1 / 19

Residue 2 residue statistics (INTRAPROTEIN) AND SOLVENT ACCESSIBLE SURFACE AREA (SASA)

Residue 2 residue statistics (INTRAPROTEIN) AND SOLVENT ACCESSIBLE SURFACE AREA (SASA). intro-VIRUSES. LIST OF RESIDUE NAMES/NUMBER. #/Code Name Hydropathy 1 R+ ARG Arginine -4.5 2 K+ L YS Lysine -3.9

apollo
Download Presentation

Residue 2 residue statistics (INTRAPROTEIN) AND SOLVENT ACCESSIBLE SURFACE AREA (SASA)

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Residue 2 residue statistics (INTRAPROTEIN)AND SOLVENT ACCESSIBLE SURFACE AREA (SASA)

  2. intro-VIRUSES

  3. LIST OF RESIDUE NAMES/NUMBER #/Code Name Hydropathy 1 R+ ARG Arginine -4.5 2 K+ L YS Lysine -3.9 3 D- ASP Aspartic Acid -3.5 4 E- GLU Glutamic Acid -3.5 5 N ASN Asparagine -3.5 6 Q GLN Glutamine -3.5 7 H+ HIS Histidine -3.2 8 P PRO Proline -1.6 9 Y TYR Tyrosine -1.3 10 W TRP Trytophan -0.9 11 S SER Serine -0.8 12 T THR Threonine -0.7 13 G GLY Glycine -0.4 14 A ALA Alanine 1.8 15 M MET Methionine 1.9 16 C CYS Cysteine* (CYX*) 2.5 17 F PHE Phenylalanine 2.8 18 L LEU Leucine 3.8 19 V VAL Valine 4.2 20 I ILE Isoleucine 4.5

  4. intro, R2R STATS • 11 viruses are used. • Residue 2 residue statistics are collected if any non-hydrogen atoms within each residue are within 3.5 Å of each other. • Statistics are ONLY collected for interactions of residues within the same protein of the viral capsid. • All viruses used have icosahedral symmetry. • A protein was used to collect statistics if it was a protein within the “identity” subunit.

  5. Distances, Cα • If two residues are neighbors then the distance between their Cα atoms was calculated. • These distances were tabulated by residue-residue type and their average and standard deviation were found.

  6. Distances, Cα: AVERAGE nmin = 23 nmax = 178

  7. Distances, Cα: AVERAGE

  8. Distances, Cα: NSET tot # of data points =14827

  9. Distance, Cα: STANDARD DEV

  10. intro, SASA • 11 viruses are used. • The SASA is calculated for every atom using the LCPO method (J Comp Chem, 22, 2, 217-230, 1999). • The LCPO method occasionally gives a negative SASA, if this occurred the SASA for that atom was set to zero. • Each residue is then assigned a SASA value based on the sum of the SASA’s of the atoms in that residue. • These values are then tabulated into averages, and standard deviations for each residue type.

  11. intro, SASA • Side Note: • When calculating the neighbor map for the LCPO algorithm on atom i only atoms that were on the same molecule of atom i were used as neighbors of atoms i. • This has the effect of finding not whether an atom is buried inside a viral capsid but rather it is buried within its own protein.

  12. SASA: Average

  13. SASA: # of amino acids

  14. SASA: Standard Deviation

  15. SASA: Histograms

  16. SASA: Histograms

  17. SASA: Histograms

  18. SASA: Histograms

  19. SASA: Conclusion • The general trend of the average seems to imply that the more hydrophilic an amino acid is the higher its SASA is going to be. • However, from the large standard deviations and the evidence given by the histograms this trend should probably not be taken as an absolute.

More Related