GETAREA 1.0 beta

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

Introduction

GETAREA is a web service provided by the Sealy Center for Structural Biology at the University of Texas Medical Branch. Originally, GETAREA was a subroutine for efficient analytical calculation of solvent accessible surface area and its gradient for proteins [1,2] implemented in our program FANTOM. This service allows a user to submit Cartesian coordinates of atoms in a molecule, stored in PDB format on her/his local disk, and to get back solvent accessible surface area (SASA) or solvation energy (depending on parameter setup) in a variety of formats. By default, the submission form is set up to calculate SASA of non-hydrogen atoms in proteins, but an appropriate change of input parameters will allow to compute any quantity proportional to SASA for any kind of molecule.

Input of atomic coordinates

Specify a path to your data file containing Cartesian coordinates in the format of Protein Data Bank. The only recognizable keywords are: ATOM, HETATM, TER and END. Lines starting with other keywords are ignored. Atom names must coincide with those defined in the atom library; otherwise an error will occur. It is especially true in the case of ambiguous atom positions marked with capital letters A, B, etc. A user must resolve this ambiguity by manual editing the PDB file, otherwise the calculated SASA would be meaningless. Input is terminated by the first encountered TER or END keyword. Other input options are self-explanatory.

Macintosh users: if you use a word processor to edit a PDB file, then save it as "MSDOS text". Submitting a file saved as regular "text file" will most likely produce an error message.

Examples:


The following output is produced for serine protease inhibitor (PDB code 1COA) with standard settings. 

 Job identifier:  get_a_16884 
 Probe radius  :  1.400

 ---------------------------------------------
 POLAR  area/energy         =         1477.33
 APOLAR area/energy         =         2948.62
 UNKNOW area/energy         =            0.00
 ---------------------------------------------
 Total  area/energy         =         4425.95
 ---------------------------------------------
 Number of surface atoms    =          316
 Number of buried atoms     =          196
 Number of atoms with ASP=0 =            0
The same job with surface area output requested per residue: 
 Job identifier:  get_a_16930 
 Probe radius  :  1.400

