Contacts of ligand P6G1543A in PDB entry 2JF0
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 P6G1543A
in PDB entry 2JF0 (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
----------------------------------------------------------
377A ALA* 3.9 16.8 - - - +
380A LEU* 3.2 45.3 - - - +
381A HIS* 3.2 66.9 + - - -
385A TRP* 4.7 0.4 - - - -
527A GLN* 3.2 60.9 + - - +
530A ALA* 4.2 1.3 - - - -
531A PHE* 3.5 38.3 - - - +
535A PHE* 3.4 33.0 - - - -
377B ALA* 3.4 29.4 - - - +
380B LEU* 3.4 37.0 - - - +
381B HIS* 3.2 85.3 + - - +
527B GLN* 3.5 42.6 + - - +
528B THR* 5.3 0.3 + - - -
530B ALA 4.6 0.2 - - - -
531B PHE* 3.4 38.0 - - - -
535B PHE* 3.4 35.9 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand P6G1543A
and protein in PDB entry 2JF0
(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
------------------------------------------------------------------------
1 O1 I HIS 381B O II 3.3 10.2
1 O1 I GLN 527A NE2 III 3.3 4.5
1 O1 I HIS 381B NE2 I 3.9 1.2
1 O1 I THR 528B OG1 I 5.3 0.3
4 O4 II HIS 381A ND1 I 3.8 0.3
7 O7 II HIS 381B ND1 I 4.4 0.5
7 O7 II HIS 381A ND1 I 4.8 0.7
10 O10 II HIS 381B ND1 I 5.1 0.3
13 O13 II HIS 381B ND1 I 4.9 0.2
16 O16 II HIS 381B ND1 I 4.0 0.2
19 O19 I HIS 381A O II 3.3 10.7
19 O19 I GLN 527B NE2 III 3.5 8.8
19 O19 I HIS 381A ND1 I 3.7 1.6
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand P6G1543A
in PDB entry 2JF0 (back
to top of page)
Total number of contacts is 110
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 O1 I HIS 381B O II 3.3 10.2
1 O1 I GLN 527A NE2 III 3.3 4.5
1 O1 I HIS 381B CE1 V 3.5 8.1
1 O1 I HIS 381B NE2 I 3.9 1.2
1 O1 I GLN 527A CG IV 4.1 1.9*
1 O1 I THR 528B OG1 I 5.3 0.3
2 C2 VI GLN 527A NE2 III 3.3 8.3
2 C2 VI HIS 381B ND1 I 3.7 5.4
2 C2 VI HIS 381B CE1 V 3.7 3.8
2 C2 VI GLN 527A CG IV 4.0 7.6
2 C2 VI GLN 527A CB IV 4.0 3.4
2 C2 VI HIS 381A CE1 V 4.4 2.2
3 C3 VIII GLN 527A NE2 III 3.2 8.7
3 C3 VIII HIS 381B O II 3.2 11.2*
3 C3 VIII HIS 381B ND1 I 3.3 13.2
4 O4 II HIS 381A CE1 V 3.5 10.6
4 O4 II HIS 381A ND1 I 3.8 0.3
5 C5 VIII GLN 527A O II 3.2 24.2*
5 C5 VIII LEU 380B O II 3.5 7.2*
5 C5 VIII GLN 527A C VI 4.0 0.4
5 C5 VIII GLN 527A NE2 III 4.0 1.8
5 C5 VIII PHE 531A N III 4.1 1.6
5 C5 VIII PHE 531A CB IV 4.2 2.7
5 C5 VIII ALA 530A CB IV 4.2 1.3
6 C6 VIII LEU 380B O II 3.4 11.4*
6 C6 VIII LEU 380B C VI 3.6 1.1
6 C6 VIII LEU 380B CB IV 3.9 4.3
6 C6 VIII PHE 531A N III 3.9 15.0
6 C6 VIII PHE 531A CA VII 3.9 2.9
6 C6 VIII PHE 531A CB IV 3.9 0.2
6 C6 VIII LEU 380B CD2 IV 4.4 1.1
7 O7 II HIS 381B CB IV 4.1 0.3*
