Contacts of ligand L7A 1B in PDB entry 3QGW
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 L7A 1B
in PDB entry 3QGW (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
----------------------------------------------------------
369B ILE* 3.8 51.0 - - + +
377B VAL* 3.7 34.2 - - + +
379B LEU* 5.9 1.1 - - + -
389B ALA* 3.2 26.8 - - + +
391B LYS* 3.5 36.1 + - + -
410B MET* 5.5 0.2 - - + -
419B VAL* 3.9 2.9 - - + -
435B PHE* 3.3 52.5 - + + -
436B GLU 2.7 22.8 + - - -
437B PHE* 3.0 37.5 - + - -
438B MET* 2.3 41.9 + - + +
439B GLU 4.5 4.9 - - - -
440B HIS 4.8 0.4 - - - -
441B GLY* 3.4 37.4 - - - -
442B CYS* 4.7 9.5 + - + +
445B ASP* 5.3 9.2 - - + -
489B LEU* 3.4 33.9 - - + +
499B SER* 3.5 25.4 - - - -
500B ASP* 3.6 24.8 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand L7A 1B
and protein in PDB entry 3QGW
(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 N1 I LYS 391B NZ III 3.5 15.8
2 N1 I ASP 500B OD2 II 3.6 5.7
2 N1 I ASP 500B OD1 II 3.8 0.4
3 O1 II MET 438B N III 2.3 27.7
5 N2 I MET 438B O II 4.0 1.6
6 O2 II CYS 442B N III 5.2 0.2
8 N3 I GLU 436B O II 2.7 17.4
8 N3 I MET 438B N III 3.7 1.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand L7A 1B
in PDB entry 3QGW (back
to top of page)
Total number of contacts is 105
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 V ILE 369B CD1 IV 3.8 2.9
1 C1 V GLY 441B CA VI 3.8 2.7
2 N1 I LYS 391B NZ III 3.5 15.8
2 N1 I LYS 391B CE VII 3.5 1.2
2 N1 I ASP 500B OD2 II 3.6 5.7
2 N1 I ASP 500B OD1 II 3.8 0.4
3 O1 II MET 438B N III 2.3 27.7
3 O1 II PHE 437B CD1 V 3.0 9.5
3 O1 II MET 438B O II 3.2 1.2*
4 C2 V ILE 369B O II 3.8 14.1
4 C2 V ILE 369B CB IV 4.0 2.0
4 C2 V GLY 441B CA VI 4.3 2.5
4 C2 V CYS 442B N III 4.7 3.4
4 C2 V CYS 442B CB IV 5.6 2.0
4 C2 V CYS 442B SG VI 6.0 0.9
5 N2 I PHE 437B CE1 V 4.0 2.6
5 N2 I MET 438B O II 4.0 1.6
5 N2 I LEU 489B CD2 IV 4.5 1.6*
5 N2 I GLY 441B CA VI 4.7 0.4
6 O2 II ILE 369B CD1 IV 4.1 2.9*
6 O2 II VAL 377B CG1 IV 4.1 5.5*
6 O2 II ILE 369B O II 4.6 1.2*
6 O2 II LEU 489B CD2 IV 4.6 1.9*
6 O2 II VAL 377B CB IV 4.9 0.2*
6 O2 II CYS 442B N III 5.2 0.2
6 O2 II VAL 377B CG2 IV 5.2 0.2*
6 O2 II CYS 442B CB IV 5.6 1.0*
7 C3 V ILE 369B O II 4.1 7.2
7 C3 V ILE 369B CB IV 4.2 4.5
7 C3 V GLY 441B CA VI 4.4 2.2
7 C3 V CYS 442B N III 5.0 0.9
7 C3 V ASP 445B OD1 II 5.3 8.1
7 C3 V CYS 442B SG VI 6.2 0.7
7 C3 V ASP 445B CB IV 6.3 1.1
8 N3 I GLU 436B O II 2.7 17.4
