Contacts of ligand TCQ 382B in PDB entry 1W4N
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 TCQ 382B
in PDB entry 1W4N (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
----------------------------------------------------------
358A LEU* 6.3 2.0 - - + -
359A TRP* 5.0 3.8 - + - -
105B PHE* 4.1 24.0 - + - -
135B ALA* 3.9 12.8 - - + -
136B PRO* 3.5 36.8 - - + -
137B LEU* 3.5 20.2 - - + -
168B TRP* 4.1 12.8 - + - -
282B VAL* 4.4 5.4 - - + -
284B TYR* 2.4 41.9 + - - -
296B TYR* 3.2 50.7 - + + -
298B ASP* 4.3 6.5 - - - -
302B TYR* 3.8 28.0 - + - -
378B THR* 3.4 2.6 - - - +
379B ILE* 2.9 64.5 + - + +
380B GLY* 3.5 32.3 - - - -
381B ASN* 1.3 107.4 + - - -
383B ASP* 1.3 70.1 + - - +
384B TYR* 3.4 37.4 + - + -
403B THR 4.0 9.2 - - - +
405B VAL 4.7 2.7 - - - +
406B VAL* 5.7 1.3 - - - -
407B PHE* 4.1 8.3 - + + -
431B HIS* 5.3 1.6 - + - -
433B HIS* 3.6 17.9 - + - -
602B MET* 6.1 1.0 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand TCQ 382B
and protein in PDB entry 1W4N
(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 ASN 381B N III 2.8 5.9
1 N I ILE 379B O II 3.0 1.4
4 O II ASP 383B N III 2.2 0.5
4 O II ILE 379B N III 2.9 24.3
8 O2 II TYR 384B OH I 3.4 4.2
8 O2 II ASN 381B ND2 III 4.0 1.0
11 O4 I TYR 284B OH I 2.4 19.1
13 N5 I ASN 381B OD1 II 3.5 0.6
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand TCQ 382B
in PDB entry 1W4N (back
to top of page)
Total number of contacts is 127
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 ASN 381B C VI 1.3 56.2
1 N I ASN 381B CA VII 2.4 4.8
1 N I ASN 381B N III 2.8 5.9
1 N I ILE 379B O II 3.0 1.4
2 CA VI ASP 383B N III 2.4 3.1
2 CA VI ASN 381B C VI 2.4 6.3
2 CA VI ASN 381B O II 2.8 1.3
2 CA VI THR 403B O II 4.0 2.2
2 CA VI VAL 405B O II 4.9 0.4
3 C VIII ASP 383B N III 1.3 44.4
3 C VIII ASP 383B CA VII 2.4 2.2
3 C VIII ASP 383B OD1 II 3.0 6.1*
3 C VIII ILE 379B N III 4.0 0.4
3 C VIII TYR 384B CE2 V 4.7 0.4
4 O II ASP 383B N III 2.2 0.5
4 O II ASP 383B CA VII 2.8 6.9
4 O II ILE 379B N III 2.9 24.3
4 O II ASP 383B OD1 II 3.2 3.1*
4 O II ASP 383B CG VI 3.4 2.1
4 O II THR 378B CA VII 3.4 0.7
4 O II THR 378B CG2 IV 3.6 1.9*
5 CB IV ASP 383B N III 3.1 1.6*
5 CB IV TYR 384B CE2 V 3.5 17.5
5 CB IV ILE 379B O II 3.6 1.1*
5 CB IV TYR 384B CZ V 3.7 0.7
5 CB IV ILE 379B N III 4.8 0.4*
6 C1 V TYR 384B OH I 3.5 2.2
7 C2 V TYR 384B OH I 3.4 5.4
7 C2 V ASN 381B ND2 III 3.5 4.9
8 O2 II TYR 384B OH I 3.4 4.2
8 O2 II HIS 433B CE1 V 3.6 9.4
8 O2 II ASN 381B ND2 III 4.0 1.0
8 O2 II TYR 384B CZ V 4.1 0.9
8 O2 II THR 403B O II 4.3 6.9*
8 O2 II TYR 384B CE1 V 4.5 0.5
8 O2 II VAL 405B O II 4.7 2.3*
8 O2 II VAL 406B CA VII 5.7 1.0
8 O2 II MET 602B SD VIII 6.1 1.0*
9 C3 V TYR 284B OH I 3.3 11.7
9 C3 V ASN 381B ND2 III 3.3 7.0
9 C3 V TYR 384B OH I 4.0 3.6
9 C3 V HIS 433B CE1 V 4.2 8.5
9 C3 V VAL 282B CG1 IV 4.4 1.3
9 C3 V PHE 407B CB IV 4.8 0.2
9 C3 V PHE 407B N III 5.2 1.1
