Complet list of 1m4f hssp file
Complete list of 1m4f.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1M4F
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 2014-05-03
HEADER ANTIMICROBIAL PROTEIN 02-JUL-02 1M4F
COMPND MOL_ID: 1; MOLECULE: HEPCIDIN; CHAIN: A; FRAGMENT: HEPCIDIN-25 (RESIDU
SOURCE MOL_ID: 1; SYNTHETIC: YES; OTHER_DETAILS: THE SEQUENCE OF THE PROTEIN
AUTHOR H.N.HUNTER,D.B.FULTON,T.GANZ,H.J.VOGEL
DBREF 1M4F A 1 25 UNP P81172 HEPC_HUMAN 60 84
SEQLENGTH 25
NCHAIN 1 chain(s) in 1M4F data set
NALIGN 56
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 : A7XEH6_PANTR 1.00 1.00 1 25 60 84 25 0 0 84 A7XEH6 Hepcidin OS=Pan troglodytes GN=HAMP PE=4 SV=1
2 : A7XEH7_PONPY 1.00 1.00 1 25 60 84 25 0 0 84 A7XEH7 Hepcidin OS=Pongo pygmaeus GN=HAMP PE=4 SV=1
3 : A7XEI4_9PRIM 1.00 1.00 1 25 60 84 25 0 0 84 A7XEI4 Hepcidin OS=Gorilla gorilla GN=HAMP PE=4 SV=1
4 : A7XEI8_NOMCO 1.00 1.00 1 25 61 85 25 0 0 85 A7XEI8 Hepcidin OS=Nomascus concolor GN=HAMP PE=4 SV=1
5 : A7XEI9_HYLLA 1.00 1.00 1 25 61 85 25 0 0 85 A7XEI9 Hepcidin OS=Hylobates lar GN=HAMP PE=4 SV=1
6 : G1RJV2_NOMLE 1.00 1.00 1 25 61 85 25 0 0 85 G1RJV2 Uncharacterized protein OS=Nomascus leucogenys GN=HAMP PE=4 SV=1
7 : G3QEQ8_GORGO 1.00 1.00 1 25 60 84 25 0 0 84 G3QEQ8 Uncharacterized protein OS=Gorilla gorilla gorilla GN=101142391 PE=4 SV=1
8 : H2NYF4_PONAB 1.00 1.00 1 25 61 85 25 0 0 85 H2NYF4 Hepcidin OS=Pongo abelii GN=HAMP PE=4 SV=1
9 : HEPC_HUMAN 1M4E 1.00 1.00 1 25 60 84 25 0 0 84 P81172 Hepcidin OS=Homo sapiens GN=HAMP PE=1 SV=2
10 : A7XEH8_PAPPA 0.96 1.00 1 25 60 84 25 0 0 84 A7XEH8 Hepcidin OS=Papio papio GN=HAMP PE=4 SV=1
11 : A7XEH9_TRAOB 0.96 1.00 1 25 60 84 25 0 0 84 A7XEH9 Hepcidin OS=Trachypithecus obscurus GN=HAMP PE=4 SV=1
12 : A7XEI0_PREME 0.96 1.00 1 25 60 84 25 0 0 84 A7XEI0 Hepcidin OS=Presbytis melalophos GN=HAMP PE=4 SV=1
13 : A7XEI1_TRACR 0.96 1.00 1 25 60 84 25 0 0 84 A7XEI1 Hepcidin OS=Trachypithecus cristatus GN=HAMP PE=4 SV=1
14 : A7XEI2_9PRIM 0.96 1.00 1 25 60 84 25 0 0 84 A7XEI2 Hepcidin OS=Macaca fuscata GN=HAMP PE=4 SV=1
15 : A7XEI3_MACFA 0.96 1.00 1 25 60 84 25 0 0 84 A7XEI3 Hepcidin OS=Macaca fascicularis GN=HAMP PE=4 SV=1
16 : A7XEI6_CHLAE 0.96 1.00 1 25 60 84 25 0 0 84 A7XEI6 Hepcidin OS=Chlorocebus aethiops GN=HAMP PE=4 SV=1
17 : F6WA25_MACMU 0.96 1.00 1 25 60 84 25 0 0 84 F6WA25 Liver-expressed antimicrobial peptide 1 OS=Macaca mulatta GN=HAMP PE=4 SV=1
18 : HEPC_PONAB 0.96 0.96 1 25 60 84 25 0 0 84 Q5NVR8 Hepcidin OS=Pongo abelii GN=HAMP PE=3 SV=1
19 : L7T7I1_DESRO 0.92 1.00 1 25 59 83 25 0 0 83 L7T7I1 Hepcidin OS=Desmodus rotundus GN=HAMP PE=4 SV=1
20 : L7T7I6_GLOSR 0.92 1.00 1 25 30 54 25 0 0 54 L7T7I6 Hepcidin (Fragment) OS=Glossophaga soricina GN=HAMP PE=4 SV=1
