Contacts of ligand AKG 702A in PDB entry 3KV6
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 AKG 702A
in PDB entry 3KV6 (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
----------------------------------------------------------
224A ASN* 3.7 10.0 + - - +
225A VAL 4.8 1.0 - - - +
226A ILE* 3.2 51.7 - - + +
271A LEU* 4.6 9.9 - - + +
277A SER* 5.0 2.1 + - - -
279A THR* 3.6 21.6 + - - +
282A HIS* 3.2 13.9 + - - -
284A ASP* 3.5 7.1 + - - -
292A TYR* 2.7 31.8 + - + -
299A LYS* 3.1 26.1 + - + -
301A PHE* 5.6 0.2 - - + -
354A HIS* 4.4 0.3 + - - -
356A VAL* 3.0 51.7 + - + +
358A THR* 3.0 25.1 + - - -
491A FE2 2.3 33.8 - - - -
492A OXY 3.8 11.4 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand AKG 702A
and protein in PDB entry 3KV6
(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 II OXY 492A O2 I 3.8 9.7
2 O1 II OXY 492A O1 I 4.1 0.7
3 O2 I TYR 292A OH I 2.7 4.0
3 O2 I HIS 282A NE2 I 3.2 5.0
3 O2 I ASP 284A OD1 II 3.5 7.1
3 O2 I OXY 492A O2 I 4.1 0.5
5 O5 II TYR 292A OH I 3.6 4.5
5 O5 II HIS 354A NE2 I 4.4 0.3
9 O3 II LYS 299A NZ III 3.6 4.0
9 O3 II ASN 224A ND2 III 3.7 3.5
10 O4 I THR 358A OG1 I 3.0 25.1
10 O4 I THR 279A OG1 I 4.3 1.4
10 O4 I VAL 356A O II 4.3 3.1
10 O4 I ASN 224A ND2 III 4.4 2.4
10 O4 I SER 277A O II 5.0 1.0
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand AKG 702A
in PDB entry 3KV6 (back
to top of page)
Total number of contacts is 63
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 C1 VI TYR 292A OH I 3.2 8.1
1 C1 VI HIS 282A NE2 I 4.1 3.8
1 C1 VI TYR 292A CZ V 4.1 0.9
1 C1 VI OXY 492A O2 I 4.2 0.4
1 C1 VI TYR 292A CE1 V 4.3 0.2
1 C1 VI ILE 226A CD1 IV 5.0 3.1
1 C1 VI THR 279A CG2 IV 5.2 0.9
2 O1 II OXY 492A O2 I 3.8 9.7
2 O1 II OXY 492A O1 I 4.1 0.7
2 O1 II ILE 226A CB IV 4.1 12.3*
2 O1 II ILE 226A O II 4.3 4.5*
2 O1 II ILE 226A CD1 IV 4.3 2.9*
2 O1 II LEU 271A CD2 IV 4.6 1.9*
3 O2 I FE2 491A FE VI 2.3 30.0
3 O2 I TYR 292A OH I 2.7 4.0
3 O2 I HIS 282A NE2 I 3.2 5.0
3 O2 I ASP 284A OD1 II 3.5 7.1
3 O2 I OXY 492A O2 I 4.1 0.5
3 O2 I HIS 282A CD2 V 4.2 0.2
4 C2 VIII TYR 292A OH I 3.6 4.3
4 C2 VIII TYR 292A CE1 V 4.2 2.0
4 C2 VIII HIS 282A NE2 I 4.5 1.3
4 C2 VIII THR 279A OG1 I 4.5 2.9
4 C2 VIII HIS 282A CE1 V 4.6 0.4
4 C2 VIII THR 279A CG2 IV 4.7 0.2
5 O5 II VAL 356A CG2 IV 3.0 20.8*
5 O5 II TYR 292A OH I 3.6 4.5
5 O5 II FE2 491A FE VI 3.6 3.8
5 O5 II HIS 282A CE1 V 4.0 3.1
5 O5 II TYR 292A CZ V 4.2 0.7
5 O5 II HIS 354A NE2 I 4.4 0.3
6 C3 IV ILE 226A CG2 IV 3.9 10.8
6 C3 IV THR 279A OG1 I 4.0 2.9*
