Contacts of ligand FBP 580D in PDB entry 2VGB
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 FBP 580D
in PDB entry 2VGB (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
----------------------------------------------------------
452D THR* 5.8 2.8 + - - +
474D LEU* 3.6 39.3 + - - +
475D THR* 2.9 20.5 + - - -
476D THR* 3.0 23.9 + - - -
477D THR* 2.7 41.1 + - - -
479D ARG* 4.0 9.4 + - - +
480D SER* 2.5 38.3 + - - -
498D ARG* 4.3 5.4 + - - +
525D TRP* 2.8 32.0 + - - -
529D VAL* 5.0 0.7 - - - +
532D ARG* 2.5 60.2 + - - -
556D THR* 4.0 1.9 - - - -
557D GLY* 2.9 38.8 + - - -
559D ARG 3.1 19.0 + - - -
560D PRO* 3.6 5.4 - - - +
561D GLY* 2.4 48.4 + - - +
562D SER* 3.2 20.4 + - - -
563D GLY* 3.0 23.3 + - - -
564D TYR* 3.1 24.6 + - - +
565D THR* 3.5 27.6 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand FBP 580D
and protein in PDB entry 2VGB
(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 O1P I ARG 532D NH2 III 2.6 22.3
2 O1P I TRP 525D NE1 III 2.8 21.8
2 O1P I ARG 498D NH1 III 5.2 0.2
3 O2P I ARG 532D NH1 III 2.5 26.2
3 O2P I ARG 532D NH2 III 3.4 0.2
3 O2P I THR 476D OG1 I 4.0 8.5
3 O2P I ARG 498D NH1 III 4.3 5.0
4 O3P I GLY 561D N III 3.0 22.5
4 O3P I THR 476D OG1 I 4.4 2.8
5 O1 II GLY 561D N III 4.0 1.0
5 O1 II THR 476D OG1 I 4.0 1.6
8 O2 I GLY 557D N III 3.6 12.5
8 O2 I LEU 474D O II 4.2 0.7
10 O3 I ARG 559D O II 3.1 9.4
10 O3 I GLY 557D N III 3.4 0.2
10 O3 I GLY 557D O II 3.9 0.9
12 O4 I GLY 561D O II 2.4 16.5
12 O4 I TYR 564D N III 3.1 21.0
14 O5 II THR 476D OG1 I 4.1 2.3
14 O5 II THR 475D N III 4.4 0.2
16 O6 II THR 476D N III 3.8 0.2
18 O4P I THR 477D N III 2.7 30.7
18 O4P I THR 476D N III 3.0 3.5
18 O4P I THR 477D OG1 I 3.1 5.7
19 O5P I GLY 563D N III 3.0 19.9
19 O5P I SER 562D OG I 3.6 1.0
19 O5P I THR 477D OG1 I 4.0 4.7
19 O5P I SER 480D OG I 4.3 0.7
19 O5P I SER 480D N III 4.7 0.2
19 O5P I THR 565D OG1 I 5.1 0.7
19 O5P I THR 452D OG1 I 5.8 0.2
20 O6P I SER 480D OG I 2.5 28.4
20 O6P I THR 475D OG1 I 2.9 15.6
20 O6P I SER 480D N III 3.3 6.4
20 O6P I ARG 479D N III 4.0 0.7
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand FBP 580D
in PDB entry 2VGB (back
to top of page)
Total number of contacts is 86
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
------------------------------------------------------------------------
2 O1P I ARG 532D NH2 III 2.6 22.3
2 O1P I TRP 525D NE1 III 2.8 21.8
2 O1P I TRP 525D CD1 V 3.8 0.7
2 O1P I PRO 560D CB IV 4.1 0.3*
2 O1P I ARG 498D NH1 III 5.2 0.2
3 O2P I ARG 532D NH1 III 2.5 26.2
3 O2P I ARG 532D CZ VI 3.3 0.3
3 O2P I ARG 532D NH2 III 3.4 0.2
