residue 2 residue statistics(intraprotein) and solvent accessible surface area (sasa)

intro-VIRUSESVirus Name PDB ID

HUMAN PAPILLOMAVIRUS 16 1DZL

BACTERIOPHAGE GA 1GAV

L-A virus 1M1C

SATELLITE PANICUM MOSAIC VIRUS

1STM

SATELLITE TOBACCO NECROSIS 2BUK

CANINE PARVOVIRUS 2CAS

Human hepatitis B virus 2G34

RYEGRASS MOTTLE VIRUS 2IZW

BACTERIOPHAGE MS2 2MS2

CARNATION MOTTLE VIRUS 1OPO

BACTERIOPHAGE PP7 1DWN

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

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: AVERAGEnmin = 23nmax = 178

Distances, Cα: AVERAGE

Distances, Cα: NSETtot # 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, 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, 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: Histograms

SASA: Histograms

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.