  Residue      Total   Apolar  Backbone Sidechain Ratio(%) In/Out
 MET     20   159.24   100.77    75.37    83.87     53.0     o
 LYS     21    79.28    64.98     8.99    70.28     42.7      
 THR     22    67.67    45.64     0.97    66.70     62.8     o
 GLU     23    73.21    20.44     1.93    71.27     50.5     o
 TRP     24     0.00     0.00     0.00     0.00      0.0     i
 PRO     25    74.82    63.67    11.15    63.67     60.5     o
 GLU     26    90.68    74.36    18.43    72.24     51.2     o
 LEU     27     3.33     3.33     0.00     3.33      2.3     i
 VAL     28    69.90    56.54    13.37    56.54     46.2      
 GLY     29    50.40    32.33    50.40     0.00     57.8     o
 LYS     30   101.48    77.54     4.37    97.11     59.0     o
 SER     31    46.95    41.54     2.40    44.56     57.6     o
 VAL     32    24.62    24.52     0.10    24.52     20.0      
 GLU     33   119.04    36.56     1.73   117.31     83.1     o
 GLU     34   101.40    25.03     0.37   101.03     71.6     o
 ALA     35     0.00     0.00     0.00     0.00      0.0     i
 LYS     36    87.49    48.29     0.00    87.49     53.2     o
 LYS     37   103.86   101.73     6.88    96.99     59.0     o
 VAL     38    47.71    47.71     1.17    46.54     38.1      
 ILE     39     0.00     0.00     0.00     0.00      0.0     i
 LEU     40    78.12    71.02     7.12    71.01     48.6      
 GLN     41   139.70    41.40    26.90   112.80     78.5     o
 ASP     42    57.28    13.31    25.09    32.19     28.5      
 LYS     43     3.84     3.66     0.98     2.86      1.7     i
 PRO     44   110.92    92.14    20.91    90.01     85.6     o
 GLU     45    90.02    68.70    15.40    74.63     52.9     o
 ALA     46     9.59     0.00     9.59     0.00      0.0     i
 GLN     47    97.29    29.11     3.77    93.52     65.1     o
 ILE     48    29.96     8.79    21.21     8.75      5.9     i
 ILE     49    76.36    76.36     3.71    72.66     49.3      
 VAL     50    67.07    47.45    19.62    47.45     38.8      
 LEU     51    39.47    39.47     0.03    39.45     27.0      
 PRO     52    89.79    89.79     0.01    89.78     85.3     o
 VAL     53    75.34    57.95    17.40    57.95     47.4      
 GLY     54    68.00    44.56    68.00     0.00     78.0     o
 THR     55    60.48    47.95    20.96    39.52     37.2      
 ILE     56   172.42   155.82    21.45   150.98    100.0     o
 VAL     57    59.65    46.84    17.25    42.40     34.7      
 THR     58   106.02    99.19    10.72    95.30     89.7     o
 MET     59   203.93   182.91    32.34   171.58    100.0     o
 GLU     60   102.74    42.72    12.14    90.60     64.2     o
 TYR     61   160.35   115.56    29.16   131.19     67.9     o
 ARG     62   128.12    46.60     4.14   123.98     63.4     o
 ILE     63   108.89   108.89     0.00   108.89     73.9     o
 ASP     64    32.13    15.45     0.19    31.94     28.3      
 ARG     65    30.99    10.92     0.00    30.99     15.9     i
 VAL     66     0.00     0.00     0.00     0.00      0.0     i
 ARG     67    41.75     6.28     1.58    40.17     20.5      
 LEU     68     0.36     0.36     0.36     0.00      0.0     i
 PHE     69    33.09    32.25     0.84    32.25     17.9     i
 VAL     70     8.44     6.86     1.58     6.86      5.6     i
 ASP     71    60.40    32.46    13.01    47.39     41.9      
 LYS     72   199.41   133.00    37.66   161.75     98.3     o
 LEU     73   144.83   128.90    20.94   123.89     84.7     o
 ASP     74    76.93    19.22     0.16    76.78     67.9     o
 ASN     75    39.89     4.92     0.00    39.89     34.9      
 VAL     76     0.79     0.03     0.76     0.03      0.0     i
 ALA     77    42.58    24.05    25.49    17.09     26.3      
 GLU     78    80.35    31.51     4.60    75.74     53.6     o
 VAL     79    42.59    35.04     7.55    35.04     28.7      
 PRO     80     3.51     3.51     3.46     0.05      0.0     i
 ARG     81   127.86    59.40     2.70   125.16     64.0     o
 VAL     82    15.67     1.74    13.93     1.74      1.4     i
 GLY     83     7.92     7.54     7.54     0.38      9.1     i
 ---------------------------------------------
 POLAR  area/energy         =         1477.33
 APOLAR area/energy         =         2948.62
 UNKNOW area/energy         =            0.00
 ---------------------------------------------
 Total  area/energy         =         4425.95
 ---------------------------------------------
 Number of surface atoms    =          316
 Number of buried atoms     =          196
 Number of atoms with ASP=0 =            0
The contributions from backbone and sidechain atoms are listed in the 5th and 6th columns respectively. The next column lists the ratio of side-chain surface area to "random coil" value per residue. The "random coil" value of a residue X is the average solvent-accessible surface area of X in the tripeptide Gly-X-Gly in an ensemble of 30 random conformations. Residues are considered to be solvent exposed if the ratio value exceeds 50% and to be buried if the ratio is less than 20%, marked as "o" and "i" respectively in the last column. The "random coil" values for 20 amino acids are:

Database of atomic types

Our basic goal was to make our service as flexible as possible. Therefore, in the "Advanced Options" section we made all the files that GETAREA depends on available to the user. In this section we describe the editable database of atomic types. The default database contains protein atom types and atomic solvation parameters (ASP) corresponding to the solvent accessible surface area of non-hydrogen atoms in squared angstroms. Comments start with a "#". Each data line contains a keyword describing a group of atom types. Keywords allow for defining global properties of atoms; in the default setting all atoms are divided into "polar", "apolar" and "unknown" groups. This affects output, since GETAREA will list SASA for each keyword. The following character strings "BB" and "SC" identify atom types as backbone and sidechain respectively. Identifiers are followed in data lines by atomic radii, whose units will determine units of the surface area. All radii, including radius of the water probe, must be in the same units. The next entry, atomic solvation parameters, are either unitless (for SASA calculations) or have units of energy/area. Changing the value of ASPs lets the user explore a wide variety of solvation models to calculate the value of solvation energy term and its gradient. ASP entry is followed by an atom type that allows to assign a radius and an ASP to every atom name specified in the library. Type PSEUD corresponds to pseudo atoms used as reference points in NMR structures. The "unknown" type UNKN_ must be always present. It allows GETAREA to continue calculations even when some atom names cannot be matched against their types. A warning message is issued in this case. Both the radius and the ASP for UNKN_ must be equal to zero. Users can modify or define their own database observing the following rules:

