GetArea

GETAREA

Calculation of Solvent Accessible Surface Areas, Atomic Solvation Energies and Their Gradients for Macromolecules
Surendra Negi, Hongyao Zhu, Robert Fraczkiewicz, Werner Braun

Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555

Quite often a biomolecular researcher wants to quickly calculate solvent accessible surface area or solvation energy of, for example, a protein molecule but does not have time/resources/skills/will to find and install an appropriate software. GETAREA, our efficient method of calculating the solvent accesible surface area [1,2] implemented in program FANTOM, can be directly accessed through this form. An on-line manual is available. Atomic coordinates should be supplied in PDB format. Please cite reference [1] in publications that use our service. Comments are welcome, please mail them to ssnegiATutmb.edu or webraunATutmb.edu .

Please select your PDB file: Please Enter radius of the water probe(A): Do you want gradient in calculations: y or n, Default is n Please enter your Email Address: For information purpose only Select desired level of output: Please note: If you are using a batch file then please use a delay of 10 sec.
ADVANCED OPTIONS: This is a default database of atomic radii and atomic solvation parameters (ASP). By changing its entries you can calculate surface areas for only specific atom types or switch the program to calculate solvation energies with different ASP sets. Please consult the manual for more info. Calculation of solvent accessible surface area of non-hydrogen atoms (for which all ASP=1.0) is the default. Please add one empty line after you add ASP values. # Radii in A from Shrake A & Rupley JA, JMB, 79:351 (1973). # ASP's for non-hydrogen solvent accessible surface area in A^2. # Key ID Radius ASP Type Comment POLAR BB 0.00 0.000 H_B_B # amid/ne H (backbone) APOLAR BB 2.00 1.000 C_A_B # aliphatic C (backbone) APOLAR BB 1.50 1.000 C_B_B # carbon C (backbone) POLAR BB 1.50 1.000 N_B_B # amide -NH- (backbone) POLAR BB 1.40 1.000 O_B_B # carboxyl O (backbone) APOLAR SC 0.00 0.000 H_ALI # aliphatic H APOLAR SC 0.00 0.000 H_ARO # aromatic H POLAR SC 0.00 0.000 H_AMI # amid/ne H POLAR SC 0.00 0.000 H_SUL # sulfur H POLAR SC 0.00 0.000 H_OXY # hydroxyl H APOLAR SC 2.00 1.000 C_ALI # aliphatic -CH2, -CH3 APOLAR SC 1.50 1.000 C_BYL # carbon/xyl C APOLAR SC 1.85 1.000 C_ARO # aromatic =CH-, =CC-, =CN- or =CO- POLAR SC 1.50 1.000 N_AMI # amide -NH- -NH2 POLAR SC 1.50 1.000 N_AMO # amine -NH3 POLAR SC 1.40 1.000 O_BYL # carbonyl O POLAR SC 1.40 1.000 O_BYX # carboxyl O POLAR SC 1.40 1.000 O_HYD # hydroxyl O APOLAR SC 1.85 1.000 S_OXY # sulfur and thiol S of S-S bridge POLAR SC 1.85 1.000 S_RED # sulfur and thiol SH or S-CH3 UNKNOW SC 0.00 0.000 PSEUD # pseudo atoms in NMR structures UNKNOW SC 0.00 0.000 UNKN_ # unknown atom type; do not change! POLAR BB 2.00 1.000 P_DNA # DNA/RNA POLAR BB 1.40 1.000 O_D_P # DNA/RNA POLAR BB 1.40 1.000 O_D_B # DNA/RNA APOLAR BB 2.00 1.000 C_D_B # DNA/RNA APOLAR BB 0.00 0.000 H_D_B # DNA/RNA POLAR SC 1.40 1.000 O_D_S # DNA/RNA APOLAR BB 2.00 1.000 C_D_S # DNA/RNA APOLAR SC 0.00 0.000 H_D_S # DNA/RNA POLAR SC 1.50 1.000 N_ARO # base ring -N-
This is a default library that assigns names of protein atoms to their respective types (the fifth column of ASP database above). Atom name entries follow IUPAC (Pure & Appl. Chem. 70, 117, 1998) plus all PDB violations of these rules. It should suffice for most of proteins. By changing library and ASP database entries you can calculate surface areas and/or solvation energies of molecules different than proteins, e.g. carbohydrates (see manual). Please add one empty line after you add atom types values. # This is the default GETAREA library of atom types for proteins RESIDUE ANY 51 HN H_AMI HN1 H_AMI HN2 H_AMI HN3 H_AMI OB O_BYX OXT O_BYX C C_B_B O O_B_B N N_B_B H H_B_B H1 H_AMI H3 H_AMI H3 H_AMI CA C_A_B HA H_B_B HA1 H_B_B HA2 H_B_B CB C_ALI HB H_ALI HB1 H_ALI HB2 H_ALI HB3 H_ALI QA