Contacts of ligand NHE 520B in PDB entry 3OB9
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 NHE 520B
in PDB entry 3OB9 (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
----------------------------------------------------------
21B GLU* 2.6 30.1 + - - +
22B PRO* 3.9 14.6 - - + -
23B ASP* 4.7 7.2 - - + +
26B LYS* 4.1 26.6 - - - +
31B TYR* 3.4 38.2 + - + +
56B PHE* 3.6 48.5 - - + -
59B TRP* 3.5 53.9 - - + -
63B TRP* 3.7 37.8 - - + +
65B ARG* 4.0 20.6 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand NHE 520B
and protein in PDB entry 3OB9
(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
------------------------------------------------------------------------
5 N I GLU 21B OE2 II 2.6 14.5
9 O1 I TYR 31B OH I 5.0 0.5
9 O1 I GLU 21B OE1 II 5.3 0.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand NHE 520B
in PDB entry 3OB9 (back
to top of page)
Total number of contacts is 62
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 C3' IV TRP 63B CE3 V 3.7 20.0
1 C3' IV ARG 65B NE III 4.0 18.4*
1 C3' IV PRO 22B CG IV 4.1 1.1
1 C3' IV ARG 65B CZ VI 4.4 0.9
1 C3' IV TRP 63B O II 4.6 1.3*
2 C2' IV GLU 21B OE2 II 3.7 5.8*
2 C2' IV PRO 22B CG IV 3.9 8.5
2 C2' IV TRP 63B CE3 V 4.2 3.8
2 C2' IV TRP 63B CZ3 V 4.3 2.7
2 C2' IV ARG 65B CZ VI 5.2 1.1
2 C2' IV ARG 65B NH2 III 5.2 0.2*
2 C2' IV ASP 23B CB IV 5.3 3.1
3 C1' VI TRP 59B CH2 V 4.2 2.0
3 C1' VI TRP 59B CZ3 V 4.4 1.6
3 C1' VI TRP 63B CZ3 V 4.5 2.7
4 C6' IV TYR 31B OH I 3.4 20.6*
4 C6' IV TYR 31B CZ V 3.5 4.3
4 C6' IV TRP 59B CH2 V 3.8 2.2
4 C6' IV TYR 31B CE1 V 3.9 2.2
4 C6' IV GLU 21B OE2 II 3.9 0.7*
5 N I GLU 21B OE2 II 2.6 14.5
5 N I ASP 23B CB IV 4.7 1.2*
6 C1 VI GLU 21B OE2 II 3.6 4.9
6 C1 VI GLU 21B OE1 II 3.8 3.6
6 C1 VI GLU 21B CD VI 4.1 0.4
6 C1 VI LYS 26B CD IV 4.3 9.9
6 C1 VI LYS 26B CG IV 4.5 1.1
6 C1 VI ASP 23B OD2 II 5.1 2.9
6 C1 VI TRP 63B CZ3 V 5.5 2.0
7 C2 IV TRP 59B CH2 V 3.5 9.2
7 C2 IV TYR 31B OH I 4.0 7.4*
7 C2 IV TRP 59B CZ3 V 4.3 0.4
7 C2 IV TRP 59B CZ2 V 4.3 0.2
7 C2 IV TRP 63B CZ3 V 5.7 0.4
8 S VI TRP 59B CZ3 V 4.9 0.2
9 O1 I LYS 26B CD IV 4.1 11.4*
9 O1 I TYR 31B OH I 5.0 0.5
9 O1 I GLU 21B OE1 II 5.3 0.2
10 O2 I LYS 26B CD IV 4.5 4.2*
10 O2 I TRP 63B CH2 V 5.5 4.0
11 O3 I TRP 59B CH2 V 3.5 13.2
11 O3 I TRP 59B CZ3 V 4.2 1.0
11 O3 I TRP 63B CH2 V 6.0 0.2
12 C5' IV TRP 59B CZ2 V 4.0 14.8
12 C5' IV TRP 59B CH2 V 4.0 1.3
12 C5' IV TRP 59B CE2 V 4.1 4.9
12 C5' IV PHE 56B CD1 V 4.2 12.1
12 C5' IV TYR 31B CZ V 4.2 3.1
12 C5' IV TRP 59B CZ3 V 4.2 1.3
12 C5' IV PHE 56B CG V 4.2 1.6
12 C5' IV TRP 59B CD2 V 4.3 1.1
12 C5' IV PHE 56B CE1 V 4.3 0.2
12 C5' IV TRP 59B CE3 V 4.3 0.2
13 C4' IV PHE 56B CZ V 3.6 28.3
13 C4' IV PHE 56B CE2 V 3.6 4.3
13 C4' IV PHE 56B CE1 V 3.9 0.9
13 C4' IV PHE 56B CD2 V 3.9 1.1
13 C4' IV PRO 22B CG IV 4.1 4.5
13 C4' IV PRO 22B CD IV 4.2 0.4
13 C4' IV TRP 63B O II 4.6 0.2*
13 C4' IV TRP 63B CE3 V 4.7 0.2
13 C4' IV TRP 63B CB IV 4.9 0.2
------------------------------------------------------------------------
Table V
Complementarity values for the ligand NHE 520B
in PDB entry 3OB9 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 380
Actual value (Å2) 134
Normalised complementarity 0.35
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand NHE 520B
in PDB entry 3OB9 (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 | C3'
| IV |
0.45 |
0.44
|
0.35 |
0.35
|
0.46 |
0.46
|
0.36 |
0.45
|
| 2 | C2'
| IV |
0.32 |
0.29
|
0.32 |
0.35
|
0.38 |
0.38
|
0.38 |
0.35
|
| 3 | C1'
| VI |
0.35 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
| 4 | C6'
| IV |
0.47 |
0.46
|
0.47 |
0.35
|
0.47 |
0.47
|
0.47 |
0.46
|
| 5 | N
| I |
0.35 |
0.28
|
0.35 |
0.28
|
0.36 |
0.36
|
0.36 |
0.28
|
| 6 | C1
| VI |
0.30 |
0.24
|
0.30 |
0.29
|
0.35 |
0.35
|
0.35 |
0.29
|
| 7 | C2
| IV |
0.39 |
0.39
|
0.39 |
0.35
|
0.39 |
0.39
|
0.39 |
0.39
|
| 8 | S
| VI |
0.35 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
| 9 | O1
| I |
0.35 |
0.35
|
0.35 |
0.41
|
0.41 |
0.41
|
0.41 |
0.41
|
| 10 | O2
| I |
0.35 |
0.35
|
0.35 |
0.37
|
0.37 |
0.37
|
0.37 |
0.37
|
| 11 | O3
| I |
0.35 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
| 12 | C5'
| IV |
0.35 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
| 13 | C4'
| IV |
0.33 |
0.33
|
0.33 |
0.35
|
0.35 |
0.35
|
0.35 |
0.35
|
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 NHE 540
1. Carbon (in rings)
1 C3' 2 C2' 3 C1' 4 C6' 12 C5' 13 C4'
3. Nitrogen ("hydrophilic")
5 N
Ligand NHE 520
1. Carbon (in rings)
1 C3' 2 C2' 3 C1' 4 C6' 12 C5' 13 C4'
3. Nitrogen ("hydrophilic")
5 N
Ligand NHE 500
1. Carbon (in rings)
1 C3' 2 C2' 3 C1' 4 C6' 12 C5' 13 C4'
3. Nitrogen ("hydrophilic")
5 N
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il