Complet list of 1i2v hssp file
Complete list of 1i2v.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1I2V
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 2014-04-30
HEADER ANTIMICROBIAL PROTEIN 12-FEB-01 1I2V
COMPND MOL_ID: 1; MOLECULE: DEFENSIN HELIOMICIN; CHAIN: A; ENGINEERED: YES; M
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: HELIOTHIS VIRESCENS; ORGANISM_COMMON:
AUTHOR M.LAMBERTY,A.CAILLE,C.LANDON,S.TASSIN-MOINDROT,C.HETRU, P.BULET,F.VOVE
DBREF 1I2V A 1 44 UNP P81544 DEFN_HELVI 1 44
SEQLENGTH 44
NCHAIN 1 chain(s) in 1I2V data set
NALIGN 14
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 : D3G9G5_HELVI 0.95 0.95 1 44 30 73 44 0 0 73 D3G9G5 Heliomicin OS=Heliothis virescens PE=4 SV=1
2 : DEFN_HELVI 1I2U 0.95 0.95 1 44 1 44 44 0 0 44 P81544 Defensin heliomicin OS=Heliothis virescens PE=1 SV=1
3 : E5D602_HELAM 0.95 0.95 1 44 30 73 44 0 0 73 E5D602 Galiomicin OS=Helicoverpa armigera GN=Gali PE=4 SV=1
4 : S5TR00_HELZE 0.93 0.93 1 44 25 68 44 0 0 68 S5TR00 Galiomicin (Fragment) OS=Helicoverpa zea GN=gali PE=4 SV=1
5 : DEFN_ARCDE 1P00 0.91 0.95 1 44 1 44 44 0 0 44 P84156 Defensin ARD1 OS=Archaeoprepona demophon PE=1 SV=1
6 : DEF2_GALME 0.88 0.91 1 43 1 43 43 0 0 44 P85215 Defensin-like peptide OS=Galleria mellonella PE=1 SV=1
7 : DEF1_GALME 0.86 0.88 1 43 30 72 43 0 0 72 P85213 Defensin OS=Galleria mellonella PE=1 SV=2
8 : E5LBK2_MANSE 0.86 0.98 1 44 27 70 44 0 0 70 E5LBK2 Defensin 2 OS=Manduca sexta PE=4 SV=1
9 : V9MG79_COTVE 0.84 0.91 1 44 30 73 44 0 0 73 V9MG79 Defensin 3 OS=Cotesia vestalis GN=def-3 PE=4 SV=1
10 : R4IXW7_BEMTA 0.82 0.84 1 44 30 73 44 0 0 75 R4IXW7 Defensin OS=Bemisia tabaci GN=Def PE=4 SV=1
11 : V9MMW2_COTVE 0.77 0.85 4 43 33 72 40 0 0 73 V9MMW2 Defensin 2 OS=Cotesia vestalis GN=def-2 PE=4 SV=1
12 : R4H5E1_MESEU 0.42 0.51 1 43 13 53 43 2 2 72 R4H5E1 Sodium channel toxin 17 (Fragment) OS=Mesobuthus eupeus PE=2 SV=1
13 : E4VP32_MESEU 0.40 0.49 1 43 27 67 45 3 6 86 E4VP32 Venom sodium channel toxin-5 OS=Mesobuthus eupeus PE=3 SV=1
14 : I6MRK9_CAERE 0.40 0.60 1 44 17 54 45 3 8 54 I6MRK9 Mycin-7 (Precursor) OS=Caenorhabditis remanei PE=2 SV=1
## ALIGNMENTS 1 - 14
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A D 0 0 135 14 15 DDDDDDDDDD DDG
2 2 A K E -A 42 0A 100 14 25 KKKKKKTKKV KKK
3 3 A L E -A 41 0A 82 14 43 LLLLLLLLLL YYF
4 4 A I E - 0 0A 22 15 69 IIIIIIIIIIITTK
5 5 A G E -A 40 0A 5 15 0 GGGGGGGGGGGGGG
6 6 A S E -Ab 39 14A 11 15 45 SSSSSSSSSSSCCP
7 7 A a + 0 0 39 15 70 CCCCCCCCCCCKEC
8 8 A V > - 0 0 47 14 0 VVVVVVVVVVVVV.
