User:Susana Retamal/Sandbox1: Difference between revisions
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Background Information
Structure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw
Protein Sequence
Physico - Chemical parameters for Rsp1275
Amino Acid Conservation Scores
Phylogenetic Tree of rsp1275
Reference
Animated Image Construction
JMol Image Construction
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=Background Information= | =Background Information= | ||
Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from ''E. coli'' have been identified in a variety of taxonomically diverse bacterial species. The bacterium ''Rhodobacter | Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from ''E. coli'' have been identified in a variety of taxonomically diverse bacterial species.<ref>Spiro, S. 1994. The FNR family of transcriptional regulators. Antonie van Leeuwenhoek 66:23–36.</ref><ref>PredictProtein: B Rost, G Yachdav and J Liu (2004). The PredictProtein Server. Nucleic Acids Research 32(Web Server issue):W321-W326.</ref>The bacterium ''Rhodobacter sphaeroides" 2.4.1 encodes 8 members of this family, however only 2 have known function. Models of 7 of them, including RSP1275, were successfully obtained using 3D-Jigsaw, all being very similar in structure to Crp (the only one with crystal structure solved). The DNA binding domain helix-turn-helix is located in the C-terminal, and the N-terminal part contains the allosteric effector domain. | ||
'' | |||
= Structure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw = | |||
'' | |||
<applet load='Rsp1275.pdb' size='300' frame='true' align='right' caption='Insert caption here' /> | |||
The highlighted <scene name='User:Susana_Retamal/Sandbox1/Rsp1275/10'>alpha-helices</scene> of the protein. | |||
This is the <scene name='User:Susana_Retamal/Sandbox1/Rsp1275/12'>Amino to Carboxyl rainbow</scene> of the protein. | |||
= | =Protein Sequence= | ||
1 mfvpapdati tncrncplrr kplflpfsds elsfmeqfkv gelvvapgvt lleegqgsah | |||
61 lftvlsglgi rstmlengrr qvinflfpgd figlqaglag emrhsvestt tmvlcvfnra | |||
121 dlwdlfreep eraydltwia aveehflget iaslgqrdat erlawallri herlsaigla | |||
181 ergrvpmpwr qqdladalgl slvhtnktir rlretghalw eggtlfvdre rlatlaladp | |||
241 drprrrpli | |||
=Physico - Chemical parameters for Rsp1275= | =Physico - Chemical parameters for Rsp1275= | ||
From http://ca.expasy.org/tools/protparam.html | |||
Number of amino acids: 249 | '''Number of amino acids: 249''' | ||
Molecular weight: 28014.2 | '''Molecular weight: 28014.2''' | ||
Theoretical pI: 6.10 | '''Theoretical pI: 6.10''' | ||
'''Atomic composition:''' | |||
Secondary Structure: | Carbon C 1249 | ||
Hydrogen H 1986 | |||
Nitrogen N 360 | |||
Oxygen O 355 | |||
Sulfur S 9 | |||
Formula: C1249H1986N360O355S9 | |||
Total number of atoms: 3959 | |||
'''Extinction coefficients:''' | |||
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. | |||
*Ext. coefficient 29115 | |||
Abs 0.1% (=1 g/l) 1.039, assuming ALL Cys residues appear as half cystines | |||
*Ext. coefficient 28990 | |||
Abs 0.1% (=1 g/l) 1.035, assuming NO Cys residues appear as half cystines | |||
'''Estimated half-life:''' | |||
The N-terminal of the sequence considered is M (Met). | |||
'''The estimated half-life is''': | |||
*30 hours (mammalian reticulocytes, in vitro). | |||
* >20 hours (yeast, in vivo). | |||
* >10 hours (Escherichia coli, in vivo). | |||
'''Instability index:''' | |||
The instability index (II) is computed to be 41.06 | |||
This classifies the protein as unstable. | |||
'''Aliphatic index:''' 97.19 | |||
'''Grand average of hydropathicity (GRAVY):''' -0.097 | |||
'''Globe Predictio'''n: it appears as compact, as a globular domain. | |||
'''Secondary Structure:''' | |||
Helix 34.94% | Helix 34.94% | ||