PSEUD QB PSEUD QD PSEUD QE PSEUD QG PSEUD QG1 PSEUD QG2 PSEUD QR PSEUD QZ PSEUD P P_DNA O1P O_D_P O2P O_D_P O5* O_D_B C5* C_D_B C4* C_D_B O4* O_D_S C3* C_D_B O3* O_D_B C2* C_D_S C1* C_D_S H5* H_D_B H51 H_D_B H52 H_D_B H4* H_D_B H3* H_D_B H2* H_D_S H21 H_D_S H22 H_D_S H1* H_D_S RESIDUE ALA 0 RESIDUE ARG 23 CG C_ALI HG H_ALI HG1 H_ALI HG2 H_ALI HG3 H_ALI CD C_ALI HD H_ALI HD1 H_ALI HD2 H_ALI HD3 H_ALI NE N_AMI HE H_AMI CZ C_ARO NH1 N_AMI NH2 N_AMI HH1 H_AMI HH2 H_AMI HH11 H_AMI HH12 H_AMI HH21 H_AMI HH22 H_AMI QH1 PSEUD QH2 PSEUD RESIDUE ASN 7 CG C_BYL OD1 O_BYL ND2 N_AMI HD2 H_AMI HD21 H_AMI HD22 H_AMI QD2 PSEUD RESIDUE ASP 5 CG C_BYL OD1 O_BYL OD2 O_HYD HD H_OXY HD2 H_OXY RESIDUE CYS 2 SG S_RED HG H_SUL RESIDUE CYSS 1 SG S_RED RESIDUE GLN 12 CG C_ALI HG H_ALI HG1 H_ALI HG2 H_ALI HG3 H_ALI CD C_BYL OE1 O_BYL NE2 N_AMI HE2 H_AMI HE21 H_AMI HE22 H_AMI QE2 PSEUD RESIDUE GLU 10 CG C_ALI HG H_ALI HG1 H_ALI HG2 H_ALI HG3 H_ALI CD C_BYL OE1 O_BYL OE2 O_HYD HE H_OXY HE2 H_OXY RESIDUE GLY 0 RESIDUE HIS 10 CG C_ARO ND1 N_AMI CD2 C_ARO HD1 H_AMI CE1 C_ARO NE2 N_AMI HD2 H_ARO HE H_ARO HE1 H_ARO HE2 H_AMI RESIDUE ILE 16 CG2 C_ALI CG1 C_ALI HG2 H_ALI HG1 H_ALI HG21 H_ALI HG22 H_ALI HG23 H_ALI HG11 H_ALI HG12 H_ALI HG13 H_ALI CD1 C_ALI HD1 H_ALI HD11 H_ALI HD12 H_ALI HD13 H_ALI QD1 PSEUD RESIDUE LEU 15 CG C_ALI HG H_ALI CD1 C_ALI CD2 C_ALI HD1 H_ALI HD2 H_ALI HD11 H_ALI HD12 H_ALI HD13 H_ALI HD21 H_ALI HD22 H_ALI HD23 H_ALI QD1 PSEUD QD2 PSEUD QQD PSEUD RESIDUE LYS 20 CG C_ALI HG H_ALI HG1 H_ALI HG2 H_ALI HG3 H_ALI CD C_ALI HD H_ALI HD1 H_ALI HD2 H_ALI HD3 H_ALI CE C_ALI HE H_ALI HE1 H_ALI HE2 H_ALI HE3 H_ALI NZ N_AMI HZ H_AMI HZ1 H_AMI HZ2 H_AMI HZ3 H_AMI RESIDUE MET 11 CG C_ALI HG H_ALI HG1 H_ALI HG2 H_ALI HG3 H_ALI SD S_OXY CE C_ALI HE H_ALI HE1 H_ALI HE2 H_ALI HE3 H_ALI RESIDUE PHE 11 CG C_ARO CD1 C_ARO CD2 C_ARO HD1 H_ARO CE1 C_ARO CE2 C_ARO HD2 H_ARO HE1 H_ARO CZ C_ARO HE2 H_ARO HZ H_ARO RESIDUE PRO 10 CG C_ALI HG H_ALI HG1 H_ALI HG2 H_ALI HG3 H_ALI CD C_ALI HD H_ALI HD1 H_ALI HD2 H_ALI HD3 H_ALI RESIDUE SER 2 OG O_HYD HG H_OXY RESIDUE THR 7 OG1 O_HYD CG2 C_ALI HG1 H_OXY HG2 H_ALI HG21 H_ALI HG22 H_ALI HG23 H_ALI RESIDUE TRP 15 CG C_ARO CD1 C_ARO CD2 C_ARO CE3 C_ARO CE2 C_ARO NE1 N_AMI HD1 H_ARO HE3 H_ARO CZ3 C_ARO CZ2 C_ARO HE1 H_AMI HZ3 H_ARO CH2 C_ARO HZ2 H_ARO HH2 H_ARO RESIDUE TYR 12 CG C_ARO CD1 C_ARO CD2 C_ARO HD1 H_ARO CE1 C_ARO CE2 C_ARO HD2 H_ARO HE1 H_ARO CZ C_ARO HE2 H_ARO OH O_HYD HH H_OXY RESIDUE VAL 11 CG1 C_ALI CG2 C_ALI HG1 H_ALI HG2 H_ALI HG11 H_ALI HG12 H_ALI HG13 H_ALI HG21 H_ALI HG22 H_ALI HG23 H_ALI QQG PSEUD RESIDUE A 15 N9 N_ARO C8 C_ARO N7 N_ARO C5 C_ARO C6 C_ARO N6 N_AMI N1 N_ARO C2 C_ARO N3 N_ARO C4 C_ARO H8 H_ARO H6 H_AMI H61 H_AMI H62 H_AMI H2 H_ARO RESIDUE G 16 N9 N_ARO C8 C_ARO N7 N_ARO C5 C_ARO C6 C_ARO O6 O_BYL N1 N_ARO C2 C_ARO N2 N_AMI N3 N_ARO C4 C_ARO H8 H_ARO H1 H_AMI H2 H_AMI H21 H_AMI H22 H_AMI RESIDUE C 13 N1 N_ARO C2 C_ARO O2 O_BYL N3 N_ARO C4 C_ARO N4 N_AMI C5 C_ARO C6 C_ARO H4 H_AMI H41 H_AMI H42 H_AMI H5 H_ARO H6 H_ARO RESIDUE T 15 N1 N_ARO C2 C_ARO O2 O_BYL N3 N_ARO C4 C_ARO O4 O_BYL C5 C_ARO C5M C_ALI C6 C_ARO H3 H_AMI H5M H_ALI H5M1 H_ALI H5M2 H_ALI H5M3 H_ALI H6 H_ARO RESIDUE U 11 N1 N_ARO C2 C_ARO O2 O_BYL N3 N_ARO C4 C_ARO O4 O_BYL C5 C_ARO H5 C_ARO C6 C_ARO H3 H_AMI H6 H_ARO RESIDUE DA 15 N9 N_ARO C8 C_ARO N7 N_ARO C5 C_ARO C6 C_ARO N6 N_AMI N1 N_ARO C2 C_ARO N3 N_ARO C4 C_ARO H8 H_ARO H6 H_AMI H61 H_AMI H62 H_AMI H2 H_ARO RESIDUE DG 16 N9 N_ARO C8 C_ARO N7 N_ARO C5 C_ARO C6 C_ARO O6 O_BYL N1 N_ARO C2 C_ARO N2 N_AMI N3 N_ARO C4 C_ARO H8 H_ARO H1 H_AMI H2 H_AMI H21 H_AMI H22 H_AMI RESIDUE DC 13 N1 N_ARO C2 C_ARO O2 O_BYL N3 N_ARO C4 C_ARO N4 N_AMI C5 C_ARO C6 C_ARO H4 H_AMI H41 H_AMI H42 H_AMI H5 H_ARO H6 H_ARO RESIDUE DT 15 N1 N_ARO C2 C_ARO O2 O_BYL N3 N_ARO C4 C_ARO O4 O_BYL C5 C_ARO C5M C_ALI C6 C_ARO H3 H_AMI H5M H_ALI H5M1 H_ALI H5M2 H_ALI H5M3 H_ALI H6 H_ARO RESIDUE DU 11 N1 N_ARO C2 C_ARO O2 O_BYL N3 N_ARO C4 C_ARO O4 O_BYL C5 C_ARO H5 C_ARO C6 C_ARO H3 H_AMI H6 H_ARO

