Contacts of ligand PTR1235A in PDB entry 3Q6W
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 PTR1235A
in PDB entry 3Q6W (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
----------------------------------------------------------
1123A GLN* 5.2 2.3 + - - -
1201A VAL* 3.8 22.2 - - + -
1203A ARG* 3.5 37.3 + - - -
1227A ARG* 2.9 62.5 + - + -
1228A ASP 4.9 7.0 - - - +
1229A MET* 4.7 1.8 - - + -
1230A TYR* 6.4 0.7 - + - -
1232A LYS* 5.7 3.1 - - - -
1234A PTR 1.3 76.9 - - - +
1236A SER* 1.3 78.2 + - - +
1237A VAL* 3.8 7.7 - - - +
1238A HIS* 2.6 38.9 + + - +
1239A ASN* 3.0 37.1 + - - +
1259A LYS* 3.5 0.3 - - - -
1260A PHE* 2.7 34.0 + + + +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand PTR1235A
and protein in PDB entry 3Q6W
(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 PHE 1260A O II 2.9 5.1
4 O II SER 1236A N III 2.3 0.3
4 O II PHE 1260A N III 2.7 27.2
12 OH II ARG 1227A NE III 3.6 2.1
12 OH II ARG 1227A NH2 III 4.2 1.7
12 OH II ARG 1203A NH2 III 4.5 0.7
14 O1P I ARG 1227A NE III 2.9 21.1
14 O1P I ARG 1227A NH2 III 3.7 2.9
14 O1P I GLN 1123A NE2 III 5.3 1.2
15 O2P I HIS 1238A ND1 I 2.6 31.4
16 O3P I ASN 1239A N III 3.0 27.4
16 O3P I HIS 1238A N III 3.5 1.7
16 O3P I ARG 1227A NH2 III 4.5 4.5
16 O3P I GLN 1123A NE2 III 5.2 1.0
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand PTR1235A
in PDB entry 3Q6W (back
to top of page)
Total number of contacts is 82
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 PTR 1234A C VIII 1.3 56.8
1 N I PTR 1234A CA VI 2.4 4.8
1 N I PHE 1260A O II 2.9 5.1
1 N I PTR 1234A CB IV 2.9 0.8*
2 CA VI SER 1236A N III 2.5 3.1
2 CA VI PTR 1234A C VIII 2.5 6.5
2 CA VI PTR 1234A O II 2.8 2.0
2 CA VI PTR 1234A CD2 V 3.9 1.1
2 CA VI PTR 1234A CE2 V 4.7 0.4
2 CA VI LYS 1232A NZ III 5.7 1.6
3 C VIII SER 1236A N III 1.3 44.0
3 C VIII SER 1236A CA VII 2.5 2.0
3 C VIII PTR 1234A C VIII 3.5 0.4*
3 C VIII SER 1236A CB VI 3.6 0.9
3 C VIII SER 1236A OG I 3.8 2.2
3 C VIII PTR 1234A CD2 V 3.8 0.4
4 O II SER 1236A N III 2.3 0.3
4 O II PHE 1260A N III 2.7 27.2
4 O II SER 1236A CA VII 2.9 5.0
4 O II LYS 1259A CA VII 3.5 0.3
4 O II PHE 1260A CB IV 3.8 0.2*
4 O II PHE 1260A CD1 V 3.8 0.3
5 CB IV PTR 1234A C VIII 3.4 2.5
5 CB IV PTR 1234A O II 3.6 1.1*
5 CB IV VAL 1201A CG1 IV 3.8 22.2
5 CB IV ARG 1227A CB IV 4.1 2.2
5 CB IV PHE 1260A O II 4.3 0.2*
5 CB IV MET 1229A CG IV 4.7 1.8
5 CB IV PHE 1260A CB IV 5.0 0.2
5 CB IV ASP 1228A O II 5.0 1.8*
6 CG V ARG 1227A CG IV 3.8 2.9
7 CD1 V SER 1236A C VI 3.8 0.7
7 CD1 V ARG 1227A CG IV 3.8 4.9
7 CD1 V ARG 1203A CD VII 3.9 13.0
7 CD1 V ARG 1203A NH1 III 4.0 0.7
7 CD1 V VAL 1237A N III 4.3 0.2
7 CD1 V PHE 1260A CD1 V 4.5 0.7
8 CD2 V ARG 1227A CG IV 3.7 6.1
8 CD2 V SER 1236A N III 3.8 2.2
8 CD2 V ARG 1227A CB IV 3.8 2.7
8 CD2 V SER 1236A O II 3.9 0.2
8 CD2 V ASP 1228A O II 4.9 5.2
8 CD2 V HIS 1238A CE1 V 5.3 1.3
8 CD2 V LYS 1232A NZ III 6.2 1.6
8 CD2 V TYR 1230A CE2 V 6.4 0.7
9 CE1 V SER 1236A O II 3.4 5.8
9 CE1 V ARG 1203A NH1 III 3.5 19.5
9 CE1 V ARG 1203A CZ VI 3.6 3.4
9 CE1 V SER 1236A C VI 3.6 4.0
9 CE1 V VAL 1237A N III 3.8 1.8
