Contacts of ligand ORN 500A in PDB entry 3THJ
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 ORN 500A
in PDB entry 3THJ (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
----------------------------------------------------------
126A HIS* 3.6 38.9 - - + +
128A ASP* 3.0 29.9 + - - +
130A ASN* 3.1 19.8 + - - -
135A THR* 4.5 4.3 + - - -
136A THR* 5.5 1.5 + - - -
137A SER* 2.5 37.8 + - - -
139A ASN* 4.2 9.5 + - - +
141A HIS* 3.2 48.2 + - - +
142A GLY* 3.7 17.4 - - - +
181A ASP* 4.8 3.6 + - - -
183A ASP* 2.9 31.2 + - - +
186A GLU* 3.6 11.7 + - - -
232A ASP* 5.1 0.2 + - - -
234A ASP* 5.2 0.2 + - - -
246A THR* 3.9 16.0 + - + -
277A GLU* 4.8 1.4 + - - -
400A CO 4.3 4.8 + - - -
401A CO 4.5 0.6 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand ORN 500A
and protein in PDB entry 3THJ
(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
------------------------------------------------------------------------
1 N I ASP 183A OD2 II 2.9 18.0
1 N I ASP 183A OD1 II 3.6 1.6
1 N I GLU 186A OE1 II 3.6 9.9
1 N I ASN 130A ND2 III 3.9 0.6
1 N I GLU 186A OE2 II 4.5 0.6
1 N I ASP 181A O II 4.8 2.8
6 NE I ASP 128A OD1 II 3.0 14.5
6 NE I HIS 141A O II 3.2 15.6
6 NE I HIS 141A NE2 I 3.2 13.5
6 NE I HIS 141A ND1 I 3.4 1.2
6 NE I ASP 128A OD2 II 4.1 0.8
6 NE I CO 400A CO I 4.3 4.8
6 NE I THR 246A OG1 I 4.3 1.2
6 NE I CO 401A CO I 4.5 0.6
6 NE I GLU 277A OE2 II 4.8 1.4
6 NE I ASP 232A OD2 II 5.1 0.2
6 NE I ASP 234A OD1 II 5.2 0.2
8 O II ASN 130A ND2 III 3.1 19.2
8 O II SER 137A OG I 3.7 3.5
8 O II THR 135A OG1 I 4.5 4.2
8 O II SER 137A N III 5.3 0.2
8 O II THR 136A N III 5.5 0.3
9 OXT I SER 137A OG I 2.5 23.6
9 OXT I ASN 139A ND2 III 4.2 5.5
9 OXT I HIS 141A NE2 I 4.5 0.7
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand ORN 500A
in PDB entry 3THJ (back
to top of page)
Total number of contacts is 71
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 N I ASP 183A OD2 II 2.9 18.0
1 N I ASP 183A CG VI 3.6 5.3
1 N I ASP 183A OD1 II 3.6 1.6
1 N I GLU 186A OE1 II 3.6 9.9
1 N I ASN 130A ND2 III 3.9 0.6
1 N I GLU 186A CD VI 4.4 1.2
1 N I GLU 186A OE2 II 4.5 0.6
1 N I HIS 126A CD2 V 4.7 5.3
1 N I ASP 181A O II 4.8 2.8
1 N I HIS 126A CB IV 5.1 1.0*
1 N I GLY 142A CA VI 5.1 0.2
1 N I ASP 181A CG VI 6.1 0.4
2 CA VI ASP 183A OD2 II 3.8 1.8
2 CA VI ASP 183A OD1 II 4.4 2.2
2 CA VI ASP 181A CG VI 6.5 0.2
3 CB IV HIS 126A CD2 V 4.0 9.4
3 CB IV HIS 126A NE2 I 4.4 0.9*
3 CB IV HIS 141A NE2 I 4.5 2.0*
3 CB IV THR 246A CG2 IV 4.7 7.2
3 CB IV ASP 181A CG VI 6.4 0.2
4 CG IV ASP 128A OD1 II 3.6 9.0*
4 CG IV GLY 142A CA VI 3.7 6.7
4 CG IV HIS 141A NE2 I 4.0 0.9*
4 CG IV HIS 126A CD2 V 4.2 1.6
4 CG IV HIS 126A CG V 4.2 0.2
4 CG IV HIS 126A CB IV 4.4 0.2
4 CG IV ASP 128A CA VII 5.4 0.2
