Contacts of ligand PTR1007A in PDB entry 3TJD
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 PTR1007A
in PDB entry 3TJD (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
----------------------------------------------------------
1001A LEU* 3.5 5.8 - - - -
1002A PRO* 3.6 9.9 - - - +
1005A LYS* 3.2 53.6 + - + +
1006A GLU* 1.3 87.0 + - + +
1008A PTR 1.3 71.8 + - - +
1009A LYS* 4.2 22.9 + - + -
1028A GLU* 5.4 0.3 + - - -
1030A LYS* 2.9 61.1 + - + -
1031A PHE 3.5 15.3 - - - +
1032A SER* 4.2 7.4 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand PTR1007A
and protein in PDB entry 3TJD
(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 N I GLU 1006A N III 2.6 7.3
1 N I LYS 1005A O II 3.5 0.2
4 O II PTR 1008A N I 2.3 0.9
14 O1P I LYS 1009A NZ III 5.8 0.3
16 O3P I LYS 1030A NZ III 2.9 27.2
16 O3P I GLU 1028A OE2 II 5.4 0.3
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand PTR1007A
in PDB entry 3TJD (back
to top of page)
Total number of contacts is 66
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 N I GLU 1006A C VI 1.3 56.8
1 N I GLU 1006A CA VII 2.4 5.5
1 N I GLU 1006A N III 2.6 7.3
1 N I LYS 1005A C VI 3.2 0.6
1 N I LYS 1005A O II 3.5 0.2
2 CA VI PTR 1008A N I 2.4 2.0
2 CA VI GLU 1006A C VI 2.4 6.5
2 CA VI GLU 1006A O II 2.8 1.8
2 CA VI PHE 1031A O II 3.5 5.8
2 CA VI LEU 1001A CD2 IV 3.5 1.3
3 C VIII PTR 1008A N I 1.3 43.7
3 C VIII PTR 1008A CA VI 2.4 2.9
3 C VIII PTR 1008A CB IV 3.3 2.7
3 C VIII LEU 1001A CD2 IV 3.5 4.5
4 O II PTR 1008A N I 2.3 0.9
4 O II PTR 1008A CA VI 2.8 6.1
4 O II LYS 1005A CB IV 3.5 14.7*
4 O II PRO 1002A CD IV 3.6 9.2*
4 O II PRO 1002A CG IV 3.9 0.7*
4 O II LYS 1005A CE VII 4.1 1.4
5 CB IV PTR 1008A N I 2.9 2.7*
5 CB IV GLU 1006A C VI 3.3 2.5
5 CB IV GLU 1006A O II 3.5 1.3*
5 CB IV PHE 1031A O II 3.8 5.2*
5 CB IV SER 1032A CB VI 4.2 7.0
5 CB IV PHE 1031A C VI 4.5 1.3
5 CB IV LYS 1030A CE VII 4.7 2.2
5 CB IV PHE 1031A N III 4.7 2.9*
5 CB IV SER 1032A OG I 4.8 0.4*
5 CB IV LYS 1030A CB IV 4.9 2.2
6 CG V LYS 1030A CE VII 3.9 2.0
7 CD1 V LYS 1030A CE VII 3.9 4.7
7 CD1 V LYS 1030A NZ III 4.0 1.6
7 CD1 V GLU 1006A C VI 4.2 2.0
7 CD1 V LYS 1005A CG IV 4.4 2.0
7 CD1 V GLU 1006A N III 4.4 1.6
7 CD1 V GLU 1006A CB IV 5.3 1.3
8 CD2 V PTR 1008A N I 3.4 3.4
8 CD2 V LYS 1030A CE VII 3.8 5.2
8 CD2 V PTR 1008A CA VI 4.1 3.6
8 CD2 V PTR 1008A C VIII 4.2 3.8
8 CD2 V LYS 1030A CG IV 4.2 2.9
8 CD2 V LYS 1009A N III 4.4 0.2
9 CE1 V LYS 1030A CE VII 3.7 1.6
9 CE1 V LYS 1030A NZ III 3.8 1.6
9 CE1 V LYS 1005A CG IV 4.0 7.9
9 CE1 V GLU 1006A N III 5.1 0.2
10 CE2 V LYS 1030A CE VII 3.7 6.3
10 CE2 V LYS 1005A CE VII 3.9 12.1
10 CE2 V LYS 1009A CG IV 4.2 13.5
10 CE2 V LYS 1009A CE VII 4.4 2.2
10 CE2 V LYS 1009A CD IV 4.7 0.2
10 CE2 V LYS 1009A N III 4.9 0.4
10 CE2 V LYS 1009A CB IV 5.1 0.2
11 CZ V LYS 1005A CG IV 4.1 5.8
12 OH II LYS 1005A CE VII 4.3 4.3
12 OH II LYS 1005A CD IV 4.4 1.6*
