Complet list of 1dkc hssp file
Complete list of 1dkc.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1DKC
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 ANTIFUNGAL PROTEIN 07-DEC-99 1DKC
COMPND MOL_ID: 1; MOLECULE: ANTIFUNGAL PEPTIDE; CHAIN: A; SYNONYM: PAFP-S
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: PHYTOLACCA AMERICANA; ORGANISM_COMMON:
AUTHOR D.C.WANG,G.H.GAO,F.SHAO,J.X.DAI,J.F.WANG
DBREF 1DKC A 1 38 UNP P81418 PAFP_PHYAM 28 65
SEQLENGTH 37
NCHAIN 1 chain(s) in 1DKC data set
NALIGN 7
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 : PAFP_PHYAM 1DKC 1.00 1.00 1 37 28 64 37 0 0 65 P81418 Antimicrobial peptide 1 OS=Phytolacca americana PE=1 SV=1
2 : Q54AI2_PHYAM 1.00 1.00 1 37 28 64 37 0 0 65 Q54AI2 Anti-fungal protein OS=Phytolacca americana GN=PAFP PE=4 SV=1
3 : Q9SDS1_PHYAM 0.83 0.97 2 37 1 36 36 0 0 37 Q9SDS1 Antimicrobial seed protein (Fragment) OS=Phytolacca americana GN=AMP-2 PE=2 SV=1
4 : AMP1_MIRJA 0.65 0.84 1 37 24 60 37 0 0 61 P25403 Antimicrobial peptide 1 (Fragment) OS=Mirabilis jalapa GN=AMP1 PE=1 SV=4
5 : AMP2_MIRJA 0.61 0.86 2 37 27 62 36 0 0 63 P25404 Antimicrobial peptide 2 OS=Mirabilis jalapa GN=AMP2 PE=1 SV=2
6 : AMP1_MESCR 0.51 0.68 1 37 27 63 37 0 0 64 O81338 Antimicrobial peptide 1 OS=Mesembryanthemum crystallinum PE=3 SV=1
7 : J4KLB7_BEAB2 0.50 0.74 3 36 28 61 34 0 0 61 J4KLB7 Uncharacterized protein OS=Beauveria bassiana (strain ARSEF 2860) GN=BBA_09080 PE=4 SV=1
## ALIGNMENTS 1 - 7
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A A 0 0 123 5 0 AA A A
2 2 A G - 0 0 77 7 78 GGAQAK
3 3 A a - 0 0 67 8 0 CCCCCCC
4 4 A I - 0 0 96 8 0 IIIIIII
5 5 A K S S+ 0 0 90 8 66 KKKGGKN
6 6 A N S S+ 0 0 133 8 0 NNNNNNN
7 7 A G S S+ 0 0 45 8 0 GGGGGGG
8 8 A G E -A 35 0A 5 8 52 GGGGGKS
9 9 A R E +A 34 0A 154 8 70 RRRRRGG
10 10 A b E -A 33 0A 9 8 0 CCCCCCC
11 11 A N > + 0 0 28 8 69 NNVNNRK
12 12 A A T 3 S+ 0 0 59 8 53 AAAEEEA
13 13 A S T 3 S+ 0 0 66 8 68 SSSNNDD
14 14 A A S < S- 0 0 76 8 77 AAGVVQG
15 15 A G - 0 0 56 8 21 GGGGGGS
16 16 A P - 0 0 81 8 54 PPPPPPW
17 17 A P - 0 0 102 8 28 PPPPPPG
18 18 A Y - 0 0 125 8 38 YYYYYFV
19 19 A c - 0 0 17 8 0 CCCCCCC
20 20 A a S S+ 0 0 24 8 0 CCCCCCC
21 21 A S S S- 0 0 30 8 0 SSSSSSS
22 22 A S S S+ 0 0 121 8 48 SSNGGGG
23 23 A Y E +B 36 0A 102 8 4 YYYFFFF
24 24 A b E -B 35 0A 46 8 0 CCCCCCC
25 25 A F E +B 34 0A 115 8 24 FFLLLYL
26 26 A Q E -B 33 0A 46 8 48 QQQRRRQ
27 27 A I E >> -B 32 0A 76 8 100 IIIQQQY
28 28 A A T 45S+ 0 0 112 8 76 AAAPPVQ
29 29 A G T 45S+ 0 0 64 8 19 GGGGNGG
30 30 A Q T 45S- 0 0 156 8 71 QQQQQWA
31 31 A S T <5S+ 0 0 51 8 47 SSSGGAS
32 32 A Y E < - B 0 27A 89 8 82 YYYYYRS
33 33 A G E -AB 10 26A 0 8 0 GGGGGGG