9 C3 V HIS 431B CD2 V 5.3 0.2
9 C3 V HIS 431B NE2 I 5.3 1.1
9 C3 V HIS 431B CE1 V 6.0 0.2
9 C3 V VAL 406B CA VII 6.0 0.2
10 C4 V TYR 284B OH I 3.2 0.2
10 C4 V ASN 381B ND2 III 3.5 5.2
10 C4 V ASN 381B OD1 II 3.8 0.2
10 C4 V TYR 296B CD1 V 4.3 1.1
10 C4 V VAL 282B CG1 IV 4.4 4.0
11 O4 I TYR 284B OH I 2.4 19.1
11 O4 I TYR 284B CZ V 3.2 5.9
11 O4 I TYR 284B CE1 V 3.3 5.0
11 O4 I TYR 296B CD1 V 3.4 3.6
11 O4 I TYR 296B CE1 V 3.7 1.7
11 O4 I PHE 407B CD1 V 4.1 3.1
12 C5 V ASN 381B OD1 II 3.3 3.6
12 C5 V TYR 296B CD1 V 4.3 0.7
12 C5 V TYR 384B OH I 4.8 0.2
12 C5 V TYR 296B CG V 4.9 0.2
12 C5 V ASP 298B OD2 II 4.9 0.9
12 C5 V TYR 296B CB IV 5.1 0.7
12 C5 V ASP 298B OD1 II 5.1 0.7
13 N5 I TYR 296B CD1 V 3.4 3.6
13 N5 I ASN 381B OD1 II 3.5 0.6
13 N5 I PHE 407B CD1 V 4.8 0.2
14 C7 V ILE 379B O II 3.9 2.5
14 C7 V TYR 296B CD1 V 4.0 0.2
14 C7 V ILE 379B CG2 IV 4.1 6.1
14 C7 V TYR 296B CG V 4.1 0.4
14 C7 V ASP 298B OD2 II 4.3 1.8
15 C9 V TYR 296B CG V 3.2 26.0
15 C9 V TYR 296B CD2 V 3.4 6.5
15 C9 V TYR 296B CE2 V 3.7 1.6
15 C9 V TYR 302B OH I 3.8 6.5
15 C9 V TYR 296B CB IV 3.8 2.2
15 C9 V TYR 302B CZ V 4.0 2.7
15 C9 V TYR 302B CE1 V 4.0 1.3
16 C8 V LEU 137B CD2 IV 3.5 9.0
16 C8 V ASN 381B OD1 II 3.9 1.6
16 C8 V TYR 296B CE1 V 4.2 2.0
16 C8 V PHE 407B CE1 V 4.7 1.8
17 C10 V LEU 137B CD2 IV 3.6 2.5
17 C10 V GLY 380B CA VI 4.1 1.1
18 C11 V GLY 380B CA VI 3.8 5.6
18 C11 V LEU 137B CD2 IV 3.8 8.7
18 C11 V ASN 381B OD1 II 3.9 8.3
18 C11 V ALA 135B CB IV 4.1 4.3
18 C11 V TRP 168B CH2 V 4.2 3.4
18 C11 V PHE 407B CE1 V 4.8 1.8
19 C12 V GLY 380B CA VI 3.5 8.3
19 C12 V PRO 136B CD IV 3.9 8.7
19 C12 V ALA 135B CB IV 3.9 8.1
19 C12 V TRP 168B CH2 V 4.1 9.0
19 C12 V ALA 135B CA VII 4.3 0.4
19 C12 V TRP 168B CZ2 V 4.8 0.4
19 C12 V TRP 359A CH2 V 5.0 2.2
19 C12 V TRP 359A CZ2 V 5.1 0.7
20 C13 V GLY 380B CA VI 3.5 9.0
20 C13 V PRO 136B CD IV 3.5 16.2
20 C13 V PRO 136B CG IV 3.9 0.9
20 C13 V PHE 105B CE2 V 4.5 4.9
20 C13 V PHE 105B CD2 V 4.7 0.9
20 C13 V TRP 359A CZ2 V 5.6 0.9
20 C13 V LEU 358A CD2 IV 6.3 2.0
21 C14 V GLY 380B CA VI 3.8 5.2
21 C14 V GLY 380B N III 3.9 2.7
21 C14 V PRO 136B O II 4.0 9.6
21 C14 V PHE 105B CE2 V 4.1 17.9
21 C14 V PRO 136B CG IV 4.1 0.4
21 C14 V TYR 302B CE2 V 4.2 2.7
21 C14 V PHE 105B CZ V 4.4 0.2
21 C14 V ILE 379B CG2 IV 4.6 0.4
22 C15 V TYR 302B OH I 3.9 9.6
22 C15 V TYR 302B CE2 V 4.0 5.2
22 C15 V ILE 379B CG2 IV 4.1 6.7
22 C15 V GLY 380B CA VI 4.1 0.4
22 C15 V PRO 136B O II 4.1 0.9
23 C6 V ILE 379B O II 3.1 17.7
23 C6 V ASN 381B OD1 II 3.5 0.4
23 C6 V TYR 384B OH I 4.2 1.8
23 C6 V ILE 379B CB IV 4.5 3.4
23 C6 V ASP 298B OD2 II 4.7 3.1
------------------------------------------------------------------------
Table V
Complementarity values for the ligand TCQ 382B
in PDB entry 1W4N (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 558
Actual value (Å2) 552
Normalised complementarity 0.99
