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)

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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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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 nset
Distances, Cα: NSET

tot # of data points =14827

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 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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