12 OH II LYS 1009A CE VII 4.9 2.3
14 O1P I LYS 1009A CE VII 5.7 1.7
14 O1P I LYS 1009A NZ III 5.8 0.3
15 O2P I LYS 1005A CG IV 4.9 2.8*
15 O2P I LYS 1005A CD IV 5.4 0.2*
16 O3P I LYS 1030A NZ III 2.9 27.2
16 O3P I LYS 1030A CE VII 3.1 3.6
16 O3P I LYS 1009A CE VII 5.2 1.7
16 O3P I GLU 1028A OE2 II 5.4 0.3
------------------------------------------------------------------------
Table V
Complementarity values for the ligand PTR1007A
in PDB entry 3TJD (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 405
Actual value (Å2) 251
Normalised complementarity 0.62
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand PTR1007A
in PDB entry 3TJD (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 | N
| I |
0.62 |
0.62
|
0.56 |
0.58
|
0.62 |
0.62
|
0.56 |
0.62
|
| 2 | CA
| VI |
0.61 |
0.58
|
0.61 |
0.57
|
0.62 |
0.62
|
0.62 |
0.58
|
| 3 | C
| VIII |
0.59 |
0.59
|
0.59 |
0.40
|
0.62 |
0.62
|
0.62 |
0.62
|
| 4 | O
| II |
0.62 |
0.62
|
0.61 |
0.74
|
0.74 |
0.74
|
0.74 |
0.74
|
| 5 | CB
| IV |
0.67 |
0.64
|
0.65 |
0.62
|
0.68 |
0.68
|
0.66 |
0.65
|
| 6 | CG
| V |
0.62 |
0.62
|
0.61 |
0.62
|
0.62 |
0.62
|
0.61 |
0.62
|
| 7 | CD1
| V |
0.60 |
0.60
|
0.57 |
0.61
|
0.62 |
0.62
|
0.58 |
0.62
|
| 8 | CD2
| V |
0.61 |
0.59
|
0.58 |
0.60
|
0.62 |
0.62
|
0.59 |
0.60
|
| 9 | CE1
| V |
0.58 |
0.58
|
0.57 |
0.61
|
0.62 |
0.62
|
0.60 |
0.62
|
| 10 | CE2
| V |
0.55 |
0.55
|
0.45 |
0.62
|
0.62 |
0.62
|
0.52 |
0.62
|
| 11 | CZ
| V |
0.59 |
0.59
|
0.59 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 12 | OH
| II |
0.62 |
0.62
|
0.59 |
0.63
|
0.63 |
0.63
|
0.60 |
0.63
|
| 14 | O1P
| I |
0.62 |
0.62
|
0.61 |
0.62
|
0.62 |
0.62
|
0.61 |
0.62
|
| 15 | O2P
| I |
0.62 |
0.62
|
0.62 |
0.64
|
0.64 |
0.64
|
0.64 |
0.64
|
| 16 | O3P
| I |
0.62 |
0.62
|
0.46 |
0.48
|
0.62 |
0.62
|
0.46 |
0.62
|
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 PTR 1007
1. Carbon (in rings)
6 CG 7 CD1 9 CE1 11 CZ 10 CE2 8 CD2
2. Oxygen ("hydroxy" or "carbonyl")
4 O
3. Nitrogen ("hydrophilic")
1 N
Ligand PTR 1008
1. Carbon (in rings)
6 CG 7 CD1 9 CE1 11 CZ 10 CE2 8 CD2
2. Oxygen ("hydroxy" or "carbonyl")
4 O
3. Nitrogen ("hydrophilic")
1 N
Ligand PTR 1007
1. Carbon (in rings)
6 CG 7 CD1 9 CE1 11 CZ 10 CE2 8 CD2
2. Oxygen ("hydroxy" or "carbonyl")
4 O
3. Nitrogen ("hydrophilic")
1 N
Ligand PTR 1008
1. Carbon (in rings)
6 CG 7 CD1 9 CE1 11 CZ 10 CE2 8 CD2
2. Oxygen ("hydroxy" or "carbonyl")
4 O
3. Nitrogen ("hydrophilic")
1 N
Ligand 6TP 1
1. Carbon (in rings)
19 C10 17 C8 18 C9 20 C11 22 C13 5 C2
25 C16 28 C19 14 C5 27 C18 26 C17
2. Oxygen ("hydroxy" or "carbonyl")
7 O2
3. Nitrogen ("hydrophilic")
2 N1 6 N2 10 N3 13 N4
Ligand 6TP 1
1. Carbon (in rings)
19 C10 17 C8 18 C9 20 C11 22 C13 5 C2
25 C16 28 C19 14 C5 27 C18 26 C17
2. Oxygen ("hydroxy" or "carbonyl")
7 O2
3. Nitrogen ("hydrophilic")
2 N1 6 N2 10 N3 13 N4
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il