Extended (sheet) 17.67% | Extended (sheet) 17.67% | ||
| Line 107: | Line 157: | ||
- POS: The position of the AA in the SEQRES derived sequence. | - POS: The position of the AA in the SEQRES derived sequence. | ||
- SEQ: The SEQRES derived sequence in one letter code. | - SEQ: The SEQRES derived sequence in one letter code. | ||
- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier. | - 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier. | ||
- SCORE: The normalized conservation scores. | - SCORE: The normalized conservation scores. | ||
- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable). | - COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable). | ||
- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores. | - CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores. | ||
- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval. | - CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval. | ||
- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position. | - MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position. | ||
- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment. | - RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment. | ||
| Line 138: | Line 196: | ||
19 L LEU65: 0.975 2* 0.108, 1.367 5,1 18/19 A,I,L,M,R,S,V | 19 L LEU65: 0.975 2* 0.108, 1.367 5,1 18/19 A,I,L,M,R,S,V | ||
20 S SER66: -0.045 5 -0.697, 0.404 7,4 18/19 E,H,R,S,T | 20 S SER66: -0.045 5 -0.697, 0.404 7,4 18/19 E,H,R,S,T | ||
21 G GLY67: -1.418 9 -1.755,-1.277 9,9 18/19 G | |||
22 L LEU68: 0.334 4 -0.344, 0.790 6,3 18/19 A,I,K,L,T,V | 22 L LEU68: 0.334 4 -0.344, 0.790 6,3 18/19 A,I,K,L,T,V | ||
23 G GLY69: 0.572 3* -0.136, 1.367 5,1 18/19 A,G,I,L,M,V | 23 G GLY69: 0.572 3* -0.136, 1.367 5,1 18/19 A,G,I,L,M,V | ||
| Line 301: | Line 359: | ||
== Phylogenetic Tree of rsp1275 == | |||
http://consurf.tau.ac.il/results/1240240806/treeView.html | |||
'' | |||
== Reference == | |||
'' | |||
<references/> | |||
'' | |||
== Animated Image Construction == | |||
'' | |||
1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html | |||
2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section. | |||
3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'. | |||
4. On "advanced structural annotation" section select 'docking models in Capri format'. | |||
5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated. | |||
'' | |||
== JMol Image Construction == | |||
'' | |||
1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/. | |||
2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL. | |||
3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing. | |||
4. You can edit your protein by using the scene authoring tools after loading the applet. | |||
Page Created by Susana Retamal, email:susana.retamal@gmail.com | |||
Acknownledment: Jill Zeilstra Ryalls, Adam Meade and Yana Fedotova. | |||
Latest revision as of 04:05, 4 May 2009
Background InformationBackground Information
Rsp1275 is a member of the Fnr-Crp family of transcriptional regulators. Homologues of the Fnr protein from E. coli have been identified in a variety of taxonomically diverse bacterial species.[1][2]The bacterium Rhodobacter sphaeroides" 2.4.1 encodes 8 members of this family, however only 2 have known function. Models of 7 of them, including RSP1275, were successfully obtained using 3D-Jigsaw, all being very similar in structure to Crp (the only one with crystal structure solved). The DNA binding domain helix-turn-helix is located in the C-terminal, and the N-terminal part contains the allosteric effector domain.
Structure of the Proposed rsp1275 modeling obtained using 3D-JigsawStructure of the Proposed rsp1275 modeling obtained using 3D-Jigsaw
|
The highlighted of the protein.
This is the of the protein.
