intro-VIRUSES Virus NamePDB ID HUMAN PAPILLOMAVIRUS 161DZL BACTERIOPHAGE GA1GAV L-A virus1M1C SATELLITE PANICUM MOSAIC VIRUS1STM SATELLITE TOBACCO NECROSIS2BUK.

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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

LIST OF RESIDUE NAMES/NUMBER #/Code Name Hydropathy 1 R+ ARG Arginine K+ L YS Lysine D- ASP Aspartic Acid E- GLU Glutamic Acid N ASN Asparagine Q GLN Glutamine H+ HIS Histidine P PRO Proline Y TYR Tyrosine W TRP Trytophan S SER Serine T THR Threonine G GLY Glycine A ALA Alanine M MET Methionine C CYS Cysteine* (CYX*) F PHE Phenylalanine L LEU Leucine V VAL Valine I ILE Isoleucine 4.5

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, 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, Cα: AVERAGE nmin = 23 nmax = 178

Distances, Cα: AVERAGE

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

Distance, Cα: STANDARD DEV

intro, SASA  11 viruses are used.  The SASA is calculated for every atom using the LCPO method (J Comp Chem, 22, 2, , 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, 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: # of amino acids

SASA: Standard Deviation

SASA: Histograms

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.