7 O7 II PHE 531A CB IV 4.2 1.2*
7 O7 II PHE 531A CD1 V 4.2 0.3
7 O7 II HIS 381B ND1 I 4.4 0.5
7 O7 II HIS 381A ND1 I 4.8 0.7
8 C8 VIII ALA 377B O II 3.4 16.8*
8 C8 VIII LEU 380B CB IV 3.5 11.9
8 C8 VIII HIS 381B N III 3.5 2.5
8 C8 VIII PHE 535A CG V 3.9 4.0
8 C8 VIII HIS 381B CA VII 3.9 2.0
8 C8 VIII HIS 381B CB IV 4.1 0.2
8 C8 VIII PHE 535A CB IV 4.1 0.2
8 C8 VIII PHE 535A CD2 V 4.1 0.2
9 C9 VIII PHE 535A CD2 V 3.4 17.3
9 C9 VIII PHE 535A CG V 3.6 2.0
9 C9 VIII ALA 377B O II 3.6 9.4*
9 C9 VIII PHE 535A CE2 V 3.6 1.1
9 C9 VIII PHE 535A CD1 V 4.0 1.3
9 C9 VIII ALA 377B CA VII 4.0 2.9
9 C9 VIII ALA 377B CB IV 4.1 0.2
9 C9 VIII PHE 531B CE1 V 4.3 2.0
9 C9 VIII HIS 381B CB IV 4.7 0.4
10 O10 II PHE 531A CD1 V 3.5 4.9
10 O10 II HIS 381B ND1 I 5.1 0.3
11 C11 VIII PHE 535B CE2 V 3.4 23.8
11 C11 VIII PHE 535B CD2 V 3.5 2.2
11 C11 VIII PHE 535A CE2 V 3.6 6.5
11 C11 VIII PHE 531B CD1 V 3.8 4.0
11 C11 VIII PHE 535A CD2 V 4.1 0.2
12 C12 VIII PHE 535B CD2 V 3.9 5.8
12 C12 VIII ALA 377A O II 3.9 15.9*
12 C12 VIII PHE 531A CE1 V 4.0 8.7
12 C12 VIII PHE 535B CE2 V 4.1 0.9
12 C12 VIII PHE 535B CG V 4.1 1.1
12 C12 VIII ALA 377A CB IV 4.2 0.9
12 C12 VIII PHE 531A CD1 V 4.3 0.7
12 C12 VIII HIS 381A CB IV 4.4 2.9
12 C12 VIII HIS 381A ND1 I 5.0 0.7
12 C12 VIII HIS 381B ND1 I 5.7 0.2
13 O13 II PHE 531B CD1 V 3.4 5.9
13 O13 II HIS 381B ND1 I 4.9 0.2
14 C14 VIII LEU 380A CB IV 3.2 20.6
14 C14 VIII LEU 380A C VI 3.7 0.4
14 C14 VIII LEU 380A CD1 IV 3.8 5.4
14 C14 VIII PHE 531B CA VII 3.9 9.2
14 C14 VIII LEU 380A CG IV 4.0 0.2
14 C14 VIII PHE 535B CB IV 4.1 2.0
15 C15 VIII LEU 380A O II 3.3 14.8*
15 C15 VIII LEU 380A C VI 3.4 1.3
15 C15 VIII HIS 381A N III 3.6 0.2
15 C15 VIII LEU 380A CB IV 3.7 1.1
15 C15 VIII PHE 531B CB IV 3.9 9.9
15 C15 VIII PHE 531B CA VII 3.9 3.1
15 C15 VIII PHE 531B N III 4.0 3.8
15 C15 VIII GLN 527B O II 4.0 1.3*
15 C15 VIII LEU 380A CD1 IV 4.1 1.3
15 C15 VIII ALA 530B C VI 4.6 0.2
15 C15 VIII TRP 385A NE1 III 4.7 0.4
16 O16 II GLN 527B O II 3.7 1.6*
16 O16 II HIS 381B CE1 V 3.8 6.9
16 O16 II HIS 381B ND1 I 4.0 0.2
17 C17 VIII HIS 381A CA VII 3.6 8.5
17 C17 VIII GLN 527B O II 3.7 14.1*
17 C17 VIII GLN 527B NE2 III 3.8 9.4
17 C17 VIII HIS 381B CE1 V 4.1 0.9
17 C17 VIII GLN 527B CB IV 4.3 0.2
18 C18 VI HIS 381A ND1 I 3.2 22.2
18 C18 VI HIS 381A CE1 V 3.7 2.5
18 C18 VI HIS 381A O II 3.7 0.2
18 C18 VI HIS 381B CE1 V 3.8 17.0
18 C18 VI GLN 527B NE2 III 4.1 0.2
18 C18 VI HIS 381B ND1 I 4.3 0.2
18 C18 VI GLN 527B CB IV 4.5 2.0
19 O19 I HIS 381A O II 3.3 10.7
19 O19 I GLN 527B NE2 III 3.5 8.8