6 C3 IV TYR 292A CE1 V 4.6 5.6
6 C3 IV LEU 271A CD1 IV 5.0 4.5
7 C4 IV VAL 356A CB IV 3.5 17.7
7 C4 IV THR 279A OG1 I 3.6 6.1*
7 C4 IV VAL 356A CG1 IV 3.7 2.5
7 C4 IV LYS 299A CE VII 4.3 1.8
7 C4 IV LYS 299A CG IV 5.2 0.2
7 C4 IV TYR 292A CE1 V 5.3 1.6
7 C4 IV PHE 301A CZ V 5.6 0.2
8 C5 VI LYS 299A CE VII 3.4 9.0
8 C5 VI THR 279A OG1 I 4.0 7.2
8 C5 VI ILE 226A CG2 IV 4.0 0.9
8 C5 VI ASN 224A ND2 III 4.2 2.2
9 O3 II ILE 226A CG2 IV 3.2 17.2*
9 O3 II LYS 299A CE VII 3.5 6.8
9 O3 II LYS 299A NZ III 3.6 4.0
9 O3 II ASN 224A ND2 III 3.7 3.5
9 O3 II ASN 224A OD1 II 3.8 1.9*
9 O3 II VAL 225A O II 4.8 1.0*
9 O3 II LEU 271A CB IV 4.8 3.5*
10 O4 I THR 358A OG1 I 3.0 25.1
10 O4 I LYS 299A CE VII 3.1 4.3
10 O4 I VAL 356A CG1 IV 3.7 6.6*
10 O4 I VAL 356A CB IV 4.0 1.0*
10 O4 I THR 279A OG1 I 4.3 1.4
10 O4 I VAL 356A O II 4.3 3.1
10 O4 I ASN 224A ND2 III 4.4 2.4
10 O4 I SER 277A O II 5.0 1.0
10 O4 I SER 277A CB VI 5.0 0.7
10 O4 I SER 277A C VI 5.3 0.3
------------------------------------------------------------------------
Table V
Complementarity values for the ligand AKG 702A
in PDB entry 3KV6 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 303
Actual value (Å2) 132
Normalised complementarity 0.44
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand AKG 702A
in PDB entry 3KV6 (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 | C1
| VI |
0.41 |
0.41
|
0.41 |
0.36
|
0.44 |
0.44
|
0.44 |
0.44
|
| 2 | O1
| II |
0.47 |
0.44
|
0.47 |
0.48
|
0.58 |
0.58
|
0.58 |
0.55
|
| 3 | O2
| I |
0.44 |
0.39
|
0.44 |
0.33
|
0.44 |
0.44
|
0.44 |
0.39
|
| 4 | C2
| VIII |
0.44 |
0.44
|
0.44 |
0.38
|
0.44 |
0.44
|
0.44 |
0.44
|
| 5 | O5
| II |
0.44 |
0.44
|
0.44 |
0.54
|
0.57 |
0.57
|
0.57 |
0.57
|
| 6 | C3
| IV |
0.36 |
0.36
|
0.36 |
0.44
|
0.46 |
0.46
|
0.46 |
0.46
|
| 7 | C4
| IV |
0.34 |
0.34
|
0.33 |
0.44
|
0.48 |
0.48
|
0.47 |
0.48
|
| 8 | C5
| VI |
0.43 |
0.43
|
0.36 |
0.37
|
0.44 |
0.44
|
0.36 |
0.44
|
| 9 | O3
| II |
0.46 |
0.44
|
0.36 |
0.52
|
0.59 |
0.59
|
0.50 |
0.57
|
| 10 | O4
| I |
0.44 |
0.41
|
0.39 |
0.27
|
0.49 |
0.49
|
0.44 |
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:
Where Sl is the sum of all
surface areas of legitimate atomic contacts between
ligand and receptor, Si 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 AKG 702
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2 5 O5 9 O3 10 O4
Ligand AKG 701
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2 5 O5 9 O3 10 O4
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il