Contacts of ligand EDO1204A in PDB entry 5KTW
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 EDO1204A
in PDB entry 5KTW (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
----------------------------------------------------------
1158A TRP* 2.9 37.8 + - - -
1161A PHE* 5.9 0.3 - - - -
1182A ALA* 4.5 9.2 + - - +
1185A PHE* 4.3 5.5 - - - -
1186A GLU* 2.7 52.6 + - - +
1203A EDO 3.5 2.5 + - - -
1112B ARG* 3.7 33.9 + - - -
1113B GLN* 3.5 26.7 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand EDO1204A
and protein in PDB entry 5KTW
(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 GLU 1186A OE2 II 2.7 15.4
2 O1 I TRP 1158A NE1 III 2.9 14.6
2 O1 I EDO 1203A O1 I 3.5 0.3
2 O1 I GLU 1186A N III 4.6 0.2
2 O1 I ALA 1182A O II 5.0 1.0
4 O2 I ALA 1182A O II 4.5 4.9
4 O2 I ARG 1112B NH1 III 4.9 0.7
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand EDO1204A
in PDB entry 5KTW (back
to top of page)
Total number of contacts is 38
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 TRP 1158A NE1 III 3.2 17.0
1 C1 VI GLU 1186A OE2 II 3.4 3.6
1 C1 VI GLN 1113B NE2 III 3.5 18.2
1 C1 VI TRP 1158A CE2 V 3.5 2.0
1 C1 VI TRP 1158A CZ2 V 3.6 2.7
1 C1 VI EDO 1203A O1 I 3.6 1.8
1 C1 VI GLN 1113B CD VI 4.0 2.2
1 C1 VI TRP 1158A CD1 V 4.2 1.1
1 C1 VI GLN 1113B CG IV 4.2 0.2
1 C1 VI ARG 1112B O II 4.2 0.2
2 O1 I GLU 1186A OE2 II 2.7 15.4
2 O1 I TRP 1158A NE1 III 2.9 14.6
2 O1 I EDO 1203A O1 I 3.5 0.3
2 O1 I GLU 1186A CB IV 3.9 4.3*
2 O1 I TRP 1158A CD1 V 3.9 0.3
2 O1 I GLU 1186A CA VII 4.2 1.9
2 O1 I PHE 1185A CD2 V 4.3 5.4
2 O1 I GLU 1186A N III 4.6 0.2
2 O1 I EDO 1203A C1 VI 4.7 0.2
2 O1 I PHE 1185A CE2 V 4.8 0.2
2 O1 I ALA 1182A O II 5.0 1.0
2 O1 I PHE 1161A CE2 V 5.9 0.3
3 C2 VI GLU 1186A OE2 II 3.4 8.7
3 C2 VI ARG 1112B CB IV 3.7 29.4
3 C2 VI GLU 1186A CD VI 3.8 3.1
3 C2 VI GLU 1186A CG IV 4.1 0.2
3 C2 VI ARG 1112B O II 4.1 0.7
3 C2 VI EDO 1203A O1 I 4.2 0.2
3 C2 VI ARG 1112B CD VII 4.3 0.4
3 C2 VI GLN 1113B NE2 III 4.3 0.9
3 C2 VI GLN 1113B CG IV 4.4 5.2
4 O2 I GLU 1186A CB IV 3.6 14.4*
4 O2 I GLU 1186A CG IV 3.7 0.7*
4 O2 I ALA 1182A O II 4.5 4.9
4 O2 I ARG 1112B CD VII 4.5 2.4
4 O2 I ARG 1112B NH1 III 4.9 0.7
4 O2 I ALA 1182A C VI 5.3 0.5
4 O2 I ALA 1182A CB IV 5.6 2.8*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand EDO1204A
in PDB entry 5KTW (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 192
Actual value (Å2) 124
Normalised complementarity 0.64
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand EDO1204A
in PDB entry 5KTW (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 |
0.64 |
0.60
|
0.28 |
0.22
|
0.64 |
0.64
|
0.28 |
0.60
|
| 2 | O1
| I |
0.64 |
0.47
|
0.47 |
0.36
|
0.69 |
0.69
|
0.52 |
0.52
|
| 3 | C2
| VI |
0.28 |
0.19
|
0.27 |
0.54
|
0.64 |
0.64
|
0.63 |
0.55
|
| 4 | O2
| I |
0.64 |
0.59
|
0.61 |
0.77
|
0.83 |
0.83
|
0.80 |
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 6XG 1201
1. Carbon (in rings)
1 C7 10 C8 2 C9 4 C10 11 C11 12 C12
14 C14 15 C15 16 C16 15 C15 16 C16 23 C23
24 C24 26 C26 20 C20 21 C21 22 C22
2. Oxygen ("hydroxy" or "carbonyl")
9 O6 28 O28
3. Nitrogen ("hydrophilic")
7 N4 13 N13 17 N17 18 N18 25 N25
Ligand EDO 1202
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1203
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1204
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand 6XG 1201
1. Carbon (in rings)
1 C7 10 C8 2 C9 4 C10 11 C11 12 C12
14 C14 15 C15 16 C16 15 C15 16 C16 23 C23
24 C24 26 C26 20 C20 21 C21 22 C22
2. Oxygen ("hydroxy" or "carbonyl")
9 O6 28 O28
3. Nitrogen ("hydrophilic")
7 N4 13 N13 17 N17 18 N18 25 N25
Ligand EDO 1202
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1203
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1204
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand 6XG 1201
1. Carbon (in rings)
1 C7 10 C8 2 C9 4 C10 11 C11 12 C12
14 C14 15 C15 16 C16 15 C15 16 C16 23 C23
24 C24 26 C26 20 C20 21 C21 22 C22
2. Oxygen ("hydroxy" or "carbonyl")
9 O6 28 O28
3. Nitrogen ("hydrophilic")
7 N4 13 N13 17 N17 18 N18 25 N25
Ligand EDO 1202
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1203
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