Contacts of ligand EDO1005A in PDB entry 4ERO
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 EDO1005A
in PDB entry 4ERO (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
----------------------------------------------------------
18A GLU* 4.4 10.0 + - - +
24A VAL* 3.7 13.2 - - - +
26A ARG* 4.0 12.3 + - - -
41A LEU* 4.3 5.8 - - - -
43A ASP* 2.4 41.6 + - - +
45A PHE* 5.3 1.4 - - - +
53A PHE* 4.1 28.1 - - - -
58A HIS* 6.0 0.2 - - - -
103A GLU* 5.6 2.2 - - - -
115A GLN* 3.8 32.2 - - - +
117A TRP* 3.8 28.1 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand EDO1005A
and protein in PDB entry 4ERO
(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 O1 I ARG 26A NH2 III 4.0 6.2
2 O1 I GLU 18A OE1 II 4.6 1.9
4 O2 I ASP 43A OD2 II 2.4 22.7
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand EDO1005A
in PDB entry 4ERO (back
to top of page)
Total number of contacts is 37
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 VI ASP 43A OD2 II 3.4 9.4
1 C1 VI TRP 117A CZ2 V 3.8 26.9
1 C1 VI ARG 26A NH2 III 4.0 6.1
1 C1 VI GLN 115A OE1 II 4.3 0.4
1 C1 VI LEU 41A CD2 IV 4.3 4.7
1 C1 VI LEU 41A CD1 IV 4.6 0.7
1 C1 VI TRP 117A CH2 V 4.6 0.4
1 C1 VI HIS 58A CE1 V 6.0 0.2
2 O1 I ARG 26A NH2 III 4.0 6.2
2 O1 I PHE 53A CD2 V 4.3 11.8
2 O1 I PHE 53A CE2 V 4.4 0.9
2 O1 I GLU 18A CB IV 4.4 7.8*
2 O1 I GLU 18A CG IV 4.4 0.3*
2 O1 I TRP 117A CZ2 V 4.6 0.5
2 O1 I GLU 18A OE1 II 4.6 1.9
2 O1 I TRP 117A CH2 V 5.1 0.2
3 C2 VI ASP 43A OD2 II 3.3 1.1
3 C2 VI GLN 115A OE1 II 3.8 17.7
3 C2 VI GLN 115A CD VI 4.1 7.0
3 C2 VI GLN 115A CB IV 4.2 5.2
3 C2 VI GLN 115A CG IV 4.3 0.4
3 C2 VI PHE 53A CE2 V 4.3 10.1
3 C2 VI LEU 41A CD2 IV 4.6 0.4
3 C2 VI PHE 53A CD2 V 4.6 1.6
3 C2 VI GLN 115A NE2 III 4.9 0.2
3 C2 VI PHE 53A CZ V 4.9 0.9
3 C2 VI PHE 53A CG V 5.4 0.2
3 C2 VI PHE 53A CE1 V 5.6 0.2
3 C2 VI GLU 103A OE2 II 5.6 2.2
4 O2 I ASP 43A OD2 II 2.4 22.7
4 O2 I ASP 43A CG VI 3.3 2.9
4 O2 I ASP 43A CB IV 3.4 5.4*
4 O2 I VAL 24A CG1 IV 3.7 13.2*
4 O2 I PHE 53A CE2 V 4.1 1.9
4 O2 I GLN 115A CB IV 4.3 1.2*
4 O2 I PHE 53A CZ V 4.5 0.5
4 O2 I PHE 45A CB IV 5.3 1.4*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand EDO1005A
in PDB entry 4ERO (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 194
Actual value (Å2) 116
Normalised complementarity 0.60
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand EDO1005A
in PDB entry 4ERO (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
| VI |
0.54 |
0.44
|
0.48 |
0.44
|
0.60 |
0.60
|
0.54 |
0.50
|
| 2 | O1
| I |
0.60 |
0.58
|
0.54 |
0.60
|
0.68 |
0.68
|
0.62 |
0.66
|
| 3 | C2
| VI |
0.54 |
0.32
|
0.54 |
0.38
|
0.60 |
0.60
|
0.60 |
0.38
|
| 4 | O2
| I |
0.60 |
0.37
|
0.60 |
0.58
|
0.82 |
0.82
|
0.82 |
0.58
|
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 EDO 1002
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1003
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1004
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1005
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il