 0 20 0 20 0 0 1.051 35 0.46
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
21 10 36 1 nTr
23 25 27 1 gAk
24 26 27 1 gAk
25 26 27 1 gAk
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