Complet list of 1e4t hssp file
Complete list of 1e4t.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1E4T
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 2014-04-14
HEADER DEFENSIN 12-JUL-00 1E4T
COMPND MOL_ID: 1; MOLECULE: BETA-DEFENSIN 7; CHAIN: A; SYNONYM: MBD-7
SOURCE MOL_ID: 1; SYNTHETIC: YES; ORGANISM_SCIENTIFIC: MUS MUSCULUS; ORGANISM
AUTHOR F.BAUER,K.SCHWEIMER,E.KLUVER,K.ADERMANN,W.G.FORSSMANN, P.ROESCH,H.STIC
DBREF 1E4T A 1 37 UNP CAC44542 CAC44542 26 62
SEQLENGTH 37
NCHAIN 1 chain(s) in 1E4T data set
NALIGN 5
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 : DEFB7_MOUSE 1E4T 1.00 1.00 1 37 26 62 37 0 0 71 Q91V70 Beta-defensin 7 OS=Mus musculus GN=Defb7 PE=1 SV=1
2 : DEFB8_MOUSE 1E4R 0.70 0.73 6 35 31 60 30 0 0 60 Q91V82 Beta-defensin 8 OS=Mus musculus GN=Defb8 PE=1 SV=1
3 : DEFB3_MOUSE 0.50 0.69 5 35 30 61 32 1 1 63 Q9WTL0 Beta-defensin 3 OS=Mus musculus GN=Defb3 PE=2 SV=1
4 : DEFB3_RAT 0.48 0.65 6 35 31 61 31 1 1 63 Q32ZI4 Beta-defensin 3 OS=Rattus norvegicus GN=Defb3 PE=3 SV=1
5 : DEFB5_RAT 0.47 0.66 5 35 30 61 32 1 1 63 Q32ZI3 Beta-defensin 5 OS=Rattus norvegicus GN=Defb5 PE=3 SV=1
## ALIGNMENTS 1 - 5
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A N 0 0 181 2 0 N
2 2 A S + 0 0 122 2 0 S
3 3 A K S S- 0 0 174 2 0 K
4 4 A R - 0 0 201 2 0 R
5 5 A A > - 0 0 56 4 60 A S S
6 6 A a H >>S+ 0 0 20 6 0 CCCCC
7 7 A Y H 45S+ 0 0 198 6 74 YILMV
8 8 A R H 45S+ 0 0 206 6 65 RRRTT
9 9 A E H <5S- 0 0 68 6 67 ENKNH
10 10 A G T <5 + 0 0 60 6 0 GGGGG
11 11 A G < - 0 0 24 6 0 GGGGG
12 12 A E E -A 34 0A 103 6 87 EIRII
13 13 A b E -A 33 0A 62 6 0 CCCCC
14 14 A L E > -A 32 0A 50 6 71 LQWWW
15 15 A Q T 3 S+ 0 0 141 6 103 QYNLG
16 16 A R T 3 S- 0 0 208 6 17 RRRKR
17 17 A c < - 0 0 26 6 0 CCCCC
18 18 A I > - 0 0 117 6 72 IIISP
19 19 A G T 3 S+ 0 0 67 6 0 GGGGG
20 20 A L T 3 S+ 0 0 102 6 100 LLNTS
21 21 A F S < S- 0 0 49 6 75 FRTFF
22 22 A H E -B 35 0A 98 6 46 HHRRR
23 23 A K E +B 34 0A 129 6 59 KKQEQ
24 24 A I E - 0 0A 81 6 0 IIIII
25 25 A G E -B 33 0A 28 6 0 GGGGG
26 26 A T E -B 32 0A 107 6 47 TTSST
27 27 A b - 0 0 19 6 0 CCCCC
28 28 A N S S- 0 0 171 6 42 NGGGG
29 29 A F S S+ 0 0 141 6 86 FSVTL
30 30 A R S S+ 0 0 191 6 71 RPprg
31 31 A F - 0 0 84 6 36 FFllv
32 32 A K E -AB 14 26A 88 6 17 KKKKR
33 33 A a E +AB 13 25A 0 6 0 CCCCC
34 34 A c E -AB 12 23A 0 6 0 CCCCC
35 35 A K E - B 0 22A 66 6 0 KKKKK
36 36 A F 0 0 135 2 0 F
37 37 A Q 0 0 181 2 0 Q
## 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 0 0 0 0 100 0 2 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 2 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 2 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 0 50 0 50 0 0 0 0 0 0 0 0 0 4 0 0 0.693 23 0.40
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
7 7 A 17 17 17 17 0 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1.561 52 0.26
8 8 A 0 0 0 0 0 0 0 0 0 0 0 33 0 0 67 0 0 0 0 0 6 0 0 0.637 21 0.34
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 17 0 33 33 0 6 0 0 1.330 44 0.32
10 10 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
12 12 A 0 0 50 0 0 0 0 0 0 0 0 0 0 0 17 0 0 33 0 0 6 0 0 1.011 33 0.12
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
14 14 A 0 33 0 0 0 50 0 0 0 0 0 0 0 0 0 0 17 0 0 0 6 0 0 1.011 33 0.29
15 15 A 0 17 0 0 0 0 17 17 0 0 0 0 0 0 0 0 33 0 17 0 6 0 0 1.561 52 -0.03
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 17 0 0 0 0 6 0 0 0.451 15 0.83
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
18 18 A 0 0 67 0 0 0 0 0 0 17 17 0 0 0 0 0 0 0 0 0 6 0 0 0.868 28 0.27
19 19 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
20 20 A 0 50 0 0 0 0 0 0 0 0 17 17 0 0 0 0 0 0 17 0 6 0 0 1.242 41 -0.01
21 21 A 0 0 0 0 67 0 0 0 0 0 0 17 0 0 17 0 0 0 0 0 6 0 0 0.868 28 0.25
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 0 0 0 0 0 6 0 0 0.693 23 0.53
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 33 17 0 0 6 0 0 1.011 33 0.40
24 24 A 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
26 26 A 0 0 0 0 0 0 0 0 0 0 33 67 0 0 0 0 0 0 0 0 6 0 0 0.637 21 0.52
27 27 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
28 28 A 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 0 0 0 33 0 6 0 0 0.637 21 0.57
29 29 A 17 17 0 0 33 0 0 0 0 0 17 17 0 0 0 0 0 0 0 0 6 0 0 1.561 52 0.14
30 30 A 0 0 0 0 0 0 0 17 0 33 0 0 0 0 50 0 0 0 0 0 6 0 3 1.011 33 0.29
31 31 A 17 33 0 0 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1.011 33 0.64
32 32 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 83 0 0 0 0 6 0 0 0.451 15 0.82
33 33 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
34 34 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
35 35 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 6 0 0 0.000 0 1.00
36 36 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
37 37 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 2 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
3 27 56 1 pFl
4 26 56 1 rQl
5 27 56 1 gKv
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