Contacts of ligand SEP 139D in PDB entry 3SQD
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 SEP 139D
in PDB entry 3SQD (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
----------------------------------------------------------
871B PHE 3.6 1.0 + - - -
872B THR* 2.8 23.4 + - - -
873B GLY* 2.8 30.6 + - - -
874B PHE 4.1 9.0 + - - -
911B THR* 3.8 15.5 + - - +
913B LYS* 2.5 54.2 + - - +
140D GLN* 1.3 65.3 + - - +
141D GLU* 3.4 11.1 + - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand SEP 139D
and protein in PDB entry 3SQD
(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
------------------------------------------------------------------------
6 O II GLN 140D N III 2.3 0.3
6 O II GLU 141D N III 3.4 2.1
8 O1P I LYS 913B NZ III 2.5 34.8
8 O1P I PHE 871B O II 3.6 1.0
9 O2P I GLY 873B N III 2.8 26.9
9 O2P I PHE 874B N III 4.1 3.8
9 O2P I PHE 874B O II 4.4 5.2
10 O3P I THR 872B OG1 I 2.8 22.3
10 O3P I THR 911B OG1 I 3.8 3.6
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand SEP 139D
in PDB entry 3SQD (back
to top of page)
Total number of contacts is 33
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 CA VI GLN 140D N III 2.4 4.3
3 CB VIII GLN 140D N III 3.4 0.2
3 CB VIII THR 911B CG2 IV 4.2 8.7
3 CB VIII GLN 140D O II 4.6 0.2*
3 CB VIII THR 911B CB VI 4.7 0.7
3 CB VIII GLY 873B N III 5.1 0.4
3 CB VIII GLY 873B CA VI 5.6 0.9
4 OG II LYS 913B CE VII 5.0 0.2
5 C VIII GLN 140D N III 1.3 43.5
5 C VIII GLN 140D CA VII 2.4 2.7
5 C VIII GLN 140D C VI 3.0 2.2
6 O II GLN 140D N III 2.3 0.3
6 O II GLN 140D CA VII 2.8 6.6
6 O II GLN 140D C VI 3.0 5.2
6 O II GLU 141D N III 3.4 2.1
6 O II GLU 141D CG IV 4.0 9.0*
6 O II THR 911B CG2 IV 4.2 1.0*
8 O1P I LYS 913B NZ III 2.5 34.8
8 O1P I LYS 913B CE VII 3.0 2.8
8 O1P I LYS 913B CD IV 3.3 0.2*
8 O1P I PHE 871B O II 3.6 1.0
9 O2P I GLY 873B N III 2.8 26.9
9 O2P I GLY 873B CA VI 3.6 2.3
9 O2P I THR 872B CA VII 3.6 1.0
9 O2P I PHE 874B N III 4.1 3.8
9 O2P I GLY 873B C VI 4.2 0.2
9 O2P I PHE 874B O II 4.4 5.2
10 O3P I THR 872B OG1 I 2.8 22.3
10 O3P I LYS 913B CD IV 3.1 14.0*
10 O3P I LYS 913B CG IV 3.7 2.1*
10 O3P I THR 911B OG1 I 3.8 3.6
10 O3P I LYS 913B CE VII 3.8 0.2
10 O3P I THR 911B CB VI 3.8 1.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand SEP 139D
in PDB entry 3SQD (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 315
Actual value (Å2) 157
Normalised complementarity 0.50
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand SEP 139D
in PDB entry 3SQD (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 | CA
| VI |
0.50 |
0.50
|
0.47 |
0.47
|
0.50 |
0.50
|
0.47 |
0.50
|
| 3 | CB
| VIII |
0.44 |
0.44
|
0.44 |
0.49
|
0.50 |
0.50
|
0.49 |
0.50
|
| 4 | OG
| II |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 5 | C
| VIII |
0.50 |
0.50
|
0.20 |
0.22
|
0.50 |
0.50
|
0.20 |
0.50
|
| 6 | O
| II |
0.50 |
0.50
|
0.44 |
0.55
|
0.56 |
0.56
|
0.50 |
0.56
|
| 8 | O1P
| I |
0.50 |
0.49
|
0.26 |
0.27
|
0.50 |
0.50
|
0.26 |
0.49
|
| 9 | O2P
| I |
0.50 |
0.46
|
0.30 |
0.27
|
0.50 |
0.50
|
0.30 |
0.46
|
| 10 | O3P
| I |
0.50 |
0.50
|
0.50 |
0.44
|
0.60 |
0.60
|
0.60 |
0.60
|
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 SEP 139
2. Oxygen ("hydroxy" or "carbonyl")
6 O
3. Nitrogen ("hydrophilic")
1 N
Ligand SEP 139
2. Oxygen ("hydroxy" or "carbonyl")
6 O
3. Nitrogen ("hydrophilic")
1 N
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il