Contacts of ligand SO41689A in PDB entry 4D4V

Ligand-Protein Contacts (LPC) are derived with the LPC software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.

On this page you will find:

3D ligand structure presentation with Jmol, an open-source Java viewer for chemical structures in 3D (top left window)
Solvent accessible surface of the ligand complexed with protein and in uncomplexed form (top right window). Clicking on "select" buttons highlights atoms in 3D picture
List of residues in contact with the ligand
List of putative hydrogen bonds formed by the ligand
Full list of atomic contacts formed by the ligand
Values of ligand complementarity (a function of atomic contact surface area and the chemical properties of contacting atoms)
Prediction of complementarity changes as a function of atomic substitution in the ligand

Table II
Residues in contact with ligand SO41689A in PDB entry 4D4V (back to top of page)

Legend:
Dist - nearest distance (Å) between atoms of the ligand and the residue
Surf - contact surface area (Å²) between the ligand and the residue
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues contacting ligand by their side chain
       (including CA atoms)

----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue      Dist    Surf    HB    Arom    Phob    DC
----------------------------------------------------------
    541A  ARG*     4.2    17.6    +      -       -      -
    600A  THR*     5.3     6.5    -      -       -      +
    601A  SER*     2.5    39.6    +      -       -      -
    668A  ARG*     3.1    28.3    +      -       -      -
----------------------------------------------------------

Table III
List of putative hydrogen bonds between ligand SO41689A and protein in PDB entry 4D4V (back to top of page)

Legend:
N     - ligand atom number in PDB entry
Dist  - distance (Å) between the ligand and protein atoms
Surf  - contact surface area (Å²) between the ligand and protein atoms
------------------------------------------------------------------------
    Ligand atom            Protein atom
-----------------   ----------------------------    Dist     Surf
  N   Name   Class    Residue       Name   Class
------------------------------------------------------------------------
  2   O1     I        ARG  668A     NH2    III       3.1     14.2
  2   O1     I        ARG  668A     NH1    III       3.9      1.4
  2   O1     I        ARG  541A     NH1    III       4.2     16.1
  3   O2     I        ARG  541A     NH1    III       5.3      1.0
  3   O2     I        SER  601A     N      III       5.5      0.2
  4   O3     I        ARG  668A     NH2    III       3.5      8.3
  4   O3     I        SER  601A     OG     I         4.2      1.0
  5   O4     I        SER  601A     OG     I         2.5     27.7
  5   O4     I        ARG  668A     NH1    III       3.5      2.8
  5   O4     I        SER  601A     N      III       4.1      3.5
------------------------------------------------------------------------

Table IV
Full list of atomic contacts with ligand SO41689A in PDB entry 4D4V (back to top of page)
Total number of contacts is 20

Legend:
N     - ligand atom number in PDB entry
Dist  - distance (A) between the ligand and protein atoms
Surf  - contact surface area (A**2) between the ligand and protein atoms
*     - indicates destabilizing contacts
------------------------------------------------------------------------
    Ligand atom            Protein atom
-----------------   ----------------------------    Dist     Surf
  N   Name   Class    Residue       Name   Class
------------------------------------------------------------------------
  1   S      VI      ARG  668A     NH2    III       3.7       1.6  
  1   S      VI      SER  601A     N      III       5.3       0.4  
  1   S      VI      ARG  541A     NH1    III       5.4       0.4  
  1   S      VI      THR  600A     CB     VI        5.8       1.3  
  2   O1     I       ARG  668A     NH2    III       3.1      14.2  
  2   O1     I       ARG  668A     NH1    III       3.9       1.4  
  2   O1     I       ARG  541A     NH1    III       4.2      16.1  
  3   O2     I       ARG  541A     NH1    III       5.3       1.0  
  3   O2     I       SER  601A     N      III       5.5       0.2  
  3   O2     I       THR  600A     CB     VI        5.7       1.7  
  3   O2     I       THR  600A     CG2    IV        6.0       0.5* 
  4   O3     I       ARG  668A     NH2    III       3.5       8.3  
  4   O3     I       SER  601A     OG     I         4.2       1.0  
  4   O3     I       THR  600A     CB     VI        5.6       2.4  
  4   O3     I       THR  600A     CG2    IV        6.0       0.3* 
  5   O4     I       SER  601A     OG     I         2.5      27.7  
  5   O4     I       SER  601A     CB     VI        3.2       6.8  
  5   O4     I       ARG  668A     NH1    III       3.5       2.8  
  5   O4     I       SER  601A     N      III       4.1       3.5  
  5   O4     I       THR  600A     CB     VI        5.3       0.2  
------------------------------------------------------------------------

Table V
Complementarity values for the ligand SO41689A in PDB entry 4D4V (back to top of page)

---------------------------------------------
Theoretical maximum (Å²)                 196
Actual value (Å²)                         90
Normalised complementarity              0.46
---------------------------------------------

Table VI
Normalised complementarity as a function of atomic substitution for ligand SO41689A in PDB entry 4D4V (back to top of page)

Legend:

N	- ligand atom number in PDB entry
Bold	- indicates atomic substitution which could stabilize the complex
Italics	- indicates atomic substitution which could destabilize the complex

Ligand atom			Atom class
N	Type	Class	I	II	III	IV	V	VI	VII	VIII
1	S	VI	0.46	0.46	0.43	0.43	0.46	0.46	0.43	0.46
2	O1	I	0.46	0.46	0.14	0.14	0.46	0.46	0.14	0.46
3	O2	I	0.46	0.46	0.45	0.45	0.47	0.47	0.45	0.47
4	O3	I	0.46	0.46	0.38	0.37	0.46	0.46	0.38	0.46
5	O4	I	0.46	0.46	0.40	0.11	0.46	0.46	0.40	0.46

A short description of the analytical approach (back to top of page)

The analysis of ligand-protein contacts used in this page is based upon the surface complementarity approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129.
The complementarity function therein is defined as:

CF=S_l-S_i-E

Where S_l is the sum of all surface areas of legitimate atomic contacts between ligand and receptor, S_i is the sum of all surface areas of illegitimate atomic contacts, and E is a repulsion term.

Legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II

For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate

------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------

WARNING !!
Atom classes for ligands are automatically assigned based on the atomic coordinates. However, in three cases the automatic assignment is currently ambiguous (due to low resolution). In these three cases, the user is advised to manually analyze the full list of contacts (Table IV).

1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

IN YOUR STRUCTURE, the following atoms fall in these ambiguous cases:

Ligand KB8 1691
1. Carbon (in rings)
                     5 CAP    6 CAG   15 CAQ   14 CAS    8 CAR    8 CAR
                     9 CAF   10 CAE   11 CAO   13 CAH   14 CAS   17 CAK
                    18 CAI   20 CAJ   21 CAL
3. Nitrogen ("hydrophilic")
                     7 NAM   16 NAT   19 NAN

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il