2. intro-VIRUSES Virus NamePDB ID HUMAN PAPILLOMAVIRUS 161DZL BACTERIOPHAGE GA1GAV L-A virus1M1C SATELLITE PANICUM MOSAIC VIRUS1STM SATELLITE TOBACCO NECROSIS2BUK CANINE PARVOVIRUS2CAS Human hepatitis B virus2G34 RYEGRASS MOTTLE VIRUS2IZW BACTERIOPHAGE MS22MS2 CARNATION MOTTLE VIRUS1OPO BACTERIOPHAGE PP71DWN

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

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.