Complet list of 1n4n hssp file
Complete list of 1n4n.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1N4N
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 2014-05-04
HEADER PLANT PROTEIN 01-NOV-02 1N4N
COMPND MOL_ID: 1; MOLECULE: FLORAL DEFENSIN-LIKE PROTEIN 1; CHAIN: A; FRAGMEN
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: PETUNIA X HYBRIDA; ORGANISM_TAXID: 410
AUTHOR B.J.C.JANSSEN,H.J.SCHIRRA,F.T.LAY,M.A.ANDERSON,D.J.CRAIK
DBREF 1N4N A 1 47 UNP Q8H6Q1 DEF1_PETHY 26 72
SEQLENGTH 47
NCHAIN 1 chain(s) in 1N4N data set
NALIGN 18
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 : DEF1_PETHY 1N4N 1.00 1.00 1 47 26 72 47 0 0 103 Q8H6Q1 Floral defensin-like protein 1 OS=Petunia hybrida GN=D1 PE=1 SV=1
2 : E9NPZ9_PETHY 1.00 1.00 1 47 26 72 47 0 0 103 E9NPZ9 Flower-derived plant defensin 1 OS=Petunia hybrida GN=Def1 PE=4 SV=1
3 : E9NQ00_PETHY 0.78 0.86 1 47 26 74 49 1 2 101 E9NQ00 Flower-derived plant defensin 2 OS=Petunia hybrida GN=Def2 PE=4 SV=1
4 : DEF2_PETHY 0.76 0.86 1 47 26 74 49 1 2 101 Q8H6Q0 Floral defensin-like protein 2 OS=Petunia hybrida GN=D2 PE=1 SV=1
5 : O24105_9SOLA 0.64 0.73 3 47 28 72 45 0 0 105 O24105 Gamma-thionin OS=Nicotiana excelsior GN=NeThio2 PE=4 SV=1
6 : DEF_NICAL 4AB0 0.62 0.71 3 47 28 72 45 0 0 105 Q8GTM0 Flower-specific defensin OS=Nicotiana alata GN=D1 PE=1 SV=1
7 : DEF_TOBAC 1MR4 0.60 0.71 3 47 28 72 45 0 0 105 P32026 Defensin-like protein OS=Nicotiana tabacum GN=FST PE=1 SV=1
8 : B2BLV8_TOBAC 0.58 0.71 3 47 28 72 45 0 0 105 B2BLV8 Putative flower-specific thionin OS=Nicotiana tabacum PE=4 SV=1
9 : DEF1_NICPA 0.57 0.68 1 47 27 73 47 0 0 106 O24115 Defensin-like protein 1 OS=Nicotiana paniculata GN=THIO1 PE=2 SV=1
10 : Q6H1M1_NICAT 0.57 0.70 1 47 27 73 47 0 0 106 Q6H1M1 Gamma-thionin OS=Nicotiana attenuata PE=4 SV=1
11 : Q40128_SOLLC 0.49 0.67 3 47 29 73 45 0 0 105 Q40128 Flower-specific gamma-thionin-like protein/acidic protein (Precursor) OS=Solanum lycopersicum GN=Solyc07g006380.2 PE=4 SV=1
12 : K4D7E6_SOLLC 0.42 0.62 3 47 29 73 45 0 0 105 K4D7E6 Uncharacterized protein OS=Solanum lycopersicum GN=Solyc11g028040.1 PE=4 SV=1
13 : K4D7E8_SOLLC 0.42 0.62 3 47 29 73 45 0 0 105 K4D7E8 Uncharacterized protein OS=Solanum lycopersicum GN=Solyc11g028070.1 PE=4 SV=1
14 : Q9XHE3_CAPCH 0.42 0.56 1 47 28 75 48 1 1 107 Q9XHE3 Putative gamma-thionin OS=Capsicum chinense PE=4 SV=1
15 : C1K3M7_VIGUN 0.39 0.63 2 47 33 78 46 0 0 78 C1K3M7 Defensin (Precursor) OS=Vigna unguiculata GN=PDEF PE=4 SV=1
16 : K4BP03_SOLLC 0.39 0.61 2 47 28 73 46 0 0 73 K4BP03 Uncharacterized protein OS=Solanum lycopersicum GN=Solyc04g008470.2 PE=4 SV=1
17 : K7L950_SOYBN 0.39 0.61 2 47 33 78 46 0 0 84 K7L950 Uncharacterized protein OS=Glycine max PE=4 SV=1
18 : M1CVT4_SOLTU 0.39 0.61 2 47 28 73 46 0 0 73 M1CVT4 Uncharacterized protein OS=Solanum tuberosum GN=PGSC0003DMG400029484 PE=4 SV=1
