Residue 2 residue statistics intraprotein and solvent accessible surface area sasa
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Residue 2 residue statistics(INTRAPROTEIN) AND SOLVENT ACCESSIBLE SURFACE AREA (SASA) PowerPoint PPT Presentation


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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

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

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Residue 2 residue statistics intraprotein and solvent accessible surface area sasa

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


Intro viruses

intro-VIRUSES


List of residue names number

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


Intro r2r stats

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.


Distances c

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.


Distances c average

Distances, Cα: AVERAGE

nmin = 23

nmax = 178


Distances c average1

Distances, Cα: AVERAGE


Distances c nset

Distances, Cα: NSET

tot # of data points =14827


Distance c standard dev

Distance, Cα: STANDARD DEV


Intro sasa

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.


Intro sasa1

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.


Sasa average

SASA: Average


Sasa of amino acids

SASA: # of amino acids


Sasa standard deviation

SASA: Standard Deviation


Sasa histograms

SASA: Histograms


Sasa histograms1

SASA: Histograms


Sasa histograms2

SASA: Histograms


Sasa histograms3

SASA: Histograms


Sasa conclusion

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.


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