Please make sure that you are using standard amino acids and atoms name. A complete list is available here : HELP

Using multipe pdb files!

Users can use Getarea_Remote.pl program to submit multiple PDB files to getarea server. Click this link to download Getarea_Remote.pl program. Please note: If you are using a batch file then please use a delay of 10 sec.

Disclaimer:

This service is provided freely to the scientific community for the purpose of scientific research. There is no warranty for the service, either expressed or implied. The entire risk as to the quality and performance of the service is with the user. In no event will Sealy Center for Structural Biology be liable for any damages, including any general, special or consequential damages arising out of the use, misuse, or inability to use this service.

References:

Fraczkiewicz, R. and Braun, W. (1998) "Exact and Efficient Analytical Calculation of the Accessible Surface Areas and Their Gradients for Macromolecules" J. Comp. Chem., 19, 319-333.
html version of the document is also available at https://web.archive.org/web/20100612022744/http://bose.utmb.edu/poster1/index.html
von Freyberg, B., Richmond, T.J. and Braun, W. Surface area included in energy refinement of proteins: a comparative study on atomic solvation parameters. J. Mol. Biol. 233(2):275-292, 1993.
von Freyberg, B. and Braun, W. Minimization of empirical energy functions in proteins including hydrophobic surface area effects. J. Comp. Chem. 14(5):510-521, 1993.
Fraczkiewicz, R. and Braun, W. "A New Efficient Algorithm for Calculating Solvent Accessible Surface Areas of Macromolecules" presented at the Third Electronic Computational Chemistry Conference; Northern Illinois University; November 1996; World Wide Web.

Last modified on Tue Friday April 17, 3:00 PM 2015 by Surendra Negi. For more information visit: http://curie.utmb.edu