Protein SequenceProtein Sequence
1 mfvpapdati tncrncplrr kplflpfsds elsfmeqfkv gelvvapgvt lleegqgsah
61 lftvlsglgi rstmlengrr qvinflfpgd figlqaglag emrhsvestt tmvlcvfnra
121 dlwdlfreep eraydltwia aveehflget iaslgqrdat erlawallri herlsaigla
181 ergrvpmpwr qqdladalgl slvhtnktir rlretghalw eggtlfvdre rlatlaladp
241 drprrrpli
Physico - Chemical parameters for Rsp1275Physico - Chemical parameters for Rsp1275
From http://ca.expasy.org/tools/protparam.html
Number of amino acids: 249
Molecular weight: 28014.2
Theoretical pI: 6.10
Atomic composition:
Carbon C 1249 Hydrogen H 1986 Nitrogen N 360 Oxygen O 355 Sulfur S 9
Formula: C1249H1986N360O355S9 Total number of atoms: 3959
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
- Ext. coefficient 29115
Abs 0.1% (=1 g/l) 1.039, assuming ALL Cys residues appear as half cystines
- Ext. coefficient 28990
Abs 0.1% (=1 g/l) 1.035, assuming NO Cys residues appear as half cystines
Estimated half-life:
The N-terminal of the sequence considered is M (Met).
The estimated half-life is:
- 30 hours (mammalian reticulocytes, in vitro).
- >20 hours (yeast, in vivo).
- >10 hours (Escherichia coli, in vivo).
Instability index:
The instability index (II) is computed to be 41.06 This classifies the protein as unstable.
Aliphatic index: 97.19
Grand average of hydropathicity (GRAVY): -0.097
Globe Prediction: it appears as compact, as a globular domain.
Secondary Structure: Helix 34.94% Extended (sheet) 17.67% Loop 47.39%
| Amino Acid | Number present | Percentage of total present |
|---|---|---|
| Ala (A) | 15 | 8.8% |
| Arg (R) | 10 | 10.4% |
| Asn (N) | 6 | 2.4% |
| Asp (D) | 10 | 4.8% |
| Cys (C) | 1 | 1.2% |
| Gln (Q) | 5 | 2.8% |
| Glu (E) | 11 | 8.0% |
| Gly (G) | 9 | 7.6% |
| His (H) | 10 | 2.4% |
| Ile (I) | 3 | 4.0% |
| Leu (L) | 21 | 14.5% |
| Lys (K) | 6 | 1.2% |
| Met (M) | 6 | 2.4% |
| Phe (F) | 2 | 4.0% |
| Pro (P) | 8 | 5.2% |
| Ser (S) | 7 | 4.4% |
| Thr (T) | 13 | 6.4% |
| Trp (W) | 2 | 2.0% |
| Tyr (Y) | 6 | 0.4% |
| Val (V) | 12 | 5.6% |
| Pyl (O) | 0 | 0.% |
| Sec (U) | 0 | 0.0% |
Amino Acid Conservation ScoresAmino Acid Conservation Scores
- POS: The position of the AA in the SEQRES derived sequence.
- SEQ: The SEQRES derived sequence in one letter code.
- 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier.
- SCORE: The normalized conservation scores.
- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).
- CONFIDENCE INTERVAL: When using the bayesian method for calculating rates, a confidence interval is assigned to each of the inferred evolutionary conservation scores.
- CONFIDENCE INTERVAL COLORS: When using the bayesian method for calculating rates. The color scale representing the lower and upper bounds of the confidence interval.
- MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position.
- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.