21 : U5TRI3_CAMDR 0.92 1.00 1 25 59 83 25 0 0 83 U5TRI3 Hepcidin OS=Camelus dromedarius PE=4 SV=1
22 : A7XEI5_CALJA 0.88 1.00 1 25 60 84 25 0 0 84 A7XEI5 Hepcidin OS=Callithrix jacchus GN=HAMP PE=4 SV=1
23 : F6TFL3_CALJA 0.88 1.00 1 25 60 84 25 0 0 84 F6TFL3 Hepcidin preproprotein OS=Callithrix jacchus GN=HAMP PE=4 SV=1
24 : G1P6H5_MYOLU 0.88 0.92 1 25 59 83 25 0 0 83 G1P6H5 Uncharacterized protein OS=Myotis lucifugus GN=HAMP PE=4 SV=1
25 : L5K339_PTEAL 0.88 0.96 1 25 58 82 25 0 0 82 L5K339 Hepcidin OS=Pteropus alecto GN=PAL_GLEAN10000930 PE=4 SV=1
26 : L5LS49_MYODS 0.88 0.92 1 25 62 86 25 0 0 86 L5LS49 Hepcidin OS=Myotis davidii GN=MDA_GLEAN10008216 PE=4 SV=1
27 : L7T9T3_ROUAE 0.88 0.96 1 25 58 82 25 0 0 82 L7T9T3 Hepcidin OS=Rousettus aegyptiacus GN=HAMP PE=4 SV=1
28 : L7TCQ0_MYOLU 0.88 0.92 1 25 58 82 25 0 0 82 L7TCQ0 Hepcidin OS=Myotis lucifugus GN=HAMP PE=4 SV=1
29 : S7P5C9_MYOBR 0.88 0.92 1 25 58 82 25 0 0 82 S7P5C9 Hepcidin OS=Myotis brandtii GN=D623_10035176 PE=4 SV=1
30 : A7XEI7_ATEFU 0.84 1.00 1 25 60 84 25 0 0 84 A7XEI7 Hepcidin OS=Ateles fusciceps GN=HAMP PE=4 SV=1
31 : D2HFQ7_AILME 0.84 1.00 1 25 40 64 25 0 0 64 D2HFQ7 Putative uncharacterized protein (Fragment) OS=Ailuropoda melanoleuca GN=PANDA_009748 PE=4 SV=1
32 : G1L056_AILME 0.84 1.00 1 25 59 83 25 0 0 83 G1L056 Uncharacterized protein OS=Ailuropoda melanoleuca GN=HAMP PE=4 SV=1
33 : G1U3P2_RABIT 0.84 0.96 1 25 59 83 25 0 0 83 G1U3P2 Uncharacterized protein OS=Oryctolagus cuniculus GN=HAMP PE=4 SV=1
34 : HEPC_CANFA 0.84 0.92 1 25 61 85 25 0 0 85 Q5U9D2 Hepcidin OS=Canis familiaris GN=HAMP PE=3 SV=1
35 : HEPC_PIG 0.84 0.96 1 25 58 82 25 0 0 82 Q8MJ80 Hepcidin OS=Sus scrofa GN=HAMP PE=3 SV=1
36 : L7T7L7_EIDHE 0.84 0.96 1 25 58 82 25 0 0 82 L7T7L7 Hepcidin OS=Eidolon helvum GN=HAMP PE=4 SV=1
37 : L7T921_LASBO 0.84 0.92 1 25 58 82 25 0 0 82 L7T921 Hepcidin OS=Lasiurus borealis GN=HAMP PE=4 SV=1
38 : L7T9T8_CARPS 0.84 1.00 1 25 30 54 25 0 0 54 L7T9T8 Hepcidin (Fragment) OS=Carollia perspicillata GN=HAMP PE=4 SV=1
39 : B0LXP0_BUBBU 0.80 0.96 1 25 58 82 25 0 0 82 B0LXP0 Hepcidin OS=Bubalus bubalis PE=4 SV=2
40 : B5ANS7_BOSMU 0.80 0.96 1 25 58 82 25 0 0 82 B5ANS7 Hepcidin OS=Bos mutus grunniens GN=HAMP PE=4 SV=1
41 : E0X9N1_SHEEP 0.80 0.96 1 25 58 82 25 0 0 82 E0X9N1 Hepcidin OS=Ovis aries GN=HAMP PE=4 SV=1
42 : F1PN62_CANFA 0.80 0.88 1 25 61 85 25 0 0 85 F1PN62 Hepcidin OS=Canis familiaris GN=HAMP PE=4 SV=1
43 : L8IKS3_9CETA 0.80 0.96 1 25 58 82 25 0 0 82 L8IKS3 Hepcidin OS=Bos mutus GN=M91_08228 PE=4 SV=1
44 : Q2NKT0_BOVIN 0.80 0.96 1 25 58 82 25 0 0 82 Q2NKT0 Hepcidin antimicrobial peptide OS=Bos taurus GN=HAMP PE=4 SV=1
45 : Q49S92_CANFA 0.80 0.88 1 25 61 85 25 0 0 85 Q49S92 Hepcidin OS=Canis familiaris PE=4 SV=1
