Basic Results

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Section 1-ASA (Accessible Surface Area) values

This section defines the polar and nonpolar ASA values for the free ligand, bound ligand, free enzyme, and bound enzyme. These values are presented in a table 1. The "free ligand ASA - bound ligand ASA" and "free enzyme ASA - bound enzyme ASA" for both polar and nonpolar quantities are what STC uses to calculate the thermodynamics of binding. All changes in ASA are given in Section 2, Table 2.

Table 1
Species     Polar ASA (A2)      Nonpolar ASA (A2)
Free Ligand         #               #
Bound Ligand        #               #
Free Enzyme         #               #
Bound Ligand        #               #

This section defines the change in ASA, nonpolar and polar, when comparing the free verses bound ligand and free verses bound enzyme. The difference in polar area upon binding for the ligand is then added to the respective polar value for the enzyme. This total change in ASA polar is what STC directly uses for thermodynamic calculations. The difference in nonpolar area upon binding for the ligand is then added to the respective nonpolar value for the enzyme. This total change is ASA nonpolar is what STC directly uses for thermodynamic calculations. These are global values, the dASA for individual atoms and residues are listed in the detailed output file Tables 1-4.

Table 2
 Species     Polar dASA (A2)     Nonpolar dASA (A2)
 ligand               222.30               740.50
 enzyme               513.14               770.96
 ligand+enzyme        735.44              1511.46

This section defines the thermodynamic values calculated from the dASA nonpolar and dASA polar contributions from the ligand + enzyme. The thermodynamic calculations listed are the global values, the individual atom or residue values are listed in the detailed output file. For exact details please see the Stc paper .

DCpbind is the heat capacity of binding and should be a negative value (positive if viewed as dissociation). This value is calculated from the dASA nonpolar and dASA polar values. The unit for heat capacity is kcal/mol/K.

DHbind is the enthalpy of binding and can be positive or negative. If it is positive then the enthalpy of binding is unfavorable, if negative then the enthalpy of binding is favorable (the opposite is true for dissociation). The enthalpy of binding is calculated from the heat capacity of binding plus the binding enthalpy at a reference temperature of 60 degrees C. The unit for enthalpy of binding is kcal/mol.

DSbind is the entropy of binding and can be positive or negative. If this number is positive then the entropy of binding turns out to be favorable, if negative then the entropy of binding turns out to be unfavorable (the opposite is true for dissociation). The unit for entropy of binding is kcal/mol/K. The entropy of binding is a sum of 3 entropies that are listed below. The first is the solvation entropy, DSsol, which is directly calculated from the dASA nonpolar and dASA polar values (unit is kcal/mol.K). The second is the overall rotational/translational entropy, DSrt, which has a set value of -0.008 kcal/mol.K. The third is the conformational entropy, DSconf, which in itself is a sum of 3 entropies. The first contribution to conformational entropy is DSbu_ex, which is the change in conformational entropy of the side chains due to tertiary or quaternary interactions during binding. The second contribution to conformational entropy is DSex_u, which is the change in conformational entropy of the side chains due to secondary structure changes upon binding. The third contribution to conformational entropy is DSbb, which is the change in conformational entropy of the backbone upon binding. The 3 types of conformational entropy are generally unfavorable with respect to binding resulting in a negative value having the unit kcal/mol.K. The overall conformational entropy of each residue is given in Tables 5 and 6 in the output file containing the detailed results. The individual contributions (DSbu_ex , DSex_u, and DSbb) to conformational entropy per residue is also given in Tables 5 and 6 in the output file containing the detailed results.

TDSbind is the entropy of binding at the temperature where the structure was determined. This value is useful in calculating free energy.

DGbind is the free energy of binding and it is calculated from DHbind - TDSbind. A negative value for DGbind indicates binding is favorable, a positive value for DGbind indicates binding in not favorable. From DGbind one can quickly calculate a Ka and Kd. Many of these thermodynamic values are given for each residue in Tables 7 and 8 in the detailed output file.

Table 3
Thermodynamic Values
 DCpbind      -0.488940  kcal/mol.K
 DHbind        6.776650  kcal/mol
 DSbind        0.064941  kcal/mol.K
  DSsol        0.151776  kcal/mol.K
  DSrt        -0.008000  kcal/mol.K
  DSconf      -0.078834  kcal/mol.K
   DSbu->ex    0.047051  kcal/mol.K
   DSex->u     0.000000  kcal/mol.K
   DSbb        0.031783  kcal/mol.K
 -TDSbind    -19.362266  kcal/mol
 DGbind      -12.585616  kcal/mol
 Ka           1.682e+09  1/M
 Kd           5.945e-10  M

STC Detailed Results File
Date:
Data File Information
Complex Data File: *.acc
Number of Atoms: #
Ligand Data File: *.acc
Number of Atoms: #
Enzyme Data File: *.acc
Number of Atoms: #

This section displays the results for atoms having a change in their ASA when comparing the free ligand with the bound ligand and free enzyme with the bound enzyme. The first table shows the results for the ligand, the second table is for the enzyme. Only atoms with a change in ASA are shown. View an Example.

Section 3-Residue dASA

This section displays the results for residues having a change in their ASA when comparing the free ligand with the bound ligand and free enzyme with the bound enzyme. The first table shows the results for the ligand, the second is for the enzyme. Only residues with a change in ASA are shown. View an Example.

Section 4- Calculating DSconf

This section displays the calculation for the conformation entropy for each residue. This is done separately for the ligand and the enzyme. It also includes the dSbu->ex, dSex->u, and dSbb values used to compute dSconf per residue. dASATot is the sum of nonpolar dASA and polar dASA for each residue. dASAsc is the change in ASA for the side chain of each residue. The next 3 entropy values deal with structural changes in side chain or backbone conformations upon binding. When added together they total dSconf. View an Example.

Section 5-Thermodynamic values for each residue

This section gives the heat capacity of binding, the enthalpy of binding, the different entropies of binding, and the free energy of binding for each residue. The entropy values are multiplied by the temperature the structure was calculated at (oK). View an Example.

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