8 N3 I ALA 389B CB IV 3.2 0.6*
8 N3 I LEU 489B CD1 IV 3.6 4.4*
8 N3 I MET 438B N III 3.7 1.2
8 N3 I MET 438B CG IV 3.9 0.6*
9 C4 V GLY 441B CA VI 4.0 4.3
9 C4 V ILE 369B CB IV 4.8 3.1
9 C4 V ILE 369B CG2 IV 4.8 2.7
10 C5 V GLY 441B CA VI 3.6 8.7
10 C5 V GLY 441B N III 3.9 2.5
10 C5 V PHE 437B CZ V 4.4 9.0
10 C5 V GLU 439B O II 4.5 4.9
10 C5 V HIS 440B C VI 4.8 0.4
10 C5 V ILE 369B CD1 IV 4.9 0.9
10 C5 V ILE 369B CG2 IV 5.1 1.3
10 C5 V LEU 379B CD1 IV 5.9 1.1
11 C6 V GLY 441B CA VI 3.4 9.9
11 C6 V PHE 437B CE1 V 3.8 16.2
11 C6 V GLY 441B N III 3.9 1.8
11 C6 V MET 438B O II 3.9 1.3
11 C6 V ILE 369B CD1 IV 4.2 1.3
12 C7 VI ILE 369B CD1 IV 3.8 6.7
12 C7 VI GLY 441B CA VI 4.5 2.5
12 C7 VI LEU 489B CD2 IV 4.7 3.4
12 C7 VI CYS 442B N III 5.0 0.4
13 C8 V ALA 389B CB IV 3.3 9.4
13 C8 V LEU 489B CD1 IV 3.4 8.1
13 C8 V GLU 436B O II 3.4 5.4
13 C8 V PHE 435B CB IV 3.5 7.6
13 C8 V VAL 419B CG2 IV 3.9 2.7
14 C9 V LEU 489B CD1 IV 3.5 3.1
14 C9 V ALA 389B CB IV 3.6 2.5
15 C10 V ALA 389B CB IV 3.8 3.1
15 C10 V LEU 489B CD1 IV 3.9 4.3
15 C10 V LEU 489B CD2 IV 4.0 1.8
15 C10 V VAL 377B CG1 IV 4.4 0.9
16 C11 V ALA 389B CB IV 3.8 3.6
16 C11 V LEU 489B CD1 IV 4.1 3.1
16 C11 V LEU 489B CD2 IV 4.2 0.4
17 C12 V MET 438B N III 3.3 2.9
17 C12 V ALA 389B CB IV 3.4 7.2
17 C12 V MET 438B CB IV 3.8 5.4
17 C12 V PHE 437B CD1 V 3.8 0.2
18 C13 V LYS 391B CE VII 3.7 16.2
18 C13 V VAL 377B CG2 IV 3.7 11.0
18 C13 V ASP 500B OD2 II 3.9 10.3
18 C13 V LYS 391B CB IV 4.8 1.3
19 C14 V PHE 435B CZ V 3.3 23.1
19 C14 V SER 499B OG I 3.5 11.0
19 C14 V PHE 435B CE1 V 3.5 0.2
19 C14 V PHE 435B CE2 V 3.6 2.2
19 C14 V ASP 500B N III 4.0 7.9
19 C14 V LYS 391B NZ III 4.4 1.3
19 C14 V ASP 500B CA VII 4.5 0.4
19 C14 V MET 410B CE IV 5.5 0.2
20 C15 V SER 499B OG I 3.5 8.7
20 C15 V PHE 435B CG V 3.6 12.8
20 C15 V PHE 435B CD2 V 3.6 2.5
20 C15 V SER 499B CB VI 4.0 2.7
20 C15 V VAL 419B CG1 IV 4.5 0.2
21 C16 V SER 499B OG I 4.2 2.0
21 C16 V LEU 489B CD1 IV 4.2 0.4
21 C16 V PHE 435B CD1 V 4.3 2.9
21 C16 V ALA 389B CB IV 4.5 0.4
21 C16 V LEU 489B CD2 IV 5.0 0.2
22 C17 V VAL 377B CG2 IV 3.8 14.1
22 C17 V VAL 377B CG1 IV 3.9 2.2
22 C17 V SER 499B OG I 4.6 0.9
22 C17 V PHE 435B CD1 V 5.0 1.1
22 C17 V LYS 391B CB IV 5.3 0.2
22 C17 V LEU 489B CD2 IV 5.4 1.1
------------------------------------------------------------------------
Table V
Complementarity values for the ligand L7A 1B