## ALIGNMENTS 1 - 18
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A A 0 0 112 8 69 AAAG SS N
2 2 A T - 0 0 114 12 18 TTTT TT ITTTT
3 3 A a E -A 45 0A 53 19 0 CCCCCCCCCCCCCCCCCC
4 4 A K E +A 44 0A 97 19 38 KKKKKKKKKKKKKKEEEE
5 5 A A E -A 43 0A 41 19 58 AAAATTTTAAASSTSSSS
6 6 A E E -A 42 0A 67 19 57 EEEEEEEEEEPTTTQQQQ
7 7 A b > - 0 0 3 19 25 CCCCSSSSSSSSSSSSSS
8 8 A P T 3 S+ 0 0 110 19 73 PPPPNNNNNNQQQKHHHH
9 9 A T T 3 S+ 0 0 107 19 58 TTTTTTTTTTTTTHRRRK
10 10 A W < + 0 0 44 19 8 WWWWFFFFFFFFFFFYFY
11 11 A D + 0 0 119 19 71 DDDEPPPPPEPKKKKKKK
12 12 A S S S- 0 0 86 19 18 SSGGGGGGGGGGGGGGGG
13 13 A V - 0 0 104 19 73 VVIIIIIILFLLLLPPPP
14 14 A c + 0 0 3 19 0 CCCCCCCCCCCCCCCCCC
15 15 A I + 0 0 155 19 36 IIIIIIIIIVFFFFVVLV
16 16 A N > - 0 0 77 19 80 NNNNTTTTTTMTTASRSR
17 17 A K H > S+ 0 0 89 19 43 KKKKKKKKKKDDDDDKDK
18 18 A K H > S+ 0 0 156 19 75 KKGAPPPPPPSSSSTNTS
19 19 A P H > S+ 0 0 55 19 69 PPPPPPPPPPSSSKNNNN
20 20 A d H X S+ 0 0 0 19 0 CCCCCCCCCCCCCCCCCC
21 21 A V H X S+ 0 0 24 19 89 VVVVRRRRRRRRRRAAGG
22 22 A A H X S+ 0 0 48 19 64 AAKKKKKKKRKKKKSNSA
23 23 A b H X S+ 0 0 11 19 71 CCCCAAAAAAYAAVVVVV
24 24 A e H <>S+ 0 0 0 19 0 CCCCCCCCCCCCCCCCCC
25 25 A K H ><5S+ 0 0 137 19 84 KKkkIIIILLIVViRKRQ
26 26 A K H 3<5S+ 0 0 148 19 71 KKppKSSSSKKTTeTTTT
27 27 A A T 3<5S- 0 0 25 19 28 AAEEEEEEEEEEEDEEEE
28 28 A K T < 5S+ 0 0 169 19 57 KKKKKKKKKKKEEKRGGG
29 29 A F < - 0 0 45 19 0 FFFFFFFFFFFFFFFFFF
30 30 A S S S- 0 0 64 19 49 SSTTTTTTTTTTTESSST
31 31 A D E -B 44 0A 59 19 32 DDDDDDDDDDGGGDGGGG
32 32 A G E -B 43 0A 0 19 0 GGGGGGGGGGGGGGGGGG
33 33 A H E -B 42 0A 69 19 18 HHHHHHHHKKHHHHHHHH
34 34 A c E -B 41 0A 23 19 0 CCCCCCCCCCCCCCCCCC
35 35 A S - 0 0 22 19 45 SSSSSSSSSSSSSSRRRR
36 36 A K S S+ 0 0 195 19 51 KKKKKKKKKKKKKKGGGG
37 37 A I S S- 0 0 155 19 35 IIVIIILLIILLLLFFFV
38 38 A L S S- 0 0 99 19 87 LLLLLLLLLLQQQQRRSR
39 39 A R + 0 0 92 19 0 RRRRRRRRRRRRRRRRRR
40 40 A R - 0 0 76 19 18 RRRRRRRRRRKKKKRRRR
41 41 A d E - B 0 34A 0 19 0 CCCCCCCCCCCCCCCCCC
42 42 A L E -AB 6 33A 23 19 15 LLLLLLLLIILLLLLFFF
43 43 A e E -AB 5 32A 0 19 0 CCCCCCCCCCCCCCCCCC
44 44 A T E +AB 4 31A 33 19 36 TTTTTTTAYYTTTTTATT
45 45 A K E -A 3 0A 50 19 0 KKKKKKKKKKKKKKKKKK
46 46 A E 0 0 114 19 77 EEPPPPPPPPPVVNHHEH
47 47 A a 0 0 98 19 0 CCCCCCCCCCCCCCCCCC
## 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 13 50 0 25 0 0 0 0 0 0 0 13 0 8 0 0 1.213 40 0.31
2 2 A 0 0 8 0 0 0 0 0 0 0 0 92 0 0 0 0 0 0 0 0 12 0 0 0.287 9 0.82
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 79 0 21 0 0 19 0 0 0.515 17 0.61
5 5 A 0 0 0 0 0 0 0 0 42 0 32 26 0 0 0 0 0 0 0 0 19 0 0 1.080 36 0.41
6 6 A 0 0 0 0 0 0 0 0 0 5 0 16 0 0 0 0 21 58 0 0 19 0 0 1.091 36 0.43
7 7 A 0 0 0 0 0 0 0 0 0 0 74 0 26 0 0 0 0 0 0 0 19 0 0 0.576 19 0.75
8 8 A 0 0 0 0 0 0 0 0 0 26 0 0 0 21 0 5 16 0 32 0 19 0 0 1.490 49 0.26