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand TCQ 382B
in PDB entry 1W4N (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 |
0.99 |
0.98
|
0.95 |
0.96
|
0.99 |
0.99
|
0.95 |
0.98
|
| 2 | CA
| VI |
0.99 |
0.97
|
0.98 |
0.96
|
0.99 |
0.99
|
0.98 |
0.97
|
| 3 | C
| VIII |
1.01 |
0.99
|
0.84 |
0.83
|
1.01 |
1.01
|
0.84 |
0.99
|
| 4 | O
| II |
1.00 |
0.99
|
0.88 |
0.91
|
1.01 |
1.01
|
0.89 |
1.00
|
| 5 | CB
| IV |
1.00 |
1.00
|
0.99 |
0.99
|
1.00 |
1.00
|
0.99 |
1.00
|
| 6 | C1
| V |
0.99 |
0.99
|
0.99 |
0.98
|
0.99 |
0.99
|
0.99 |
0.99
|
| 7 | C2
| V |
0.99 |
0.99
|
0.97 |
0.95
|
0.99 |
0.99
|
0.97 |
0.99
|
| 8 | O2
| II |
1.03 |
0.99
|
1.02 |
0.97
|
1.03 |
1.03
|
1.02 |
0.99
|
| 9 | C3
| V |
0.98 |
0.98
|
0.95 |
0.90
|
0.99 |
0.99
|
0.96 |
0.99
|
| 10 | C4
| V |
0.97 |
0.97
|
0.96 |
0.97
|
0.99 |
0.99
|
0.97 |
0.99
|
| 11 | O4
| I |
0.99 |
0.99
|
0.99 |
0.92
|
0.99 |
0.99
|
0.99 |
0.99
|
| 12 | C5
| V |
0.99 |
0.97
|
0.99 |
0.97
|
0.99 |
0.99
|
0.99 |
0.97
|
| 13 | N5
| I |
0.99 |
0.99
|
0.99 |
0.99
|
0.99 |
0.99
|
0.99 |
0.99
|
| 14 | C7
| V |
0.97 |
0.95
|
0.97 |
0.97
|
0.99 |
0.99
|
0.99 |
0.97
|
| 15 | C9
| V |
0.98 |
0.98
|
0.98 |
0.97
|
0.99 |
0.99
|
0.99 |
0.99
|
| 16 | C8
| V |
0.96 |
0.95
|
0.96 |
0.98
|
0.99 |
0.99
|
0.99 |
0.98
|
| 17 | C10
| V |
0.98 |
0.98
|
0.98 |
0.99
|
0.99 |
0.99
|
0.99 |
0.99
|
| 18 | C11
| V |
0.94 |
0.91
|
0.94 |
0.96
|
0.99 |
0.99
|
0.99 |
0.96
|
| 19 | C12
| V |
0.93 |
0.93
|
0.93 |
0.99
|
0.99 |
0.99
|
0.99 |
0.99
|
| 20 | C13
| V |
0.92 |
0.92
|
0.92 |
0.99
|
0.99 |
0.99
|
0.99 |
0.99
|
| 21 | C14
| V |
0.99 |
0.95
|
0.98 |
0.94
|
0.99 |
0.99
|
0.98 |
0.95
|
| 22 | C15
| V |
0.96 |
0.96
|
0.96 |
0.95
|
0.99 |
0.99
|
0.99 |
0.99
|
| 23 | C6
| V |
0.98 |
0.90
|
0.98 |
0.91
|
0.99 |
0.99
|
0.99 |
0.91
|
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 TCQ 382
1. Carbon (in rings)
6 C1 7 C2 9 C3 10 C4 12 C5 23 C6
14 C7 15 C9 16 C8 17 C10 18 C11 19 C12
20 C13 21 C14 22 C15
2. Oxygen ("hydroxy" or "carbonyl")
4 O 8 O2 11 O4
3. Nitrogen ("hydrophilic")
1 N 13 N5
Ligand TCQ 382
1. Carbon (in rings)
6 C1 7 C2 9 C3 10 C4 12 C5 23 C6
14 C7 15 C9 16 C8 17 C10 18 C11 19 C12
20 C13 21 C14 22 C15
2. Oxygen ("hydroxy" or "carbonyl")
4 O 8 O2 11 O4
3. Nitrogen ("hydrophilic")
1 N 13 N5
Ligand GOL 751
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand GOL 752
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand GOL 753
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand GOL 755
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand GOL 751
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand GOL 752
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand GOL 753
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand GOL 754
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand GOL 755
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il