19 O19 I HIS 381A ND1 I 3.7 1.6
19 O19 I HIS 381A CE1 V 3.8 3.5
19 O19 I GLN 527B CB IV 4.1 3.6*
19 O19 I GLN 527B CG IV 4.2 1.2*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand P6G1543A
in PDB entry 2JF0 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 523
Actual value (Å2) 258
Normalised complementarity 0.49
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand P6G1543A
in PDB entry 2JF0 (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 | O1
| I |
0.49 |
0.46
|
0.48 |
0.44
|
0.50 |
0.50
|
0.49 |
0.46
|
| 2 | C2
| VI |
0.45 |
0.45
|
0.42 |
0.44
|
0.49 |
0.49
|
0.46 |
0.49
|
| 3 | C3
| VIII |
0.54 |
0.49
|
0.50 |
0.41
|
0.54 |
0.54
|
0.50 |
0.49
|
| 4 | O4
| II |
0.49 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
| 5 | C5
| VIII |
0.60 |
0.48
|
0.59 |
0.48
|
0.62 |
0.62
|
0.60 |
0.49
|
| 6 | C6
| VIII |
0.52 |
0.47
|
0.45 |
0.44
|
0.54 |
0.54
|
0.47 |
0.49
|
| 7 | O7
| II |
0.49 |
0.49
|
0.49 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 8 | C8
| VIII |
0.51 |
0.45
|
0.49 |
0.49
|
0.56 |
0.56
|
0.54 |
0.49
|
| 9 | C9
| VIII |
0.53 |
0.49
|
0.52 |
0.49
|
0.53 |
0.53
|
0.52 |
0.49
|
| 10 | O10
| II |
0.49 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
| 11 | C11
| VIII |
0.49 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
| 12 | C12
| VIII |
0.54 |
0.48
|
0.54 |
0.49
|
0.56 |
0.56
|
0.56 |
0.49
|
| 13 | O13
| II |
0.49 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
| 14 | C14
| VIII |
0.39 |
0.39
|
0.35 |
0.49
|
0.49 |
0.49
|
0.46 |
0.49
|
| 15 | C15
| VIII |
0.51 |
0.45
|
0.48 |
0.48
|
0.56 |
0.56
|
0.53 |
0.49
|
| 16 | O16
| II |
0.50 |
0.49
|
0.50 |
0.49
|
0.50 |
0.50
|
0.50 |
0.49
|
| 17 | C17
| VIII |
0.55 |
0.49
|
0.48 |
0.46
|
0.55 |
0.55
|
0.48 |
0.49
|
| 18 | C18
| VI |
0.49 |
0.49
|
0.49 |
0.41
|
0.49 |
0.49
|
0.49 |
0.49
|
| 19 | O19
| I |
0.49 |
0.45
|
0.46 |
0.43
|
0.51 |
0.51
|
0.48 |
0.47
|
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 SUN 203
2. Oxygen ("hydroxy" or "carbonyl")
6 O
3. Nitrogen ("hydrophilic")
1 N 9 N1
Ligand SUN 203
2. Oxygen ("hydroxy" or "carbonyl")
6 O
3. Nitrogen ("hydrophilic")
1 N 9 N1
Ligand P6G 1543
2. Oxygen ("hydroxy" or "carbonyl")
1 O1 19 O19
Ligand HBP 1544
1. Carbon (in rings)
6 C7 7 C6 12 C5A 8 C4 9 C3 18 C21
19 C22 20 C23 21 C24 22 C25
3. Nitrogen ("hydrophilic")
4 N9 10 N2 17 N20 24 N27
Ligand HBP 1545
1. Carbon (in rings)
6 C7 7 C6 12 C5A 8 C4 9 C3 18 C21
19 C22 20 C23 21 C24 22 C25
3. Nitrogen ("hydrophilic")
4 N9 10 N2 17 N20 24 N27
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il