Complet list of 1c2u hssp file
Complete list of 1c2u.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1C2U
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 2014-04-27
HEADER TOXIN 27-JUL-99 1C2U
COMPND MOL_ID: 1; MOLECULE: SYNTHETIC PEPTIDE ANALOGUE OF SHK TOXIN; CHAIN: A
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY S
AUTHOR M.W.PENNINGTON,M.D.LANIGAN,K.KALMAN,V.M.MANHIR,H.RAUER, C.T.MCVAUGH,D.
DBREF 1C2U A 1 35 UNP P29187 TXSHK_STOHE 1 35
SEQLENGTH 35
NCHAIN 1 chain(s) in 1C2U 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 : TXT1A_STIME 0.94 0.94 1 34 40 73 34 0 0 74 E2S063 Kappa-stichotoxin-Sm1a OS=Stichodactyla mertensii PE=3 SV=1
2 : TXT1A_STOHE 1ROO 0.94 0.94 1 34 1 34 34 0 0 35 P29187 Potassium channel toxin kappa-stichotoxin-She1a OS=Stoichactis helianthus PE=1 SV=1
3 : TXT1A_HETHE 0.91 0.94 1 34 41 74 34 0 0 75 E2S065 Kappa-thalatoxin-Hh1a OS=Heterodactyla hemprichii PE=3 SV=1
4 : TXT1A_STIGI 0.91 0.94 1 34 40 73 34 0 0 74 E2S061 Kappa-stichotoxin-Sg1a OS=Stichodactyla gigantea PE=3 SV=1
5 : TXT1A_STIHA 0.91 0.94 1 34 40 73 34 0 0 74 E2S062 Kappa-stichotoxin-Sha1a OS=Stichodactyla haddoni PE=3 SV=1
6 : TXT1A_THAAS 0.91 0.94 1 34 41 74 34 0 0 75 E2S066 Kappa-thalatoxin-Ta1a OS=Thalassianthus aster PE=3 SV=1
7 : TXT1A_CRYAD 0.88 0.94 1 34 41 74 34 0 0 75 E2S064 Kappa-thalatoxin-Sm1a OS=Cryptodendrum adhaesivum PE=3 SV=1
8 : TXT1A_HETMG 0.56 0.76 1 34 40 73 34 0 0 74 O16846 Potassium channel toxin kappa-stichotoxin-Hm1a OS=Heteractis magnifica PE=1 SV=2
9 : TXT1A_ANEER 0.53 0.74 1 34 49 82 34 0 0 83 Q0EAE5 Potassium channel toxin kappa-actitoxin-Aer1a OS=Anemonia erythraea 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 0 227 10 0 RRRRRRRRR
2 2 A S - 0 0 78 10 62 SSTSSTTTA
3 3 A X - 0 0 41 9 0 CCCCCCCCC
4 4 A I - 0 0 46 10 88 IIIIIIIKK
5 5 A D S S+ 0 0 113 10 0 DDDDDDDDD
6 6 A T S S+ 0 0 105 10 92 TTTTTTTLY
7 7 A I S S- 0 0 9 10 21 IIIIIIIIL
8 8 A P - 0 0 53 10 0 PPPPPPPPP
9 9 A K S S+ 0 0 177 10 60 KKKQQKKVK
10 10 A S S S- 0 0 47 10 0 SSSSSSSSS
11 11 A R S S+ 0 0 183 10 78 RRRRRRREE
12 12 A a + 0 0 2 10 0 CCCCCCCCC
13 13 A T >>> - 0 0 0 10 0 TTTTTTTTT
14 14 A A T 345S+ 0 0 2 10 67 AAAAAAADQ
15 15 A F T 345S- 0 0 108 10 21 FFFFFFFIF
16 16 A Q T X45S+ 0 0 58 10 57 QQQQQQQRR
17 17 A b T 3<5S- 0 0 6 10 0 CCCCCCCCC
18 18 A K T 3 < - 0 0 80 10 36 KKKKKKKRR
19 19 A H S X S+ 0 0 111 10 85 HHHHHHNTT
20 20 A S T 3 S+ 0 0 93 10 0 SSSSSSSSS
21 21 A A T >> + 0 0 1 10 18 MMMMMMMMM
22 22 A K T <4 S+ 0 0 109 10 0 KKKKKKKKK
23 23 A Y T 34 S+ 0 0 160 10 0 YYYYYYYYY
24 24 A R T <4 S+ 0 0 152 10 21 RRRRRRRRK
25 25 A L S < S- 0 0 23 10 36 LLLLLLLLY
26 26 A S S S- 0 0 74 10 66 SSSSSSSNT
27 27 A F S S+ 0 0 79 10 68 FFFFFFFLN
28 28 A a + 0 0 2 10 0 CCCCCCCCC
29 29 A R >> + 0 0 82 10 21 RRRRRRRRK
30 30 A K T 34 S+ 0 0 141 10 0 KKKKKKKKK
31 31 A T T 34 S+ 0 0 92 10 0 TTTTTTTTT
32 32 A b T <4 S- 0 0 11 10 0 CCCCCCCCC
33 33 A G S < S+ 0 0 79 10 0 GGGGGGGGG
34 34 A T 0 0 74 10 32 TTTTTTTST
35 35 A X 0 0 98 0 0
## 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 0 100 0 0 0 0 0 10 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 10 0 50 40 0 0 0 0 0 0 0 0 10 0 0 0.943 31 0.38
3 3 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
4 4 A 0 0 80 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 0 0 10 0 0 0.500 16 0.11
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 10 0 0 0.000 0 1.00
6 6 A 0 10 0 0 0 0 10 0 0 0 0 80 0 0 0 0 0 0 0 0 10 0 0 0.639 21 0.07
7 7 A 0 10 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.325 10 0.79
8 8 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
9 9 A 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 70 20 0 0 0 10 0 0 0.802 26 0.39
10 10 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 0 0 20 0 0 10 0 0 0.500 16 0.22
12 12 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
13 13 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
14 14 A 0 0 0 0 0 0 0 0 80 0 0 0 0 0 0 0 10 0 0 10 10 0 0 0.639 21 0.32
15 15 A 0 0 10 0 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.325 10 0.78
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 80 0 0 0 10 0 0 0.500 16 0.42
17 17 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
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 80 0 0 0 0 10 0 0 0.500 16 0.63
19 19 A 0 0 0 0 0 0 0 0 0 0 0 20 0 70 0 0 0 0 10 0 10 0 0 0.802 26 0.14
20 20 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
21 21 A 0 0 0 90 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.325 10 0.82
22 22 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
23 23 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 10 0 0 0 0 10 0 0 0.325 10 0.79
25 25 A 0 90 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0.325 10 0.63
26 26 A 0 0 0 0 0 0 0 0 0 0 80 10 0 0 0 0 0 0 10 0 10 0 0 0.639 21 0.33
27 27 A 0 10 0 0 80 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 10 0 0 0.639 21 0.32
28 28 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
29 29 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 10 0 0 0 0 10 0 0 0.325 10 0.79
30 30 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
31 31 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 10 0 0 0.000 0 1.00
32 32 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
33 33 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
34 34 A 0 0 0 0 0 0 0 0 0 0 10 90 0 0 0 0 0 0 0 0 10 0 0 0.325 10 0.67
35 35 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
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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