34 34 A V E -AB 9 25A 66 8 53 VVVYVYV
35 35 A c E +AB 8 24A 3 8 0 CCCCCCC
36 36 A K E B 0 23A 73 8 12 KKKKRKK
37 37 A N 0 0 108 7 20 NNKNNN
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 43 29 0 0 0 0 0 0 14 14 0 0 0 7 0 0 1.277 42 0.21
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
4 4 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 63 0 0 13 0 8 0 0 0.900 30 0.33
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 8 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 75 0 0 13 0 0 0 0 13 0 0 0 0 8 0 0 0.736 24 0.47
9 9 A 0 0 0 0 0 0 0 25 0 0 0 0 0 0 75 0 0 0 0 0 8 0 0 0.562 18 0.30
10 10 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
11 11 A 13 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 0 0 63 0 8 0 0 1.074 35 0.30
12 12 A 0 0 0 0 0 0 0 0 63 0 0 0 0 0 0 0 0 38 0 0 8 0 0 0.662 22 0.47
13 13 A 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 25 25 8 0 0 1.040 34 0.31
14 14 A 25 0 0 0 0 0 0 25 38 0 0 0 0 0 0 0 13 0 0 0 8 0 0 1.321 44 0.23
15 15 A 0 0 0 0 0 0 0 88 0 0 13 0 0 0 0 0 0 0 0 0 8 0 0 0.377 12 0.79
16 16 A 0 0 0 0 0 13 0 0 0 88 0 0 0 0 0 0 0 0 0 0 8 0 0 0.377 12 0.45
17 17 A 0 0 0 0 0 0 0 13 0 88 0 0 0 0 0 0 0 0 0 0 8 0 0 0.377 12 0.72
18 18 A 13 0 0 0 13 0 75 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.736 24 0.61
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 50 0 0 38 0 0 0 0 0 0 0 13 0 8 0 0 0.974 32 0.52
23 23 A 0 0 0 0 50 0 50 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.693 23 0.95
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
25 25 A 0 50 0 0 38 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.974 32 0.76
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 0 63 0 0 0 8 0 0 0.662 22 0.51
27 27 A 0 0 50 0 0 0 13 0 0 0 0 0 0 0 0 0 38 0 0 0 8 0 0 0.974 32 -0.01
28 28 A 13 0 0 0 0 0 0 0 50 25 0 0 0 0 0 0 13 0 0 0 8 0 0 1.213 40 0.24
29 29 A 0 0 0 0 0 0 0 88 0 0 0 0 0 0 0 0 0 0 13 0 8 0 0 0.377 12 0.80
30 30 A 0 0 0 0 0 13 0 0 13 0 0 0 0 0 0 0 75 0 0 0 8 0 0 0.736 24 0.28
31 31 A 0 0 0 0 0 0 0 25 13 0 63 0 0 0 0 0 0 0 0 0 8 0 0 0.900 30 0.53
32 32 A 0 0 0 0 0 0 75 0 0 0 13 0 0 0 13 0 0 0 0 0 8 0 0 0.736 24 0.17
33 33 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
34 34 A 75 0 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0.562 18 0.46
35 35 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 8 0 0 0.000 0 1.00
36 36 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 88 0 0 0 0 8 0 0 0.377 12 0.87
37 37 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 86 0 7 0 0 0.410 13 0.79
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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