Complet list of 1fry hssp file
Complete list of 1fry.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1FRY
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 2014-04-29
HEADER ANTIMICROBIAL PROTEIN 07-SEP-00 1FRY
COMPND MOL_ID: 1; MOLECULE: MYELOID ANTIMICROBIAL PEPTIDE; CHAIN: A; SYNONYM:
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS SEQUENCE OCCURS NATURAL
AUTHOR B.F.TACK,M.V.SAWAI,W.R.KEARNEY,A.D.ROBERTSON,M.A.SHERMAN, W.WANG,T.HON
DBREF 1FRY A 1 29 UNP P49928 SC51_SHEEP 132 160
SEQLENGTH 29
NCHAIN 1 chain(s) in 1FRY data set
NALIGN 9
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 : SC51_SHEEP 1.00 1.00 1 29 132 160 29 0 0 160 P49928 Cathelin-related peptide SC5 OS=Ovis aries PE=1 SV=1
2 : SC52_SHEEP 1.00 1.00 1 29 132 160 29 0 0 160 P49929 Cathelin-related peptide SC5 OS=Ovis aries PE=1 SV=1
3 : W5NVS8_SHEEP 0.83 0.86 1 29 134 162 29 0 0 162 W5NVS8 Uncharacterized protein OS=Ovis aries GN=SC5 PE=4 SV=1
4 : V9LY96_BUBBU 0.64 0.79 2 29 133 160 28 0 0 160 V9LY96 Cathelicidin-5 OS=Bubalus bubalis PE=2 SV=1
5 : B9UKL4_BOBOX 0.63 0.81 2 28 133 159 27 0 0 159 B9UKL4 Cathelicidin 5 OS=Bos indicus x Bos taurus GN=CATHL5 PE=4 SV=1
6 : B9UKL5_BOSIN 0.63 0.81 2 28 133 159 27 0 0 159 B9UKL5 Cathelicidin 5 OS=Bos indicus GN=CATHL5 PE=4 SV=1
7 : B9UKL8_BOVIN 0.63 0.81 2 28 133 159 27 0 0 159 B9UKL8 Cathelicidin 5 OS=Bos taurus GN=CATHL5 PE=4 SV=1
8 : B9UKL9_BOSIN 0.63 0.81 2 28 133 159 27 0 0 159 B9UKL9 Cathelicidin 5 OS=Bos indicus GN=CATHL5 PE=4 SV=1
9 : CTHL5_BOVIN 0.63 0.81 2 28 133 159 27 0 0 159 P54229 Cathelicidin-5 OS=Bos taurus GN=CATHL5 PE=1 SV=1
## ALIGNMENTS 1 - 9
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A R 0 0 279 4 0 RRR
2 2 A G + 0 0 55 10 0 GGGGGGGGG
3 3 A L + 0 0 88 10 0 LLLLLLLLL
4 4 A R S S+ 0 0 158 10 33 RRGRRRRRR
5 5 A R S S+ 0 0 184 10 75 RRRRSSSSS
6 6 A L S S- 0 0 150 10 0 LLLLLLLLL
7 7 A G S >> S+ 0 0 37 10 0 GGGGGGGGG
8 8 A R T 34 S+ 0 0 118 10 0 RRRRRRRRR
9 9 A K T 34 S+ 0 0 104 10 0 KKKKKKKKK
10 10 A I T <4 S+ 0 0 156 10 0 IIIIIIIII
11 11 A A S < S+ 0 0 18 10 83 AAVVLLLLL
12 12 A H S S+ 0 0 42 10 45 HHRRRRRRR
13 13 A G S >S+ 0 0 0 10 45 GGGAAAAAA
14 14 A V T 5S+ 0 0 54 10 132 VVVWWWWWW
15 15 A K T 5S+ 0 0 169 10 0 KKKKKKKKK
16 16 A K T 5S+ 0 0 124 10 0 KKKKKKKKK
17 17 A Y T 5S- 0 0 133 10 0 YYYYYYYYY
18 18 A G S