46 : D1KKA2_HORSE 0.76 0.88 1 25 62 86 25 0 0 86 D1KKA2 Hepcidin antimicrobial peptide OS=Equus caballus GN=Hamp PE=4 SV=1
47 : F8THJ3_EQUAS 0.76 0.88 1 25 62 86 25 0 0 86 F8THJ3 Hepcidin antimicrobial peptide OS=Equus asinus GN=Hamp PE=4 SV=1
48 : G5BXJ4_HETGA 0.76 0.92 1 25 59 83 25 0 0 83 G5BXJ4 Hepcidin OS=Heterocephalus glaber GN=GW7_18377 PE=4 SV=1
49 : HEPC_MOUSE 0.76 0.92 1 25 59 83 25 0 0 83 Q9EQ21 Hepcidin OS=Mus musculus GN=Hamp PE=1 SV=1
50 : HEPC_RAT 0.68 0.80 1 25 60 84 25 0 0 84 Q99MH3 Hepcidin OS=Rattus norvegicus GN=Hamp PE=3 SV=1
51 : L8XZ67_TUPCH 0.65 0.83 1 23 59 81 23 0 0 83 L8XZ67 Hepcidin OS=Tupaia chinensis GN=TREES_T100004869 PE=4 SV=1
52 : F6U2Q9_MONDO 0.62 0.88 1 24 60 83 24 0 0 83 F6U2Q9 Uncharacterized protein OS=Monodelphis domestica GN=HAMP PE=4 SV=1
53 : HEPC2_MOUSE 0.61 0.83 1 23 59 81 23 0 0 83 Q80T19 Hepcidin-2 OS=Mus musculus GN=Hamp2 PE=2 SV=1
54 : Q5M9M1_MOUSE 0.61 0.83 1 23 60 82 23 0 0 84 Q5M9M1 Hepcidin antimicrobial peptide 2 OS=Mus musculus GN=Hamp2 PE=4 SV=1
55 : A1YWG4_XENTR 0.59 0.77 3 23 57 78 22 1 1 80 A1YWG4 Hepcidin 2 OS=Xenopus tropicalis GN=hamp2 PE=4 SV=1
56 : E8ZAD0_CROSI 0.56 0.80 1 25 75 99 25 0 0 99 E8ZAD0 Hepcidin OS=Crocodylus siamensis PE=4 SV=1
## ALIGNMENTS 1 - 56
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A D 0 0 149 56 7 DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDNDD N
2 2 A T - 0 0 77 56 24 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTSII S
3 3 A H S S+ 0 0 191 57 14 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHNNHHNNHH
4 4 A F S S+ 0 0 176 57 1 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFLF
5 5 A P - 0 0 30 57 6 PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPNP
6 6 A I - 0 0 121 57 1 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIVIIIII
7 7 A a - 0 0 24 57 1 CCCCCCCCCCCCCCCCCYCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
8 8 A I E -A 22 0A 97 57 50 IIIIIIIIIIIIIIIIIIIIVIIIIIIIIILLIIIVIMIIIIIIITTVILHSRRVS
9 9 A F E +A 21 0A 144 57 2 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFLLFFFFFFFYY
10 10 A b E -A 20 0A 43 57 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
11 11 A c E -A 19 0A 66 57 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
12 12 A G + 0 0 26 57 40 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGSGGGGGGGGGGGGGGGKKNNQQKN
13 13 A d S S- 0 0 100 57 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
14 14 A d S S+ 0 0 93 57 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
15 15 A H S S+ 0 0 180 57 74 HHHHHHHHHHHHHHHHHHHHHRRYYYYYYRNNRKRYYHRRRKRRKNNKNKSHNNKR
16 16 A R S S- 0 0 161 57 60 RRRRRRRRRRRRRRRRRRKKKQQPKPKPPQKKNTKKPKKKKTKKTKKNNNKNKKKN