9 9 A W T 3 S+ 0 0 220 14 0 WWWWWWWWWWWWW.
10 10 A G T 3 S+ 0 0 68 14 54 GGGGGGGGGGGCC.
11 11 A A S X S- 0 0 47 14 64 AAAAAAAAAGGVV.
12 12 A V T 3 S+ 0 0 112 14 40 VVVVVTTVTVVII.
13 13 A N T 3 S- 0 0 101 14 7 NNNNNNNDNNNNN.
14 14 A Y B < -b 6 0A 63 15 53 YYYYYYYYYYYNNY
15 15 A T + 0 0 8 15 70 TTTTTTTTTTVEEs
16 16 A S S S+ 0 0 73 13 0 SSSSSSSSSSS..s
17 17 A D >> + 0 0 83 15 58 DDDDNDDNNDNSSN
18 18 A b H 3> S+ 0 0 17 15 0 CCCCCCCCCCCCCC
19 19 A N H 3> S+ 0 0 73 15 32 NNNNNNNNNLLNNN
20 20 A G H <> S+ 0 0 20 15 41 GGGGAAAAAKDGGG
21 21 A E H X S+ 0 0 42 15 31 EEEEEEEEEEEEEV
22 22 A c H ><>S+ 0 0 0 15 0 CCCCCCCCCCCCCC
23 23 A L H ><5S+ 0 0 109 15 35 KKKKKKKVKKKKKR
24 24 A L H 3<5S+ 0 0 123 15 38 RRRRRRRRRRRRRD
25 25 A R T <<5S- 0 0 114 15 27 RRRRRRRRRRRRRE
26 26 A G T < 5S+ 0 0 65 15 0 GGGGGGGGGGGGGG
27 27 A Y < - 0 0 67 14 75 YYYYYYYFFYYG.H
28 28 A K - 0 0 109 14 47 KKKKKKKKKKKY.K
29 29 A G S S- 0 0 28 14 67 GGGGGGGGGGGY.S
30 30 A G - 0 0 14 15 0 GGGGGGGGGGGGGG
31 31 A H E -C 41 0A 70 15 40 HHHHHHHHHHHYYH
32 32 A a E -C 40 0A 50 15 8 CCCCCCCCCCCCYC
33 33 A G - 0 0 15 14 20 GGGGGGGGGGG.gS
34 34 A S S S+ 0 0 125 15 87 SSSSSSSSSSSYyH
35 35 A F S S+ 0 0 207 15 20 FFFFFFFFFAFFFW
36 36 A A > - 0 0 54 15 95 AAAAAWLAWLAWWS
37 37 A N T 3 S+ 0 0 136 15 55 NNNNNNNNNNNKKG
38 38 A V T 3 S+ 0 0 68 15 58 VVVVVVVVVVNLLA
39 39 A N E < -A 6 0A 54 14 68 NNNNNNNNNNIAA.