5 CD VI ASP 128A OD1 II 3.4 4.0
5 CD VI HIS 141A NE2 I 3.6 5.8
5 CD VI HIS 126A CG V 3.6 16.4
5 CD VI HIS 126A ND1 I 3.8 2.9
5 CD VI HIS 126A CD2 V 3.8 0.9
5 CD VI HIS 141A CE1 V 3.8 3.1
5 CD VI THR 246A OG1 I 3.9 7.4
5 CD VI THR 246A CG2 IV 4.3 0.2
6 NE I ASP 128A OD1 II 3.0 14.5
6 NE I HIS 141A O II 3.2 15.6
6 NE I HIS 141A NE2 I 3.2 13.5
6 NE I HIS 141A CE1 V 3.3 5.3
6 NE I HIS 141A ND1 I 3.4 1.2
6 NE I ASP 128A CG VI 3.9 1.4
6 NE I ASP 128A OD2 II 4.1 0.8
6 NE I CO 400A CO I 4.3 4.8
6 NE I THR 246A OG1 I 4.3 1.2
6 NE I CO 401A CO I 4.5 0.6
6 NE I GLU 277A OE2 II 4.8 1.4
6 NE I ASP 232A OD2 II 5.1 0.2
6 NE I ASP 234A OD1 II 5.2 0.2
7 C VI SER 137A OG I 3.5 2.7
7 C VI ASP 183A OD2 II 4.0 2.0
7 C VI SER 137A CB VI 4.2 2.5
7 C VI GLY 142A CA VI 4.4 2.0
7 C VI SER 137A N III 5.3 0.4
7 C VI THR 136A OG1 I 6.0 0.9
7 C VI THR 136A N III 6.0 0.2
8 O II ASN 130A ND2 III 3.1 19.2
8 O II ASP 183A OD2 II 3.6 0.2*
8 O II SER 137A OG I 3.7 3.5
8 O II GLY 142A CA VI 4.0 7.8
8 O II GLY 142A O II 4.1 0.2*
8 O II GLY 142A C VI 4.4 0.5
8 O II THR 135A OG1 I 4.5 4.2
8 O II ASN 139A O II 4.8 0.3*
8 O II SER 137A N III 5.3 0.2
8 O II THR 135A CA VII 5.4 0.2
8 O II THR 136A N III 5.5 0.3
9 OXT I SER 137A OG I 2.5 23.6
9 OXT I SER 137A CB VI 3.2 5.0
9 OXT I ASN 139A ND2 III 4.2 5.5
9 OXT I ASN 139A CB IV 4.3 3.6*
9 OXT I HIS 141A NE2 I 4.5 0.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand ORN 500A
in PDB entry 3THJ (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 302
Actual value (Å2) 240
Normalised complementarity 0.80
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand ORN 500A
in PDB entry 3THJ (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 | N
| I |
0.80 |
0.58
|
0.79 |
0.58
|
0.80 |
0.80
|
0.80 |
0.59
|
| 2 | CA
| VI |
0.80 |
0.77
|
0.80 |
0.77
|
0.80 |
0.80
|
0.80 |
0.77
|
| 3 | CB
| IV |
0.77 |
0.77
|
0.77 |
0.80
|
0.82 |
0.82
|
0.82 |
0.82
|
| 4 | CG
| IV |
0.86 |
0.80
|
0.86 |
0.80
|
0.86 |
0.86
|
0.86 |
0.80
|
| 5 | CD
| VI |
0.79 |
0.77
|
0.79 |
0.66
|
0.80 |
0.80
|
0.80 |
0.77
|
| 6 | NE
| I |
0.80 |
0.58
|
0.80 |
0.44
|
0.80 |
0.80
|
0.80 |
0.58
|
| 7 | C
| VI |
0.80 |
0.78
|
0.79 |
0.75
|
0.80 |
0.80
|
0.79 |
0.78
|
| 8 | O
| II |
0.80 |
0.80
|
0.67 |
0.62
|
0.80 |
0.80
|
0.67 |
0.80
|
| 9 | OXT
| I |
0.80 |
0.80
|
0.76 |
0.62
|
0.82 |
0.82
|
0.78 |
0.82
|
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 ORN 500
2. Oxygen ("hydroxy" or "carbonyl")
8 O 9 OXT
3. Nitrogen ("hydrophilic")
1 N 6 NE
Ligand ORN 600
2. Oxygen ("hydroxy" or "carbonyl")
8 O 9 OXT
3. Nitrogen ("hydrophilic")
1 N 6 NE
Ligand ORN 500
2. Oxygen ("hydroxy" or "carbonyl")
8 O 9 OXT
3. Nitrogen ("hydrophilic")
1 N 6 NE
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il