17 17 A S S S+ 0 0 113 57 56 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSPSSSPASSSGGGPGGPQQASSPTPPQK
18 18 A K S S- 0 0 126 57 57 KKKKKKKKKKKKKKKKKKKKKNNKKKKKKNKKKKIKRKTTTKTTKKKRQSGNSSkG
19 19 A c E +A 11 0A 81 57 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcC
20 20 A G E -A 10 0A 27 57 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
21 21 A M E -A 9 0A 117 57 42 MMMMMMMMMMMMMMMMMMIIMMMIIIIIIMIIILMIIIMMIFMMLWWIILIIIIML
22 22 A b E +A 8 0A 50 57 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
23 23 A a + 0 0 39 57 0 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
24 24 A K 0 0 127 53 33 KKKKKKKKKRRRRRRRRKKKKKKKKKKKKKKKKKKKKKRRKRRRIKKKKI R R
25 25 A T 0 0 194 52 0 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT T
## 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 4 96 56 0 0 0.154 5 0.92
2 2 A 0 0 4 0 0 0 0 0 2 0 4 91 0 0 0 0 0 0 0 0 56 0 0 0.395 13 0.76
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 0 93 0 0 0 0 7 0 57 0 0 0.254 8 0.86
4 4 A 0 2 0 0 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 0 0 0.088 2 0.99
5 5 A 0 0 0 0 0 0 0 0 0 98 0 0 0 0 0 0 0 0 2 0 57 0 0 0.088 2 0.93
6 6 A 2 0 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 0 0 0.088 2 0.99
7 7 A 0 0 0 0 0 0 2 0 0 0 0 0 98 0 0 0 0 0 0 0 57 0 0 0.088 2 0.99
8 8 A 7 5 74 2 0 0 0 0 0 0 4 4 0 2 4 0 0 0 0 0 57 0 0 1.061 35 0.49
9 9 A 0 4 0 0 93 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 57 0 0 0.303 10 0.97
10 10 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 57 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 57 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 84 0 0 2 0 0 0 0 5 4 0 5 0 57 0 0 0.643 21 0.59
13 13 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 57 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 57 0 0 0.000 0 1.00
15 15 A 0 0 0 0 0 0 14 0 0 0 2 0 0 42 19 11 0 0 12 0 57 0 0 1.523 50 0.26
16 16 A 0 0 0 0 0 0 0 0 0 9 0 5 0 0 33 37 5 0 11 0 57 0 0 1.494 49 0.39
17 17 A 0 0 0 0 0 0 0 9 4 12 67 2 0 0 0 2 5 0 0 0 57 0 0 1.156 38 0.44
18 18 A 0 0 2 0 0 0 0 4 0 0 5 9 0 0 4 68 2 0 7 0 57 0 1 1.191 39 0.43
19 19 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 57 0 0 0.000 0 1.00
20 20 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 57 0 0 0.000 0 1.00
21 21 A 0 7 37 51 2 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 0 0 1.087 36 0.57
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 57 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 57 0 0 0.000 0 1.00
24 24 A 0 0 4 0 0 0 0 0 0 0 0 0 0 0 28 68 0 0 0 0 53 0 0 0.744 24 0.66
25 25 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 52 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
55 17 73 1 kGc
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