POS SEQ 3LATOM SCORE COLOR CONFIDENCE INTERVAL CONFIDENCE INTERVAL COLORS MSA DATA RESIDUE VARIETY (normalized) 1 P PRO47: -1.063 8* -1.567,-0.697 9,7 3/19 P 2 G GLY48: -0.916 8 -1.417,-0.529 9,7 13/19 G,K 3 V VAL49: 1.226 2 0.404, 2.816 4,1 13/19 C,E,Q,R,V 4 T THR50: 1.816 1 0.790, 2.816 3,1 14/19 A,E,Q,T 5 L LEU51: 0.649 3* -0.136, 1.367 5,1 18/19 I,L,V 6 L LEU52: -0.142 5 -0.697, 0.404 7,4 18/19 F,I,L,Y 7 E GLU53: 1.061 2* 0.108, 1.367 5,1 18/19 A,E,I,K,Q,S,W 8 E GLU54: 0.909 2* 0.108, 1.367 5,1 18/19 A,E,Q,S 9 G GLY55: -0.349 6 -0.852, 0.108 7,5 18/19 D,E,G,P 10 Q GLN56: -0.600 7 -0.998,-0.344 8,6 18/19 D,E,Q,S 11 G GLY57: 2.391 1 2.816, 2.816 1,1 18/19 E,G,I,K,L,P,S,T,V 12 S SER58: 0.521 4* -0.136, 1.367 5,1 18/19 A,L,M,N,S,T 13 A ALA59: 2.175 1 1.367, 2.816 1,1 18/19 A,D,K,N,R,S,T 14 H HIS60: -0.278 6 -0.852, 0.108 7,5 18/19 F,H,K,S 15 L LEU61: 1.898 1 0.790, 2.816 3,1 18/19 C,F,I,L,V,Y 16 F PHE62: 0.468 4 -0.136, 0.790 5,3 18/19 A,F,L,S,Y 17 T THR63: 0.156 5* -0.529, 0.790 7,3 18/19 A,N,Q,S,T,V 18 V VAL64: -0.901 8 -1.277,-0.697 9,7 18/19 I,L,V 19 L LEU65: 0.975 2* 0.108, 1.367 5,1 18/19 A,I,L,M,R,S,V 20 S SER66: -0.045 5 -0.697, 0.404 7,4 18/19 E,H,R,S,T 21 G GLY67: -1.418 9 -1.755,-1.277 9,9 18/19 G 22 L LEU68: 0.334 4 -0.344, 0.790 6,3 18/19 A,I,K,L,T,V 23 G GLY69: 0.572 3* -0.136, 1.367 5,1 18/19 A,G,I,L,M,V 24 I ILE70: -0.318 6 -0.852, 0.108 7,5 18/19 I,K,R,T 25 R ARG71: 0.405 4 -0.344, 0.790 6,3 18/19 I,L,R,S,T 26 S SER72: -0.248 6 -0.852, 0.108 7,5 18/19 C,S,T,Y 27 T THR73: -0.039 5 -0.529, 0.404 7,4 18/19 K,Q,R,T 28 M MET74: -0.296 6 -0.852, 0.108 7,5 19/19 I,L,M,T,V 29 L LEU75: -0.075 5 -0.529, 0.404 7,4 19/19 A,L,M,S,T 30 E GLU76: 0.959 2* 0.108, 1.367 5,1 19/19 E,G,P,S,T 31 N ASN77: 0.131 5 -0.344, 0.404 6,4 19/19 D,E,N,Q,S,T 32 G GLY78: -1.441 9 -1.755,-1.277 9,9 19/19 G 33 R ARG79: -0.815 7 -1.139,-0.529 8,7 19/19 D,E,K,R 34 R ARG80: -0.887 8 -1.277,-0.529 9,7 19/19 E,Q,R 35 Q GLN81: -1.577 9 -1.755,-1.417 9,9 19/19 Q 36 V VAL82: -0.767 7 -1.139,-0.529 8,7 19/19 I,L,M,V 37 I ILE83: -0.369 6 -0.852, 0.108 7,5 19/19 E,I,L,T,V 38 N ASN84: 0.834 3* 0.108, 1.367 5,1 19/19 A,G,N,R,S 39 F PHE85: -0.749 7 -1.139,-0.344 8,6 19/19 