Complet list of 2amn hssp file
Complete list of 2amn.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2AMN
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 09-AUG-05 2AMN
COMPND MOL_ID: 1; MOLECULE: CATHELICIDIN; CHAIN: A; FRAGMENT: C-TERMINAL DOMA
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THIS SEQUENCE OCCURS NATURAL
AUTHOR Y.XIAO,H.DAI,Y.R.BOMMINENI,O.PRAKASH,G.ZHANG
DBREF 2AMN A 1 26 UNP Q2IAM1 Q2IAM1_CHICK 123 148
SEQLENGTH 26
NCHAIN 1 chain(s) in 2AMN data set
NALIGN 11
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 : C4PFJ7_CHICK 1.00 1.00 1 26 123 148 26 0 0 148 C4PFJ7 Fowlicidin-1 OS=Gallus gallus GN=CATHL1 PE=2 SV=1
2 : CTHL1_CHICK 2AMN 1.00 1.00 1 26 123 148 26 0 0 148 Q6QLQ5 Cathelicidin-1 OS=Gallus gallus GN=CATHL1 PE=1 SV=1
3 : D2KMV8_COTCO 0.92 0.96 1 26 123 148 26 0 0 148 D2KMV8 Cathelicidin OS=Coturnix coturnix PE=2 SV=1
4 : D1MJ07_PHACC 0.85 0.96 1 26 123 148 26 0 0 148 D1MJ07 Cathelicidin CATH3 OS=Phasianus colchicus PE=2 SV=1
5 : G1MVE2_MELGA 0.66 0.72 1 26 119 147 29 1 3 147 G1MVE2 Uncharacterized protein OS=Meleagris gallopavo PE=4 SV=2
6 : G3USW4_MELGA 0.66 0.72 1 26 119 147 29 1 3 147 G3USW4 Uncharacterized protein OS=Meleagris gallopavo PE=4 SV=1
7 : C4PFJ9_CHICK 0.62 0.72 1 26 123 151 29 1 3 151 C4PFJ9 Fowlicidin-3 OS=Gallus gallus GN=CATHL3 PE=2 SV=1
8 : CTHL3_CHICK 2HFR 0.62 0.72 1 26 123 151 29 1 3 151 Q2IAL6 Cathelicidin-3 OS=Gallus gallus GN=CATHL3 PE=1 SV=1
9 : D1MFT1_PHACC 0.62 0.72 1 26 123 151 29 1 3 151 D1MFT1 Cathelicidin CATH1 OS=Phasianus colchicus PE=2 SV=1
10 : G1K357_CHICK 0.62 0.72 1 26 121 149 29 1 3 149 G1K357 Uncharacterized protein OS=Gallus gallus PE=4 SV=2
11 : D1MJ09_COTCO 0.59 0.72 1 26 123 151 29 1 3 151 D1MJ09 Cathelicidin CATH3 OS=Coturnix coturnix PE=2 SV=1
## ALIGNMENTS 1 - 11
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A R 0 0 268 12 0 RRRRRRRRRRR
2 2 A V - 0 0 98 12 9 VVVIVVVVIVV
3 3 A K S S- 0 0 192 12 7 KKKKKKKKKKR
4 4 A R + 0 0 221 12 0 RRRRRRRRRRR
5 5 A V S S+ 0 0 82 12 63 VVVFFFFFFFF
6 6 A W > + 0 0 142 12 13 WWLWWWWWWWW
7 7 A P T 4 S+ 0 0 97 12 0 PPPPPPPPPPP
8 8 A L T > S+ 0 0 122 12 11 LLLVLLLLLLL
9 9 A V H >> S+ 0 0 64 12 0 VVVVVVVVVVV
10 10 A I H 3X S+ 0 0 66 12 97 IIIIppppppp
11 11 A R H 3> S+ 0 0 194 12 80 RRRRnnnnnnn
12 12 A T H S+ 0 0 115 12 0 YYYYYYYYYYY
21 21 A R H > S+ 0 0 127 12 40 RRRRKKKKKKK
22 22 A A H >4 S+ 0 0 28 12 0 AAAAAAAAAAA
23 23 A I H >4 S+ 0 0 79 12 0 IIIIIIIIIII
24 24 A K H 3< S+ 0 0 182 12 26 KKKKKKRRKRR
25 25 A K T << 0 0 149 12 33 KKRKRRRRRRR
26 26 A K < 0 0 220 12 0 KKKKKKKKKKK
## 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 0 100 0 0 0 0 0 12 0 0 0.000 0 1.00
2 2 A 83 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.451 15 0.91
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 92 0 0 0 0 12 0 0 0.287 9 0.92
4 4 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 12 0 0 0.000 0 1.00
5 5 A 33 0 0 0 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.637 21 0.37
6 6 A 0 8 0 0 0 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.287 9 0.86
7 7 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
8 8 A 8 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.287 9 0.89
9 9 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
10 10 A 0 0 42 0 0 0 0 0 0 58 0 0 0 0 0 0 0 0 0 0 12 0 7 0.679 22 0.03
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 0 0 0 58 0 12 0 0 0.679 22 0.20
12 12 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
13 13 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
14 14 A 8 0 33 0 0 0 0 0 58 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.888 29 0.15
15 15 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
17 17 A 0 0 58 0 0 0 42 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.679 22 0.20
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 12 0 0 0.000 0 1.00
19 19 A 0 100 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
20 20 A 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 58 0 0 0 0 12 0 0 0.679 22 0.60
22 22 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.000 0 1.00
23 23 A 0 0 100 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
24 24 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 67 0 0 0 0 12 0 0 0.637 21 0.73
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 33 0 0 0 0 12 0 0 0.637 21 0.66
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 12 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
5 11 129 3 pVAIn
6 11 129 3 pVAIn
7 11 133 3 pVAIn
8 11 133 3 pVAIn
9 11 133 3 pVAIn
10 11 131 3 pVAIn
11 11 133 3 pVAIn
//