Complet list of 1zwu hssp file
Complete list of 1zwu.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1ZWU
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 2014-05-16
HEADER ANTIMICROBIAL PROTEIN 06-JUN-05 1ZWU
COMPND MOL_ID: 1; MOLECULE: AMARANTHUS CAUDATUS ANTIMICROBIAL PEPTIDE 2 (ACMP
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE RESIDUE PHE 18 OF THE NA
AUTHOR M.I.CHAVEZ,C.ANDREU,P.VIDAL,F.FREIRE,N.ABOITIZ,P.GROVES,J.L.ASENSIO, G
DBREF 1ZWU A 1 30 UNP P27275 AMP_AMACA 26 55
SEQLENGTH 30
NCHAIN 1 chain(s) in 1ZWU data set
NALIGN 12
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 : A0SZX9_9CARY 0.97 0.97 1 30 26 55 30 0 0 86 A0SZX9 Anti-microbial protein 2 OS=Amaranthus albus PE=4 SV=1
2 : A0SZY0_AMACA 0.97 0.97 1 30 26 55 30 0 0 86 A0SZY0 Anti-microbial protein 2 OS=Amaranthus caudatus PE=4 SV=1
3 : A0SZY1_AMACR 0.97 0.97 1 30 26 55 30 0 0 86 A0SZY1 Anti-microbial protein 2 OS=Amaranthus cruentus PE=4 SV=1
4 : A0SZY2_9CARY 0.97 0.97 1 30 26 55 30 0 0 86 A0SZY2 Anti-microbial protein 2 OS=Amaranthus blitum PE=4 SV=1
5 : A0SZY3_AMAHY 0.97 0.97 1 30 26 55 30 0 0 86 A0SZY3 Anti-microbial protein 2 OS=Amaranthus hybridus PE=4 SV=1
6 : A0SZY4_AMAHP 0.97 0.97 1 30 26 55 30 0 0 86 A0SZY4 Anti-microbial protein 2 OS=Amaranthus hypochondriacus PE=4 SV=1
7 : A0SZY5_AMARE 0.97 0.97 1 30 26 55 30 0 0 86 A0SZY5 Anti-microbial protein 2 OS=Amaranthus retroflexus PE=4 SV=1
8 : A0SZY6_AMATR 0.97 0.97 1 30 26 55 30 0 0 86 A0SZY6 Anti-microbial protein 2 OS=Amaranthus tricolor PE=4 SV=1
9 : AMP_AMACA 1ZNT 0.97 0.97 1 30 26 55 30 0 0 86 P27275 Antimicrobial peptide 2 OS=Amaranthus caudatus PE=1 SV=2
10 : Q71U16_AMAHP 0.97 0.97 1 30 26 55 30 0 0 86 Q71U16 Antimicrobial protein OS=Amaranthus hypochondriacus GN=AMP PE=4 SV=1
11 : Q9S8Z7_AMACA 0.97 0.97 1 30 1 30 30 0 0 30 Q9S8Z7 AC-AMP2=ANTIMICROBIAL peptide OS=Amaranthus caudatus PE=4 SV=1
12 : AMP_AMARE 0.90 0.97 2 30 27 55 29 0 0 89 Q5I2B2 Antimicrobial peptide Ar-AMP OS=Amaranthus retroflexus PE=1 SV=1
## ALIGNMENTS 1 - 12
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A V 0 0 92 12 0 VVVVVVVVVVV
2 2 A G E +A 21 0A 33 13 0 GGGGGGGGGGGG
3 3 A E E S-A 20 0A 76 13 0 EEEEEEEEEEEE
4 4 A a > - 0 0 8 13 0 CCCCCCCCCCCC
5 5 A V B > S-C 8 0B 77 13 0 VVVVVVVVVVVV
6 6 A R T 3 S- 0 0 165 13 51 RRRRRRRRRRRQ
7 7 A G T < S+ 0 0 40 13 0 GGGGGGGGGGGG
8 8 A R B < -C 5 0B 168 13 0 RRRRRRRRRRRR
9 9 A b - 0 0 44 13 0 CCCCCCCCCCCC
10 10 A P S > S- 0 0 60 13 0 PPPPPPPPPPPP
11 11 A S T 3 S- 0 0 128 13 0 SSSSSSSSSSSS
12 12 A G T 3 S+ 0 0 58 13 0 GGGGGGGGGGGG
13 13 A M < - 0 0 74 13 0 MMMMMMMMMMMM
14 14 A c E -B 22 0A 27 13 0 CCCCCCCCCCCC
15 15 A a E -B 21 0A 42 13 0 CCCCCCCCCCCC
16 16 A S > - 0 0 6 13 0 SSSSSSSSSSSS
17 17 A Q T 3 S+ 0 0 78 13 0 QQQQQQQQQQQQ
18 18 A X T 3 S- 0 0 192 12 0 FFFFFFFFFFFF
19 19 A G S < S+ 0 0 34 13 0 GGGGGGGGGGGG
20 20 A Y E -A 3 0A 137 13 0 YYYYYYYYYYYY
21 21 A b E +AB 2 15A 3 13 0 CCCCCCCCCCCC
22 22 A G E - B 0 14A 8 13 0 GGGGGGGGGGGG
23 23 A K S S+ 0 0 139 13 32 KKKKKKKKKKKR
24 24 A G S >>>S- 0 0 27 13 0 GGGGGGGGGGGG
25 25 A P H 3>5S+ 0 0 108 13 0 PPPPPPPPPPPP
26 26 A K H 345S+ 0 0 94 13 0 KKKKKKKKKKKK
27 27 A Y H <45S+ 0 0 81 13 0 YYYYYYYYYYYY
28 28 A c H <5S+ 0 0 66 13 0 CCCCCCCCCCCC
29 29 A G << 0 0 42 13 0 GGGGGGGGGGGG
30 30 A R 0 0 139 13 0 RRRRRRRRRRRR
## 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 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 13 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
5 5 A 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 92 0 8 0 0 0 13 0 0 0.271 9 0.49
7 7 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 13 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
11 11 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
12 12 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
13 13 A 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
14 14 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
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 0 0 0 0 0 0 100 0 0 0 13 0 0 0.000 0 1.00
18 18 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
19 19 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 92 0 0 0 0 13 0 0 0.271 9 0.67
24 24 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 13 0 0 0.000 0 1.00
27 27 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 13 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 13 0 0 0.000 0 1.00
29 29 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 13 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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