Contacts of ligand NHE 354A in PDB entry 1Q1Q
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 354A
in PDB entry 1Q1Q (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
----------------------------------------------------------
25A PRO* 4.3 1.7 - - - +
28A LEU* 4.5 19.0 - - + +
29A TYR* 3.4 33.6 + - - -
54A PRO* 3.3 15.7 - - + +
55A LYS* 4.5 4.6 - - + +
83A TRP* 4.5 21.1 - + + -
88A TRP* 3.4 46.4 - + - -
91A THR* 3.8 26.7 - - + -
110A HIS* 4.4 16.8 - - + +
144A TYR* 3.5 29.2 + - + +
150A GLN* 2.4 45.0 + - - +
151A LEU* 3.9 2.6 - - - +
170A GLN* 2.6 43.3 + - - -
171A PHE* 3.4 11.6 - - - -
242A TYR* 4.7 14.1 - + - -
245A LEU* 4.1 27.8 - - + -
249A LEU* 4.5 17.0 - - + -
257A PHE* 5.4 9.5 - + + -
352A A3P 5.8 1.8 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand NHE 354A
and protein in PDB entry 1Q1Q
(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 TYR 144A OH I 4.7 1.2
9 O1 I GLN 170A OE1 II 2.9 9.4
9 O1 I TYR 29A OH I 3.4 17.2
10 O2 I GLN 170A OE1 II 2.6 14.4
10 O2 I GLN 170A NE2 III 3.0 12.3
11 O3 I GLN 150A NE2 III 2.4 32.7
11 O3 I GLN 170A OE1 II 3.3 5.7
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand NHE 354A
in PDB entry 1Q1Q (back
to top of page)
Total number of contacts is 83
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' V TRP 88A CE3 V 3.8 10.1
1 C3' V THR 91A CG2 IV 3.8 15.3
1 C3' V THR 91A CB VI 4.7 1.3
1 C3' V TRP 83A CB IV 5.0 0.4
1 C3' V LEU 28A CD1 IV 5.1 3.8
1 C3' V LEU 28A CB IV 5.4 1.6
1 C3' V LEU 28A CD2 IV 5.7 0.2
2 C2' V TRP 88A CE3 V 3.4 15.0
2 C2' V THR 91A CG2 IV 4.0 10.1
2 C2' V TRP 88A CD2 V 4.0 0.9
2 C2' V TYR 29A OH I 4.5 3.4
2 C2' V LEU 28A CD1 IV 4.8 2.7
3 C1' V TRP 88A CZ3 V 3.8 4.3
3 C1' V LEU 28A CD1 IV 4.8 0.7
4 C6' V TRP 88A CZ3 V 4.4 3.8
4 C6' V TYR 242A CE1 V 4.7 12.3
4 C6' V LEU 245A CD2 IV 4.9 1.3
4 C6' V TYR 144A OH I 4.9 6.7
4 C6' V TYR 242A CD1 V 4.9 1.3
4 C6' V LEU 245A CD1 IV 5.1 2.7
4 C6' V LEU 28A CD1 IV 5.1 2.9
4 C6' V LEU 249A CD2 IV 5.3 0.9
4 C6' V GLN 150A NE2 III 5.5 0.2
4 C6' V PHE 257A CE1 V 5.6 0.7
4 C6' V LEU 249A CG IV 5.7 0.9
5 N I TRP 88A CH2 V 4.2 10.1
5 N I TRP 88A CZ2 V 4.5 1.6
5 N I TYR 144A OH I 4.7 1.2
5 N I TRP 88A CE2 V 4.7 0.6
5 N I PHE 257A CE1 V 5.4 3.0
5 N I PHE 257A CZ V 5.5 1.6
5 N I TYR 242A CE1 V 5.5 0.2
6 C1 VI GLN 150A NE2 III 3.9 8.3
6 C1 VI TYR 29A OH I 4.1 5.2
6 C1 VI TYR 144A OH I 4.4 0.7
6 C1 VI LEU 28A CD1 IV 4.5 3.1
6 C1 VI HIS 110A CD2 V 5.1 0.4
7 C2 IV GLN 150A NE2 III 4.3 0.2*
7 C2 IV HIS 110A CD2 V 4.4 13.7
7 C2 IV HIS 110A NE2 I 4.4 2.7*
7 C2 IV TYR 144A OH I 4.4 4.7*
7 C2 IV TYR 144A CE2 V 4.6 2.9
7 C2 IV TYR 144A CZ V 4.9 0.4
7 C2 IV PRO 54A CB IV 5.2 0.4
7 C2 IV PHE 257A CZ V 5.6 4.3
7 C2 IV LYS 55A NZ III 5.7 1.6*
7 C2 IV A3P 352A O4P I 5.8 1.8*
7 C2 IV LYS 55A CD IV 5.9 0.2
8 S VI GLN 170A OE1 II 3.1 1.3
8 S VI TYR 144A CE2 V 4.4 0.2