3 O2P I THR 476D OG1 I 4.0 8.5
3 O2P I ARG 498D NH1 III 4.3 5.0
3 O2P I ARG 498D CG IV 5.9 0.2*
4 O3P I GLY 561D N III 3.0 22.5
4 O3P I PRO 560D CA IV 3.6 2.1*
4 O3P I PRO 560D CB IV 3.6 2.9*
4 O3P I GLY 561D CA VI 3.9 2.1
4 O3P I THR 476D OG1 I 4.4 2.8
5 O1 II GLY 561D N III 4.0 1.0
5 O1 II THR 476D OG1 I 4.0 1.6
6 C1 VIII ARG 532D NH1 III 4.1 8.1
6 C1 VIII ARG 532D NH2 III 4.1 2.5
6 C1 VIII TRP 525D CZ2 V 4.2 8.3
6 C1 VIII ARG 532D CZ VI 4.4 0.7
6 C1 VIII LEU 474D CB IV 4.5 3.4
6 C1 VIII LEU 474D CD2 IV 4.6 2.0
6 C1 VIII THR 476D OG1 I 5.0 0.2
6 C1 VIII VAL 529D CG2 IV 5.0 0.2
7 C2 VI LEU 474D CB IV 4.4 0.2
8 O2 I LEU 474D CB IV 3.6 15.9*
8 O2 I GLY 557D N III 3.6 12.5
8 O2 I LEU 474D CD2 IV 4.0 3.1*
8 O2 I THR 556D C VI 4.0 1.7
8 O2 I THR 556D CA VII 4.2 0.2
8 O2 I LEU 474D O II 4.2 0.7
8 O2 I TRP 525D CZ2 V 5.1 0.3
8 O2 I VAL 529D CG2 IV 5.4 0.5*
9 C3 VI ARG 559D O II 3.4 9.4
9 C3 VI GLY 561D O II 3.6 1.1
10 O3 I GLY 557D CA VI 2.9 24.3
10 O3 I ARG 559D O II 3.1 9.4
10 O3 I GLY 557D N III 3.4 0.2
10 O3 I GLY 557D C VI 3.5 1.0
10 O3 I GLY 557D O II 3.9 0.9
10 O3 I ARG 559D C VI 4.1 0.2
10 O3 I TRP 525D CZ2 V 4.2 0.9
11 C4 VI THR 565D N III 4.0 11.2
11 C4 VI THR 565D OG1 I 4.0 1.6
12 O4 I GLY 561D O II 2.4 16.5
12 O4 I TYR 564D N III 3.1 21.0
12 O4 I TYR 564D CA VII 3.6 2.3
12 O4 I TYR 564D CB IV 3.7 1.4*
13 C5 VIII GLY 561D O II 3.5 5.2*
13 C5 VIII THR 476D OG1 I 4.1 4.9
14 O5 II LEU 474D O II 3.9 3.8*
14 O5 II LEU 474D C VI 4.1 2.3
14 O5 II THR 476D OG1 I 4.1 2.3
14 O5 II THR 475D CA VII 4.3 0.5
14 O5 II THR 475D N III 4.4 0.2
15 C6 VIII THR 565D OG1 I 3.5 14.1
15 C6 VIII SER 480D OG I 3.7 2.5
15 C6 VIII LEU 474D O II 3.8 7.9*
15 C6 VIII THR 475D CA VII 3.9 4.3
15 C6 VIII GLY 563D N III 4.5 0.2
16 O6 II SER 562D CA VII 3.3 7.6
16 O6 II THR 476D N III 3.8 0.2
18 O4P I THR 477D N III 2.7 30.7
18 O4P I THR 476D N III 3.0 3.5
18 O4P I THR 477D OG1 I 3.1 5.7
18 O4P I SER 562D CB VI 3.2 9.0
19 O5P I GLY 563D N III 3.0 19.9
19 O5P I SER 562D CB VI 3.4 2.8
19 O5P I SER 562D OG I 3.6 1.0
19 O5P I GLY 563D CA VI 3.8 3.1
19 O5P I THR 477D OG1 I 4.0 4.7
19 O5P I ARG 479D CB IV 4.3 7.8*
19 O5P I SER 480D OG I 4.3 0.7
19 O5P I SER 480D N III 4.7 0.2
19 O5P I ARG 479D CG IV 5.1 0.3*
19 O5P I THR 565D OG1 I 5.1 0.7
19 O5P I SER 480D CB VI 5.2 0.2
19 O5P I ARG 479D CD VII 5.5 0.5
19 O5P I THR 452D CG2 IV 5.8 2.6*
19 O5P I THR 452D OG1 I 5.8 0.2
20 O6P I SER 480D OG I 2.5 28.4
20 O6P I THR 475D OG1 I 2.9 15.6
20 O6P I SER 480D N III 3.3 6.4
20 O6P I ARG 479D N III 4.0 0.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand FBP 580D