Examples:

An alternative ASP database classifies atoms by element and uses solvation model of Wesson and Eisenberg [5]: 

# Key   ID Radius  ASP   Type            Comment
HYDROG  BB  0.00  0.000  H_B_B   # amid/ne H   (backbone)
CARBON  BB  2.00  0.012  C_A_B   # aliphatic C (backbone) 
CARBON  BB  1.50  0.012  C_B_B   # carbon C    (backbone)
NITROG  BB  1.50 -0.116  N_B_B   # amide -NH-  (backbone)
OXYGEN  BB  1.40 -0.116  O_B_B   # carboxyl O  (backbone)
HYDROG  SC  0.00  0.000  H_ALI   # aliphatic H
HYDROG  SC  0.00  0.000  H_ARO   # aromatic H
HYDROG  SC  0.00  0.000  H_AMI   # amid/ne H
HYDROG  SC  0.00  0.000  H_SUL   # sulfur H
HYDROG  SC  0.00  0.000  H_OXY   # hydroxyl H
CARBON  SC  2.00  0.012  C_ALI   # aliphatic -CH2, -CH3
CARBON  SC  1.50  0.012  C_BYL   # carbon/xyl C
CARBON  SC  1.85  0.012  C_ARO   # aromatic =CH-, =CC-, =CN- or =CO-
NITROG  SC  1.50 -0.116  N_AMI   # amide -NH- -NH2
NITROG  SC  1.50 -0.186  N_AMO   # amine -NH3
OXYGEN  SC  1.40 -0.116  O_BYL   # carbonyl O
OXYGEN  SC  1.40 -0.175  O_BYX   # carboxyl O
OXYGEN  SC  1.40 -0.116  O_HYD   # hydroxyl O
SULFUR  SC  1.85 -0.018  S_OXY   # sulfur and thiol S of S-S bridge
SULFUR  SC  1.85 -0.018  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!
Atomic solvation parameters are in kcal/mol/angstrom2. The same PDB input as in a previous section produces solvation energy in kcal/mol split into chemical element contributions: 
 Job identifier:  get_a_17094 
 Probe radius  :  1.400

 ---------------------------------------------
 HYDROG area/energy         =            0.00
 CARBON area/energy         =           34.64
 NITROG area/energy         =          -56.58
 OXYGEN area/energy         =         -114.81
 SULFUR area/energy         =           -1.11
 UNKNOW area/energy         =            0.00
 ---------------------------------------------
 Total  area/energy         =         -137.86
 ---------------------------------------------
 Number of surface atoms    =          316
 Number of buried atoms     =          196
 Number of atoms with ASP=0 =            0

Library of atom names

Atom library matches atom names with respective atom types; the latter must be consistent with ASP database entries described above. The default library contains protein atoms named according to the latest IUPAC recommendations [4] plus all PDB violations of these rules. The library is scanned by GETAREA to assign an appropriate keyword, radius and atomic solvation parameter from ASP database to every atom entry read from the supplied PDB file. It is built of residue blocks. To save space, the first residue block contains atoms common to all residues and all the remaining blocks contain only residue-specific atoms. The first block is scanned for atom name match regardless of the residue name, if no match is found GETAREA scans the block beginning with a given residue name. Atom names that cannot be found in the library are automatically associated with the type UNKN_ (see previous section); a warning message is issued in such a case. Users can modify or define their own library observing the following rules:

Examples:

In this example the library and ASP database are redefined to calculate the solvent accessible surface area of a molecule of trimethylamine oxide (TMAO). First, the x-ray structure of TMAO is expressed in PDB format: 