in PDB entry 3QGW (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 525
Actual value (Å2) 409
Normalised complementarity 0.78
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand L7A 1B
in PDB entry 3QGW (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
| V |
0.77 |
0.77
|
0.77 |
0.78
|
0.78 |
0.78
|
0.78 |
0.78
|
| 2 | N1
| I |
0.78 |
0.76
|
0.72 |
0.70
|
0.78 |
0.78
|
0.72 |
0.76
|
| 3 | O1
| II |
0.78 |
0.78
|
0.68 |
0.67
|
0.78 |
0.78
|
0.68 |
0.78
|
| 4 | C2
| V |
0.76 |
0.71
|
0.75 |
0.71
|
0.78 |
0.78
|
0.77 |
0.73
|
| 5 | N2
| I |
0.78 |
0.77
|
0.78 |
0.78
|
0.79 |
0.79
|
0.79 |
0.78
|
| 6 | O2
| II |
0.78 |
0.78
|
0.78 |
0.82
|
0.83 |
0.83
|
0.83 |
0.82
|
| 7 | C3
| V |
0.76 |
0.70
|
0.76 |
0.72
|
0.78 |
0.78
|
0.78 |
0.72
|
| 8 | N3
| I |
0.78 |
0.71
|
0.78 |
0.73
|
0.80 |
0.80
|
0.80 |
0.73
|
| 9 | C4
| V |
0.76 |
0.76
|
0.76 |
0.78
|
0.78 |
0.78
|
0.78 |
0.78
|
| 10 | C5
| V |
0.77 |
0.75
|
0.76 |
0.75
|
0.78 |
0.78
|
0.77 |
0.76
|
| 11 | C6
| V |
0.77 |
0.77
|
0.77 |
0.77
|
0.78 |
0.78
|
0.77 |
0.77
|
| 12 | C7
| VI |
0.74 |
0.74
|
0.74 |
0.78
|
0.78 |
0.78
|
0.78 |
0.78
|
| 13 | C8
| V |
0.67 |
0.65
|
0.67 |
0.76
|
0.78 |
0.78
|
0.78 |
0.76
|
| 14 | C9
| V |
0.76 |
0.76
|
0.76 |
0.78
|
0.78 |
0.78
|
0.78 |
0.78
|
| 15 | C10
| V |
0.74 |
0.74
|
0.74 |
0.78
|
0.78 |
0.78
|
0.78 |
0.78
|
| 16 | C11
| V |
0.75 |
0.75
|
0.75 |
0.78
|
0.78 |
0.78
|
0.78 |
0.78
|
| 17 | C12
| V |
0.73 |
0.73
|
0.72 |
0.77
|
0.78 |
0.78
|
0.77 |
0.78
|
| 18 | C13
| V |
0.73 |
0.69
|
0.67 |
0.74
|
0.78 |
0.78
|
0.72 |
0.74
|
| 19 | C14
| V |
0.78 |
0.78
|
0.74 |
0.70
|
0.78 |
0.78
|
0.74 |
0.78
|
| 20 | C15
| V |
0.78 |
0.78
|
0.78 |
0.75
|
0.78 |
0.78
|
0.78 |
0.78
|
| 21 | C16
| V |
0.78 |
0.78
|
0.78 |
0.77
|
0.78 |
0.78
|
0.78 |
0.78
|
| 22 | C17
| V |
0.71 |
0.71
|
0.71 |
0.78
|
0.78 |
0.78
|
0.78 |
0.78
|
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 PQC 1
1. Carbon (in rings)
1 C1 2 C2 14 C14 13 C13 4 C4 3 C3
8 C8 9 C9 30 C30 12 C12 11 C11 10 C10
13 C13 14 C14 15 C15 18 C18 20 C20 21 C21
25 C25 24 C24 23 C23 22 C22
3. Nitrogen ("hydrophilic")
16 N16 17 N17 19 N19 29 N29
Ligand L7A 1
1. Carbon (in rings)
1 C1 4 C2 7 C3 9 C4 10 C5 11 C6
18 C13 22 C17 21 C16 20 C15 19 C14 13 C8
14 C9 15 C10 16 C11 17 C12
2. Oxygen ("hydroxy" or "carbonyl")
3 O1 6 O2
3. Nitrogen ("hydrophilic")
2 N1 5 N2 8 N3
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il