8 S VI PRO 54A CG IV 4.7 0.7
9 O1 I GLN 170A OE1 II 2.9 9.4
9 O1 I TYR 29A OH I 3.4 17.2
9 O1 I PHE 171A CE2 V 3.4 11.6
9 O1 I TYR 29A CE2 V 3.7 8.0
9 O1 I PRO 25A CG IV 4.3 1.7*
9 O1 I LEU 28A CD1 IV 5.2 0.2*
10 O2 I GLN 170A OE1 II 2.6 14.4
10 O2 I GLN 170A NE2 III 3.0 12.3
10 O2 I GLN 170A CD VI 3.2 0.2
10 O2 I PRO 54A CB IV 3.3 14.6*
10 O2 I TYR 144A CE2 V 4.5 4.7
10 O2 I LYS 55A CD IV 4.5 2.8*
10 O2 I LEU 151A CD1 IV 4.9 0.3*
11 O3 I GLN 150A NE2 III 2.4 32.7
11 O3 I GLN 170A OE1 II 3.3 5.7
11 O3 I GLN 150A CD VI 3.4 1.2
11 O3 I TYR 144A CE2 V 3.5 7.6
11 O3 I GLN 150A CG IV 3.8 2.3*
11 O3 I LEU 151A CD1 IV 3.9 2.3*
12 C5' V LEU 245A CD2 IV 4.1 23.6
12 C5' V LEU 249A CD2 IV 4.5 10.1
12 C5' V TRP 83A CB IV 4.7 5.6
12 C5' V LEU 245A CD1 IV 4.9 0.2
12 C5' V TRP 83A CD2 V 5.1 0.2
12 C5' V TYR 242A CE1 V 5.2 0.2
12 C5' V LEU 28A CD1 IV 5.4 0.4
13 C4' V TRP 83A CB IV 4.5 10.8
13 C4' V TRP 83A CG V 4.8 1.8
13 C4' V LEU 249A CD2 IV 4.9 5.2
13 C4' V TRP 83A CD1 V 5.1 2.2
13 C4' V LEU 28A CD1 IV 5.3 1.8
13 C4' V LEU 28A CD2 IV 5.6 1.6
------------------------------------------------------------------------
Table V
Complementarity values for the ligand NHE 354A
in PDB entry 1Q1Q (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 402
Actual value (Å2) 317
Normalised complementarity 0.79
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand NHE 354A
in PDB entry 1Q1Q (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'
| V |
0.68 |
0.68
|
0.68 |
0.79
|
0.79 |
0.79
|
0.79 |
0.79
|
| 2 | C2'
| V |
0.73 |
0.73
|
0.73 |
0.77
|
0.79 |
0.79
|
0.79 |
0.79
|
| 3 | C1'
| V |
0.79 |
0.79
|
0.79 |
0.79
|
0.79 |
0.79
|
0.79 |
0.79
|
| 4 | C6'
| V |
0.75 |
0.75
|
0.74 |
0.75
|
0.79 |
0.79
|
0.79 |
0.79
|
| 5 | N
| I |
0.79 |
0.79
|
0.79 |
0.78
|
0.79 |
0.79
|
0.79 |
0.79
|
| 6 | C1
| VI |
0.77 |
0.77
|
0.73 |
0.72
|
0.79 |
0.79
|
0.75 |
0.79
|
| 7 | C2
| IV |
0.84 |
0.84
|
0.83 |
0.79
|
0.84 |
0.84
|
0.83 |
0.84
|
| 8 | S
| VI |
0.79 |
0.78
|
0.79 |
0.78
|
0.79 |
0.79
|
0.79 |
0.78
|
| 9 | O1
| I |
0.79 |
0.74
|
0.79 |
0.67
|
0.80 |
0.80
|
0.80 |
0.75
|
| 10 | O2
| I |
0.79 |
0.72
|
0.73 |
0.74
|
0.88 |
0.88
|
0.82 |
0.81
|
| 11 | O3
| I |
0.79 |
0.76
|
0.63 |
0.62
|
0.81 |
0.81
|
0.65 |
0.78
|
| 12 | C5'
| V |
0.59 |
0.59
|
0.59 |
0.79
|
0.79 |
0.79
|
0.79 |
0.79
|
| 13 | C4'
| V |
0.69 |
0.69
|
0.69 |
0.79
|
0.79 |
0.79
|
0.79 |
0.79
|
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 A3P 352
1. Carbon (in rings)
11 C4' 17 C1' 15 C2' 13 C3' 19 C8 21 C5
27 C4 21 C5 22 C6 25 C2 27 C4
2. Oxygen ("hydroxy" or "carbonyl")
16 O2'
3. Nitrogen ("hydrophilic")
18 N9 20 N7 23 N6 24 N1 26 N3
Ligand NHE 353
1. Carbon (in rings)
1 C3' 2 C2' 3 C1' 4 C6' 12 C5' 13 C4'
3. Nitrogen ("hydrophilic")
5 N
Ligand NHE 354
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