40 40 A b E -AC 5 32A 0 15 0 CCCCCCCCCCCCCC
41 41 A W E -AC 3 31A 84 15 6 WWWWWWWWWWWFFW
42 42 A c E -A 2 0A 3 15 8 CCCGCCCCCCCCCC
43 43 A E 0 0 114 15 34 EEEEEEEEEEEQQD
44 44 A T 0 0 85 10 0 TTTTT TTT T
## 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 7 0 0 0 0 0 0 0 0 0 0 0 93 14 0 0 0.257 8 0.84
2 2 A 7 0 0 0 0 0 0 0 0 0 0 7 0 0 0 86 0 0 0 0 14 0 0 0.509 16 0.75
3 3 A 0 79 0 0 7 0 14 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0.656 21 0.56
4 4 A 0 0 80 0 0 0 0 0 0 0 0 13 0 0 0 7 0 0 0 0 15 0 0 0.628 20 0.30
5 5 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 7 80 0 13 0 0 0 0 0 0 0 15 0 0 0.628 20 0.54
7 7 A 0 0 0 0 0 0 0 0 0 0 0 0 87 0 0 7 0 7 0 0 15 1 0 0.485 16 0.29
8 8 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 86 0 0 0 0 14 0 0 0 0 0 0 0 14 0 0 0.410 13 0.45
11 11 A 14 0 0 0 0 0 0 14 71 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0.796 26 0.36
12 12 A 64 0 14 0 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 0 14 0 0 0.892 29 0.60
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 7 14 0 0 0.257 8 0.93
14 14 A 0 0 0 0 0 0 87 0 0 0 0 0 0 0 0 0 0 0 13 0 15 0 0 0.393 13 0.46
15 15 A 7 0 0 0 0 0 0 0 0 0 7 73 0 0 0 0 0 13 0 0 15 2 1 0.857 28 0.30
16 16 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
17 17 A 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 33 53 15 0 0 0.970 32 0.41
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
19 19 A 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 87 0 15 0 0 0.393 13 0.68
20 20 A 0 0 0 0 0 0 0 53 33 0 0 0 0 0 0 7 0 0 0 7 15 0 0 1.063 35 0.59
21 21 A 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 0 0 15 0 0 0.245 8 0.69
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
23 23 A 7 7 0 0 0 0 0 0 0 0 0 0 0 0 7 80 0 0 0 0 15 0 0 0.720 24 0.64
24 24 A 0 7 0 0 0 0 0 0 0 0 0 0 0 0 87 0 0 0 0 7 15 0 0 0.485 16 0.61
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 0 0 7 0 0 15 0 0 0.245 8 0.72
26 26 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 15 1 0 0.000 0 1.00
27 27 A 0 0 0 0 14 0 71 7 0 0 0 0 0 7 0 0 0 0 0 0 14 0 0 0.895 29 0.25
28 28 A 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 93 0 0 0 0 14 0 0 0.257 8 0.52
29 29 A 0 0 0 0 0 0 7 86 0 0 7 0 0 0 0 0 0 0 0 0 14 0 0 0.509 16 0.32
30 30 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
31 31 A 0 0 0 0 0 0 13 0 0 0 0 0 0 87 0 0 0 0 0 0 15 0 0 0.393 13 0.60
32 32 A 0 0 0 0 0 0 7 0 0 0 0 0 93 0 0 0 0 0 0 0 15 1 0 0.245 8 0.92
33 33 A 0 0 0 0 0 0 0 93 0 0 7 0 0 0 0 0 0 0 0 0 14 0 1 0.257 8 0.80
34 34 A 0 0 0 0 0 0 13 0 0 0 80 0 0 7 0 0 0 0 0 0 15 0 0 0.628 20 0.13
35 35 A 0 0 0 0 87 7 0 0 7 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.485 16 0.79
36 36 A 0 13 0 0 0 27 0 0 53 0 7 0 0 0 0 0 0 0 0 0 15 0 0 1.137 37 0.05
37 37 A 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 13 0 0 80 0 15 0 0 0.628 20 0.45
38 38 A 73 13 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 7 0 15 1 0 0.857 28 0.41
39 39 A 0 0 7 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 79 0 14 0 0 0.656 21 0.32
40 40 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
41 41 A 0 0 0 0 13 87 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.393 13 0.93
42 42 A 0 0 0 0 0 0 0 7 0 0 0 0 93 0 0 0 0 0 0 0 15 0 0 0.245 8 0.92
43 43 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 80 0 7 15 0 0 0.628 20 0.66
44 44 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
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
13 30 56 2 gYCy
14 10 26 1 sDs
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