9 CE1 V ARG 1227A CG IV 3.9 0.2
9 CE1 V VAL 1237A CA VII 3.9 0.4
10 CE2 V SER 1236A O II 3.6 2.7
10 CE2 V ARG 1227A CG IV 3.7 4.7
10 CE2 V ARG 1227A CD VII 3.8 1.8
10 CE2 V HIS 1238A ND1 I 4.5 1.1
10 CE2 V HIS 1238A CE1 V 4.8 1.1
11 CZ V SER 1236A O II 3.3 3.8
11 CZ V ARG 1227A NE III 3.6 3.8
12 OH II ARG 1227A NE III 3.6 2.1
12 OH II SER 1236A O II 3.7 1.0*
12 OH II VAL 1237A CA VII 3.8 2.8
12 OH II ARG 1227A NH2 III 4.2 1.7
12 OH II VAL 1237A CB IV 4.3 0.9*
12 OH II ARG 1203A NH2 III 4.5 0.7
12 OH II VAL 1237A CG2 IV 4.7 0.2*
14 O1P I ARG 1227A NE III 2.9 21.1
14 O1P I ARG 1227A NH2 III 3.7 2.9
14 O1P I ARG 1227A CZ VI 3.7 0.2
14 O1P I ARG 1227A CD VII 3.8 0.5
14 O1P I GLN 1123A NE2 III 5.3 1.2
15 O2P I HIS 1238A ND1 I 2.6 31.4
15 O2P I HIS 1238A CG V 3.4 0.5
15 O2P I HIS 1238A CB IV 3.5 1.4*
16 O3P I ASN 1239A N III 3.0 27.4
16 O3P I HIS 1238A N III 3.5 1.7
16 O3P I ASN 1239A CB IV 3.7 8.5*
16 O3P I HIS 1238A CB IV 3.9 0.3*
16 O3P I ASN 1239A C VI 4.4 1.2
16 O3P I ARG 1227A NH2 III 4.5 4.5
16 O3P I VAL 1237A CG2 IV 4.6 1.4*
16 O3P I GLN 1123A NE2 III 5.2 1.0
------------------------------------------------------------------------
Table V
Complementarity values for the ligand PTR1235A
in PDB entry 3Q6W (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 411
Actual value (Å2) 373
Normalised complementarity 0.91
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand PTR1235A
in PDB entry 3Q6W (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 |
0.91 |
0.61
|
0.91 |
0.89
|
0.91 |
0.91
|
0.91 |
0.61
|
| 2 | CA
| VI |
0.91 |
0.87
|
0.88 |
0.87
|
0.91 |
0.91
|
0.88 |
0.87
|
| 3 | C
| VIII |
0.91 |
0.91
|
0.69 |
0.68
|
0.91 |
0.91
|
0.69 |
0.91
|
| 4 | O
| II |
0.91 |
0.91
|
0.75 |
0.77
|
0.91 |
0.91
|
0.75 |
0.91
|
| 5 | CB
| IV |
0.79 |
0.77
|
0.79 |
0.91
|
0.92 |
0.92
|
0.92 |
0.89
|
| 6 | CG
| V |
0.89 |
0.89
|
0.89 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 7 | CD1
| V |
0.88 |
0.88
|
0.82 |
0.90
|
0.91 |
0.91
|
0.84 |
0.91
|
| 8 | CD2
| V |
0.86 |
0.84
|
0.85 |
0.86
|
0.91 |
0.91
|
0.89 |
0.88
|
| 9 | CE1
| V |
0.91 |
0.88
|
0.80 |
0.77
|
0.91 |
0.91
|
0.80 |
0.88
|
| 10 | CE2
| V |
0.88 |
0.87
|
0.88 |
0.89
|
0.91 |
0.91
|
0.90 |
0.89
|
| 11 | CZ
| V |
0.91 |
0.89
|
0.89 |
0.87
|
0.91 |
0.91
|
0.89 |
0.89
|
| 12 | OH
| II |
0.91 |
0.91
|
0.88 |
0.89
|
0.92 |
0.92
|
0.88 |
0.91
|
| 14 | O1P
| I |
0.91 |
0.91
|
0.78 |
0.78
|
0.91 |
0.91
|
0.78 |
0.91
|
| 15 | O2P
| I |
0.91 |
0.91
|
0.91 |
0.76
|
0.91 |
0.91
|
0.91 |
0.91
|
| 16 | O3P
| I |
0.91 |
0.91
|
0.74 |
0.79
|
0.96 |
0.96
|
0.79 |
0.96
|
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 1234
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 1235
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 Q6W 1
1. Carbon (in rings)
1 C 4 C1 12 C9 11 C8 10 C7 7 C4
8 C5 16 C13 15 C12 14 C11 13 C10 17 C14
23 C20 26 C23 27 C24 28 C25 29 C26 31 C28
32 C29 34 C31 36 C33 37 C34 38 C35 39 C36
2. Oxygen ("hydroxy" or "carbonyl")
3 O 22 O19
3. Nitrogen ("hydrophilic")
2 N 21 N18 24 N21 25 N22 30 N27 35 N32
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il