9 9 A 0 0 0 0 0 0 0 0 0 0 0 74 0 5 16 5 0 0 0 0 19 0 0 0.826 27 0.42
10 10 A 0 0 0 0 63 26 11 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0.879 29 0.91
11 11 A 0 0 0 0 0 0 0 0 0 32 0 0 0 0 0 37 0 11 0 21 19 0 0 1.297 43 0.28
12 12 A 0 0 0 0 0 0 0 84 0 0 16 0 0 0 0 0 0 0 0 0 19 0 0 0.436 14 0.81
13 13 A 16 26 32 0 5 0 0 0 0 21 0 0 0 0 0 0 0 0 0 0 19 0 0 1.490 49 0.27
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
15 15 A 21 5 53 0 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1.149 38 0.63
16 16 A 0 0 0 5 0 0 0 0 5 0 11 42 0 0 11 0 0 0 26 0 19 0 0 1.499 50 0.20
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 68 0 0 0 32 19 0 0 0.624 20 0.57
18 18 A 0 0 0 0 0 0 0 5 5 32 26 11 0 0 0 16 0 0 5 0 19 0 0 1.709 57 0.25
19 19 A 0 0 0 0 0 0 0 0 0 58 16 0 0 0 0 5 0 0 21 0 19 0 0 1.091 36 0.31
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
21 21 A 26 0 0 0 0 0 0 11 11 0 0 0 0 0 53 0 0 0 0 0 19 0 0 1.163 38 0.11
22 22 A 0 0 0 0 0 0 0 0 21 0 11 0 0 0 5 58 0 0 5 0 19 0 0 1.191 39 0.35
23 23 A 26 0 0 0 0 0 5 0 42 0 0 0 26 0 0 0 0 0 0 0 19 0 0 1.222 40 0.29
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
25 25 A 11 11 32 0 0 0 0 0 0 0 0 0 0 0 11 32 5 0 0 0 19 0 3 1.594 53 0.15
26 26 A 0 0 0 0 0 0 0 0 0 11 21 32 0 0 0 32 0 5 0 0 19 0 0 1.448 48 0.28
27 27 A 0 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 0 79 0 5 19 0 0 0.633 21 0.71
28 28 A 0 0 0 0 0 0 0 16 0 0 0 0 0 0 5 68 0 11 0 0 19 0 0 0.943 31 0.43
29 29 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 0 0 0 0 32 63 0 0 0 0 0 5 0 0 19 0 0 0.809 27 0.50
31 31 A 0 0 0 0 0 0 0 37 0 0 0 0 0 0 0 0 0 0 0 63 19 0 0 0.658 21 0.67
32 32 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
33 33 A 0 0 0 0 0 0 0 0 0 0 0 0 0 89 0 11 0 0 0 0 19 0 0 0.336 11 0.82
34 34 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
35 35 A 0 0 0 0 0 0 0 0 0 0 79 0 0 0 21 0 0 0 0 0 19 0 0 0.515 17 0.55
36 36 A 0 0 0 0 0 0 0 21 0 0 0 0 0 0 0 79 0 0 0 0 19 0 0 0.515 17 0.48
37 37 A 11 32 42 0 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 1.257 41 0.65
38 38 A 0 58 0 0 0 0 0 0 0 0 5 0 0 0 16 0 21 0 0 0 19 0 0 1.091 36 0.13
39 39 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 19 0 0 0.000 0 1.00
40 40 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 79 21 0 0 0 0 19 0 0 0.515 17 0.81
41 41 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
42 42 A 0 74 11 0 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0.753 25 0.84
43 43 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
44 44 A 0 0 0 0 0 0 11 0 11 0 0 79 0 0 0 0 0 0 0 0 19 0 0 0.661 22 0.63
45 45 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 19 0 0 0.000 0 1.00
46 46 A 11 0 0 0 0 0 0 0 0 47 0 0 0 16 0 0 0 21 5 0 19 0 0 1.365 45 0.23
47 47 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
3 26 51 2 kAQp
4 26 51 2 kAQp
14 26 53 1 iQe
//