F,L,V 40 L LEU86: 0.791 3* 0.108, 1.367 5,1 19/19 A,C,D,H,L,Q 41 F PHE87: -0.246 6 -0.852, 0.108 7,5 19/19 F,G,L 42 P PRO88: -0.534 7 -0.998,-0.136 8,5 19/19 A,P,V 43 G GLY89: -0.907 8 -1.277,-0.697 9,7 19/19 G,P,S 44 D ASP90: -1.388 9 -1.567,-1.277 9,9 19/19 D,E 45 F PHE91: 0.303 4 -0.344, 0.790 6,3 19/19 A,F,L,M,V,Y 46 I ILE92: -0.023 5 -0.697, 0.404 7,4 19/19 E,F,I,L,V 47 G GLY93: -1.441 9 -1.755,-1.277 9,9 19/19 G 48 L LEU94: 0.935 2* 0.108, 1.367 5,1 19/19 E,F,L,M,R,W 49 Q GLN95: 0.552 3* -0.136, 1.367 5,1 19/19 A,D,E,N,P,Q 50 A ALA96: -0.391 6 -1.139, 0.108 8,5 13/19 A,G 51 G GLY97: 0.022 5 -0.697, 0.404 7,4 13/19 G,I,L 52 L LEU98: 2.561 1 2.816, 2.816 1,1 19/19 A,F,G,H,L,M,P,S,T 53 A ALA99: 2.362 1 1.367, 2.816 1,1 19/19 A,G,N,Q,R,S,T,V 54 G GLY100: 2.565 1 2.816, 2.816 1,1 19/19 D,E,G,I,L,M,N,Q,R,S 55 E GLU101: 1.976 1 1.367, 2.816 1,1 19/19 A,E,H,K,N,Q,R,S,T 56 M MET102: 0.254 4 -0.344, 0.790 6,3 19/19 H,M,N,S,V,Y 57 R ARG103: 1.111 2 0.404, 1.367 4,1 19/19 A,N,P,Q,R,S,T,V 58 H HIS104: 0.562 3* -0.136, 1.367 5,1 19/19 F,G,H,L,N,S,Y 59 S SER105: -0.561 7 -0.998,-0.136 8,5 19/19 D,F,S,Y 60 V VAL106: -1.054 8 -1.417,-0.852 9,7 19/19 A,T,V 61 E GLU107: -0.753 7 -1.139,-0.529 8,7 19/19 D,E,Q,T 62 S SER108: -1.062 8 -1.417,-0.852 9,7 19/19 A,S,T 63 T THR109: -0.040 5 -0.529, 0.404 7,4 19/19 A,I,L,T,V 64 T THR110: -0.845 7 -1.277,-0.529 9,7 19/19 E,G,S,T 65 T THR111: 0.081 5* -0.529, 0.790 7,3 19/19 A,D,E,G,T 66 M MET112: 0.816 3* 0.108, 1.367 5,1 19/19 A,C,L,M,S,T,V 67 V VAL113: 0.008 5 -0.529, 0.404 7,4 19/19 E,L,M,R,T,V 68 L LEU114: -0.103 5 -0.697, 0.404 7,4 19/19 I,L,M,V 69 C CYS115: -0.836 7 -1.277,-0.529 9,7 19/19 A,C,V 70 V VAL116: 2.036 1 1.367, 2.816 1,1 19/19 C,E,I,K,Q,R,T,V 71 F PHE117: -0.769 7 -1.277,-0.344 9,6 19/19 F,I,V 72 N ASN118: 1.494 1 0.790, 2.816 3,1 19/19 A,F,G,K,N,P,R,S 73 R ARG119: -0.223 6 -0.697, 0.108 7,5 19/19 A,F,K,R,Y 74 A ALA120: 1.689 1 0.790, 2.816 3,1 18/19 A,D,E,G,K,N,S,T 75 D ASP121: 1.492 1 0.790, 2.816 3,1 18/19 D,I,L,P,T,V 76 L LEU122: -0.309 6 -0.852, 0.108 7,5 18/19 F,L 77 W TRP123: 1.635 1 0.790, 2.816 3,1 18/19 D,E,F,G,L,Q,W 78 D ASP124: 0.991 2* 0.108, 1.367 5,1 18/19 A,D,E,Q,R 79 L LEU125: -0.503 6 -0.998,-0.136 8,5 18/19 F,L,M,R 80 F PHE126: 0.962 2* 0.108, 1.367 5,1 18/19 A,F,I,L,M,S 81 R ARG127: 1.061 2* 0.108, 1.367 5,1 19/19 E,G,L,Q,R,S 82 E GLU128: 0.612 3* -0.136, 1.367 5,1 19/19 E,K,N,S,T 83 E GLU129: 0.413 4 -0.344, 0.790 6,3 19/19 D,E,M,Q,R,T 84 P PRO130: -1.243 9 -1.567,-0.998 9,8 19/19 P,Q 85 E GLU131: -0.080 5 -0.697, 0.404 7,4 19/19 E,H,K,N,Q 86 R ARG132: 0.801 3* 0.108, 1.367 5,1 19/19 I,L,M,R,V 87 A ALA133: 0.460 4 -0.344, 0.790 6,3 19/19 A,G,L,Q,R,S 88 Y TYR134: 0.879 2* 0.108, 1.367 5,1 19/19 C,H,L,Q,R,Y 89 D ASP135: 0.376 4 -0.344, 0.790 6,3 19/19 A,D,E,Q,R,S 90 L LEU136: -0.372 6 -0.852, 0.108 7,5 19/19 I,L,M 91 T THR137: 0.789 3* 0.108, 1.367 5,1 19/19 H,L,M,N,T,W 92 W TRP138: 0.918 2* 0.108, 1.367 5,1 19/19 A,D,E,R,T,W 93 I ILE139: 0.435 4 -0.344, 0.790 6,3 19/19 E,F,I,L,M,Q 94 A ALA140: -0.562 7 -0.998,-0.136 8,5 19/19 A,M,N,S,T 95 A ALA141: 0.604 3* -0.136, 1.367 5,1 19/19 A,F,I,L,S,T 96 V VAL142: 1.537 1 0.790, 2.816 3,1 19/19 A,D,G,K,N,R,S,T,V 97 E GLU143: -1.054 8 -1.417,-0.852 9,7 19/19 E,G,K 98 E GLU144: -0.200 6 -0.697, 0.108 7,5 19/19 E,I,L,M 99 H HIS145: 0.536 3* -0.136, 1.367 5,1 19/19 A,D,H,K,M,Q,S 100 F PHE146: 1.103 2* 0.108, 2.816 5,1 19/19 A,F,G,L,N,Q,R,S 101 L LEU147: -0.661 7 -1.139,-0.344 8,6 19/19 A,D,L 102 G GLY148: -0.441 6 -0.852,-0.136 7,5 19/19 E,G,Q,R 103 E GLU149: -0.539 7 -0.998,-0.136 8,5 19/19 D,E,K,Q 104 T THR150: 0.063 5 -0.529, 0.404 7,4 19/19 H,M,Q,T,W 105 I ILE151: -0.555 7 -0.998,-0.136 8,5 19/19 A,I,L,M 106 A ALA152: -0.041 5 -0.697, 0.404 7,4 19/19 A,G,L,V 107 S SER153: 0.364 4 -0.344, 0.790 6,3 19/19 L,S,T,V,Y 108 L LEU154: -1.173 8 -1.567,-0.998 9,8 19/19 I,L 109 G GLY155: -1.243 9 -1.567,-0.998 9,8 19/19 G,S 110 Q GLN156: -0.805 7 -1.139,-0.529 8,7 19/19 K,N,Q,R 111 R ARG157: 0.138 5 -0.344, 0.404 6,4 19/19 D,K,M,Q,R 112 D ASP158: -0.224 6 -0.697, 0.108 7,5 19/19 C,D,N,S,T 113 A ALA159: -1.362 9 -1.567,-1.139 9,8 19/19 A,I 114 T THR160: 0.916 2* 0.108, 1.367 5,1 19/19 D,E,N,Q,R,T,V 115 E GLU161: -1.294 9 -1.567,-1.139 9,8 19/19 E,V 116 R ARG162: -0.855 7 -1.277,-0.529 9,7 19/19 K,R 117 L LEU163: -0.418 6 -0.852,-0.136 7,5 19/19 I,L,V 118 A ALA164: -1.261 9 -1.567,-1.139 9,8 19/19 A,G,T 119 W TRP165: -0.387 6 -0.852,-0.136 7,5 19/19 A,H,S,W 120 A ALA166: -0.327 6 -0.852, 0.108 7,5 19/19 A,F,L,Y 121 L LEU167: -0.623 7 -1.139,-0.344 8,6 19/19 I,L 122 L LEU168: 2.061 1 1.367, 2.816 1,1 19/19 A,H,L,S,V,Y 123 R ARG169: 0.245 4 -0.344, 0.790 6,3 19/19 D,G,I,L,N,R 124 I ILE170: -0.525 6 -0.998,-0.136 8,5 19/19 I,L,W 125 H HIS171: 0.296 4 -0.344, 0.790 6,3 19/19 A,C,H,R,S 126 E GLU172: 2.674 1 2.816, 2.816 1,1 19/19 C,D,E,H,K,N,Q,R,T 127 R ARG173: -1.085 8 -1.417,-0.852 9,7 19/19 A,H,R 128 L LEU174: 1.821 1 0.790, 2.816 3,1 19/19 A,D,F,L,Q,S,Y 129 S SER175: 1.545 1 0.790, 2.816 3,1 19/19 A,E,G,L,S 130 A ALA176: 0.878 2* -0.136, 1.367 5,1 19/19 A,G,N,P,Q,R,T 131 I ILE177: 1.408 1 0.404, 2.816 4,1 17/19 E,I,K,P,Q,R,T 132 G GLY178: -0.288 6 -0.852, 0.108 7,5 17/19 G,N,S,T 133 L LEU179: 0.548 3* -0.344, 1.367 6,1 17/19 A,F,L,N,V 134 A ALA180: -0.547 7 -0.998,-0.136 8,5 17/19 A,G,S,T 135 E GLU181: 1.841 1 0.790, 2.816 3,1 18/19 A,D,E,G,H,K,P,S 136 R ARG182: 0.783 3* -0.136, 1.367 5,1 17/19 D,K,M,R,T,V 137 G GLY183: 0.172 5* -0.697, 0.790 7,3 2/19 G,T 138 R ARG184: 0.226 4* -0.529, 0.790 7,3 19/19 A,E,Q,R,T 139 V VAL185: -0.496 6 -1.139,-0.136 8,5 19/19 F,L,V 140 P PRO186: 0.687 3* -0.136, 1.367 5,1 19/19 D,P,R,S,T 141 M MET187: -0.889 8 -1.277,-0.529 9,7 19/19 L,M,V 142 P PRO188: -0.993 8 -1.417,-0.697 9,7 19/19 A,P,T 143 W TRP189: -1.104 8 -1.417,-0.852 9,7 19/19 L,M,W 144 R ARG190: -0.591 7 -0.998,-0.344 8,6 19/19 A,G,R,S,T 145 Q GLN191: -1.107 8 -1.417,-0.852 9,7 19/19 Q,R,W 146 Q GLN192: -0.300 6 -0.852, 0.108 7,5 19/19 A,E,G,Q,T 147 D ASP193: -0.990 8 -1.277,-0.697 9,7 19/19 D,E,Q 148 L LEU194: -0.925 8 -1.277,-0.697 9,7 19/19 I,L,M 149 A ALA195: -1.427 9 -1.755,-1.277 9,9 19/19 A,G 150 D ASP196: -1.403 9 -1.567,-1.277 9,9 19/19 D,N 151 A ALA197: 0.072 5 -0.529, 0.404 7,4 19/19 A,F,Y 152 L LEU198: -1.443 9 -1.755,-1.277 9,9 19/19 L 153 G GLY199: -1.441 9 -1.755,-1.277 9,9 19/19 G 154 L LEU200: -1.044 8 -1.417,-0.697 9,7 19/19 L,T 155 S SER201: -1.493 9 -1.755,-1.417 9,9 19/19 S,T 156 L LEU202: -0.226 6 -0.697, 0.108 7,5 19/19 I,L,P,V 157 V VAL203: -1.296 9 -1.567,-1.139 9,8 19/19 E,V 158 H HIS204: -1.435 9 -1.755,-1.277 9,9 19/19 H,T 159 T THR205: -1.190 8 -1.417,-0.998 9,8 19/19 I,T,V 160 N ASN206: -1.519 9 -1.755,-1.417 9,9 19/19 N,S 161 K LYS207: -1.390 9 -1.567,-1.277 9,9 19/19 K,R 162 T THR208: -0.802 7 -1.277,-0.529 9,7 19/19 L,Q,T,V 163 I ILE209: 0.127 5* -0.529, 0.790 7,3 19/19 F,I,L,M,V 164 R ARG210: -0.459 6 -0.852,-0.136 7,5 19/19 G,K,R,S,T 165 R ARG211: -0.501 6 -0.998,-0.136 8,5 19/19 A,K,R,Y 166 L LEU212: -0.866 7 -1.277,-0.529 9,7 19/19 F,L 167 R ARG213: 0.305 4 -0.344, 0.790 6,3 18/19 A,E,K,Q,R 168 E GLU214: -0.134 5 -0.697, 0.404 7,4 18/19 E,K,R 169 T THR215: 1.641 1 0.790, 2.816 3,1 16/19 D,H,I,L,M,Q,S,T 170 G GLY216: -1.323 9 -1.755,-1.139 9,8 14/19 G 171 H HIS217: 0.687 3* -0.136, 1.367 5,1 4/19 A,H,M,V 172 A ALA218: -0.749 7* -1.277,-0.344 9,6 4/19 A,I 173 L LEU219: -0.200 6* -0.852, 0.404 7,4 4/19 A,L,T 174 W TRP220: 0.478 4* -0.344, 1.367 6,1 4/19 I,L,V,W 175 E GLU221: 0.163 5* -0.697, 0.790 7,3 4/19 E,I,Q 176 G GLY222: -0.526 7* -1.139,-0.136 8,5 4/19 G,H 177 G GLY223: -0.842 7* -1.417,-0.529 9,7 2/19 G 178 T THR224: 0.181 4* -0.697, 0.790 7,3 2/19 G,T 179 L LEU225: -0.327 6* -1.139, 0.404 8,4 1/19 L 180 F PHE226: -0.327 6* -1.139, 0.404 8,4 1/19 F 181 V VAL227: -0.327 6* -1.139, 0.404 8,4 1/19 V
Phylogenetic Tree of rsp1275Phylogenetic Tree of rsp1275
http://consurf.tau.ac.il/results/1240240806/treeView.html
ReferenceReference
Animated Image ConstructionAnimated Image Construction
1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html
2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.
3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.
4. On "advanced structural annotation" section select 'docking models in Capri format'.
5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.
JMol Image ConstructionJMol Image Construction
1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.
2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.
3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.
4. You can edit your protein by using the scene authoring tools after loading the applet.
Page Created by Susana Retamal, email:susana.retamal@gmail.com
Acknownledment: Jill Zeilstra Ryalls, Adam Meade and Yana Fedotova.