COMPND    Trimethylamine oxide
ATOM      1  O   TMAO    1       1.123   1.621   5.991
ATOM      2  N   TMAO    1       1.970   0.633   5.482
ATOM      3  C1  TMAO    1       1.316  -0.014   4.322
ATOM      4  C2  TMAO    1       2.230  -0.377   6.539
ATOM      5  C3  TMAO    1       3.245   1.258   5.052
ATOM      6  H11 TMAO    1       1.889  -0.706   3.984
ATOM      7  H12 TMAO    1       1.149   0.630   3.630
ATOM      8  H13 TMAO    1       0.484  -0.399   4.609
ATOM      9  H21 TMAO    1       2.790  -1.053   6.149
ATOM     10  H22 TMAO    1       1.398  -0.770   6.812
ATOM     11  H23 TMAO    1       2.671   0.002   7.303
ATOM     12  H31 TMAO    1       3.850   0.596   4.715
ATOM     13  H32 TMAO    1       3.656   1.725   5.785
ATOM     14  H33 TMAO    1       3.031   1.883   4.355
END
Second, the new library of atom names is created: 
# Atom names for TMAO
RESIDUE  TMAO 14
 O   OXYGE 
 N   NITRO
 C1  CARBO
 C2  CARBO
 C3  CARBO
 H11 HYDRO
 H12 HYDRO
 H13 HYDRO
 H21 HYDRO
 H22 HYDRO
 H23 HYDRO
 H31 HYDRO
 H32 HYDRO
 H33 HYDRO
Third, the corresponding ASP database is defined (radii values are used here for illustrative purposes only): 
# Key   ID Radius  ASP   Type    #         Comment
HYDROG  NO  0.50  1.000  HYDRO   # hydrogen 
CARBON  NO  1.50  1.000  CARBO   # carbon
NITROG  NO  1.50  1.000  NITRO   # nitrogen
OXYGEN  NO  1.40  1.000  OXYGE   # oxygen
UNKNOW  NO  0.00  0.000  UNKN_   # unknown atom type; do not change!
With the most detailed output option GETAREA generates the following: 
 Job identifier:  get_a_17047 
 Probe radius  :  1.400

 ATOM  NAME  RESIDUE   AREA/ENERGY
     1 O    TMA     1    42.54
     2 N    TMA     1     0.00
     3 C1   TMA     1    50.10
     4 C2   TMA     1    50.26
     5 C3   TMA     1    50.23
     6 H11  TMA     1    12.27
     7 H12  TMA     1    12.73
     8 H13  TMA     1    12.47
     9 H21  TMA     1    11.91
    10 H22  TMA     1    12.55
    11 H23  TMA     1    13.13
    12 H31  TMA     1    12.59
    13 H32  TMA     1    12.86
    14 H33  TMA     1    12.12
 ---------------------------------------------
 HYDROG area/energy         =          112.62
 CARBON area/energy         =          150.58
 NITROG area/energy         =            0.00
 OXYGEN area/energy         =           42.54
 UNKNOW area/energy         =            0.00
 ---------------------------------------------
 Total  area/energy         =          305.74
 ---------------------------------------------
 Number of surface atoms    =           13
 Number of buried atoms     =            1

 Number of atoms with ASP=0 =            0
Nitrogen atom in TMAO is inaccessible to the 1.4-angstrom water probe.

References

  1. Fraczkiewicz, R; Braun, W. (1998) J. Comp. Chem., 19, 319.
  2. Fraczkiewicz, R; Braun, W. A New Efficient Algorithm for Calculating Solvent Accessible Surface Areas of Macromolecules, ECCC3; Nov. 1996; Northern Illinois Univ.
  3. Eisenberg, D; McLachlan, AD. (1986) Nature, 319, 199.
  4. Markley, JL; Bax, A; Arata, Y; Hilbers, CW; Kaptein, R; Sykes, BD; Wright, PE; Wuthrich, K. (1998) Pure & Appl. Chem., 70, 117.
  5. Wesson, L; Eisenberg, D. (1992) Protein Sci., 1, 227.

Last modified on Wed 17th April, 3:00 PM, 2015  by  Surendra S Negi