in PDB entry 2VGB (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 486
Actual value (Å2) 374
Normalised complementarity 0.77
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand FBP 580D
in PDB entry 2VGB (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 |
|---|
| 2 | O1P
| I |
0.77 |
0.77
|
0.59 |
0.59
|
0.77 |
0.77
|
0.59 |
0.77
|
| 3 | O2P
| I |
0.77 |
0.77
|
0.64 |
0.61
|
0.77 |
0.77
|
0.64 |
0.77
|
| 4 | O3P
| I |
0.77 |
0.77
|
0.68 |
0.69
|
0.79 |
0.79
|
0.70 |
0.79
|
| 5 | O1
| II |
0.77 |
0.77
|
0.77 |
0.76
|
0.77 |
0.77
|
0.77 |
0.77
|
| 6 | C1
| VIII |
0.75 |
0.75
|
0.70 |
0.73
|
0.77 |
0.77
|
0.73 |
0.77
|
| 7 | C2
| VI |
0.77 |
0.77
|
0.77 |
0.77
|
0.77 |
0.77
|
0.77 |
0.77
|
| 8 | O2
| I |
0.77 |
0.77
|
0.72 |
0.80
|
0.85 |
0.85
|
0.80 |
0.85
|
| 9 | C3
| VI |
0.77 |
0.73
|
0.77 |
0.73
|
0.77 |
0.77
|
0.77 |
0.73
|
| 10 | O3
| I |
0.77 |
0.73
|
0.77 |
0.73
|
0.77 |
0.77
|
0.77 |
0.73
|
| 11 | C4
| VI |
0.77 |
0.77
|
0.72 |
0.72
|
0.77 |
0.77
|
0.72 |
0.77
|
| 12 | O4
| I |
0.77 |
0.70
|
0.68 |
0.62
|
0.78 |
0.78
|
0.68 |
0.71
|
| 13 | C5
| VIII |
0.79 |
0.77
|
0.79 |
0.75
|
0.79 |
0.79
|
0.79 |
0.77
|
| 14 | O5
| II |
0.79 |
0.77
|
0.78 |
0.76
|
0.79 |
0.79
|
0.78 |
0.77
|
| 15 | C6
| VIII |
0.80 |
0.77
|
0.78 |
0.70
|
0.80 |
0.80
|
0.78 |
0.77
|
| 16 | O6
| II |
0.77 |
0.77
|
0.74 |
0.77
|
0.77 |
0.77
|
0.74 |
0.77
|
| 18 | O4P
| I |
0.77 |
0.77
|
0.63 |
0.61
|
0.77 |
0.77
|
0.63 |
0.77
|
| 19 | O5P
| I |
0.77 |
0.77
|
0.69 |
0.70
|
0.82 |
0.82
|
0.73 |
0.82
|
| 20 | O6P
| I |
0.77 |
0.77
|
0.74 |
0.56
|
0.77 |
0.77
|
0.74 |
0.77
|
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 FBP 580
1. Carbon (in rings)
7 C2 9 C3 11 C4 13 C5
2. Oxygen ("hydroxy" or "carbonyl")
8 O2 10 O3 12 O4
Ligand PGA 581
2. Oxygen ("hydroxy" or "carbonyl")
8 O1 9 O2
Ligand MN 583
3. Nitrogen ("hydrophilic")
1 N
Ligand FBP 580
1. Carbon (in rings)
7 C2 9 C3 11 C4 13 C5
2. Oxygen ("hydroxy" or "carbonyl")
8 O2 10 O3 12 O4
Ligand PGA 581
2. Oxygen ("hydroxy" or "carbonyl")
8 O1 9 O2
Ligand MN 587
3. Nitrogen ("hydrophilic")
1 N
Ligand FBP 580
1. Carbon (in rings)
7 C2 9 C3 11 C4 13 C5
2. Oxygen ("hydroxy" or "carbonyl")
8 O2 10 O3 12 O4
Ligand PGA 581
2. Oxygen ("hydroxy" or "carbonyl")
8 O1 9 O2
Ligand MN 591
3. Nitrogen ("hydrophilic")
1 N
Ligand FBP 580
1. Carbon (in rings)
7 C2 9 C3 11 C4 13 C5
2. Oxygen ("hydroxy" or "carbonyl")
8 O2 10 O3 12 O4
Ligand PGA 581
2. Oxygen ("hydroxy" or "carbonyl")
8 O1 9 O2
Ligand MN 595
3. Nitrogen ("hydrophilic")
1 N
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il