Contacts of ligand PNT 25B in PDB entry 1D64
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 PNT 25B
in PDB entry 1D64 (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
----------------------------------------------------------
4A G* 4.3 2.4 + - - -
5A A* 2.8 31.5 + - - -
6A A* 2.8 52.9 + - - -
7A T* 3.6 33.4 - - - +
8A T* 2.8 56.9 - - - +
9A C* 3.2 41.9 + - - +
10A G* 4.1 22.3 + - - -
16B G* 4.4 2.2 + - - -
17B A* 2.9 21.8 + - - -
18B A* 2.7 60.8 + - - -
19B T* 3.4 46.7 - - - +
20B T* 2.8 58.6 - - - +
21B C* 3.0 53.8 + - - +
22B G* 4.5 14.8 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand PNT 25B
and protein in PDB entry 1D64
(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
------------------------------------------------------------------------
22 N1 I A 5A N3 II 2.8 27.5
22 N1 I A 6A O4' II 2.9 7.1
22 N1 I C 21B O2 II 3.3 4.4
22 N1 I G 4A N2 III 4.3 2.4
22 N1 I A 5A C1' I 4.7 0.4
23 N2 I C 21B O2 II 4.1 3.6
23 N2 I A 6A O4' II 4.1 0.8
23 N2 I C 21B C1' I 4.3 3.6
23 N2 I G 22B O4' II 4.8 1.2
24 N1' I A 18B O4' II 2.7 17.8
24 N1' I A 17B N3 II 2.9 19.4
24 N1' I C 9A O2 II 3.5 4.4
24 N1' I G 16B N2 III 4.4 2.2
24 N1' I A 17B C1' I 4.9 0.2
25 N2' I C 9A O4' II 3.9 2.6
25 N2' I C 9A O2 II 4.5 0.4
25 N2' I A 18B O3' II 4.7 0.8
25 N2' I G 10A OP1 I 5.0 0.4
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand PNT 25B
in PDB entry 1D64 (back
to top of page)
Total number of contacts is 117
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 V C 21B C5' VIII 3.6 2.7
1 C1 V T 7A C4' VIII 3.9 5.6
2 C2 V T 20B O2 II 2.8 6.1
2 C2 V A 6A N3 II 3.0 9.9
2 C2 V T 7A O4' II 3.6 4.9
3 C3 V T 20B O2 II 2.8 10.8
3 C3 V A 6A N3 II 2.8 12.6
3 C3 V A 6A O4' II 3.7 2.0
3 C3 V A 6A C1' I 3.8 0.9
4 C4 V C 21B O4' II 3.5 2.5
4 C4 V A 6A O4' II 3.7 0.9
4 C4 V A 6A C1' I 4.2 0.7
4 C4 V A 6A C4' VIII 4.3 0.7
5 C5 V C 21B C4' VIII 3.0 11.4
5 C5 V C 21B O3' II 4.3 1.1
5 C5 V T 7A C5' VIII 4.5 3.1
5 C5 V A 6A C4' VIII 5.1 0.2
5 C5 V A 6A O3' II 5.1 0.2
6 C6 V C 21B C5' VIII 3.0 17.0
6 C6 V T 7A C5' VIII 4.2 5.4
7 C7 VIII T 20B O4' II 3.2 13.7*
7 C7 VIII T 20B C1' I 3.4 2.2
7 C7 VIII T 20B C4' VIII 3.6 0.2*
7 C7 VIII T 20B O2 II 3.6 0.4*
7 C7 VIII A 6A C2 V 4.2 1.1
7 C7 VIII T 7A O4' II 4.3 1.3*
8 C8 IV T 20B C4' VIII 3.5 9.6
8 C8 IV T 20B C5' VIII 4.1 0.2
8 C8 IV T 8A C5' VIII 4.4 11.4
8 C8 IV T 7A C4' VIII 4.7 1.8
8 C8 IV T 7A O3' II 4.9 0.2*
8 C8 IV C 21B OP1 I 5.7 0.4*
9 C9 VI A 6A O4' II 3.3 5.8
9 C9 VI C 21B O2 II 3.7 4.0
9 C9 VI A 6A C4' VIII 3.8 0.9
10 C10 IV T 19B O2 II 3.4 9.0*
10 C10 IV T 20B O4' II 3.5 1.1*
10 C10 IV T 7A O2 II 3.8 9.0*
10 C10 IV T 8A O4' II 4.2 3.4*
10 C10 IV T 7A C1' I 4.5 0.2*
11 C1' V T 19B O4' II 3.6 3.1
11 C1' V T 19B C4' VIII 3.8 0.2
11 C1' V T 8A O2 II 3.8 0.4
11 C1' V C 9A C5' VIII 4.0 4.7
12 C2' V T 8A O2 II 2.8 11.9
12 C2' V A 18B N3 II 3.0 8.3
12 C2' V T 19B O4' II 3.6 0.9
13 C3' V A 18B N3 II 2.8 14.6
13 C3' V T 8A O2 II 2.9 10.8
13 C3' V C 9A O4' II 3.5 0.4
13 C3' V A 18B C1' I 3.9 0.2
14 C4' V C 9A O4' II 3.2 2.9
14 C4' V A 18B O4' II 4.0 0.7
14 C4' V A 18B C1' I 4.1 1.1
15 C5' V C 9A O4' II 3.3 5.8
15 C5' V C 9A C4' VIII 3.5 3.1
15 C5' V T 19B C5' VIII 4.1 7.9
15 C5' V C 9A O3' II 4.5 0.9
15 C5' V G 10A OP1 I 5.4 1.1
16 C6' V C 9A C4' VIII 3.6 9.2
16 C6' V T 19B C4' VIII 3.8 8.7
16 C6' V C 9A C5' VIII 3.9 1.3
16 C6' V T 19B C5' VIII 4.1 0.4
17 C7' VIII T 19B O2 II 3.5 10.5*
17 C7' VIII T 19B O4' II 3.9 2.9*
17 C7' VIII T 8A O4' II 3.9 6.1*
17 C7' VIII T 19B C1' I 4.0 0.7
17 C7' VIII A 18B C2 V 4.1 1.8
18 C8' IV T 19B O2 II 3.9 0.7*
18 C8' IV T 20B C5' VIII 3.9 14.1
18 C8' IV T 8A C4' VIII 3.9 10.3
18 C8' IV T 8A C5' VIII 4.4 0.2
19 C9' VI A 18B O4' II 3.4 4.5
19 C9' VI C 9A O4' II 3.6 4.5
19 C9' VI A 18B C4' VIII 3.8 0.7
19 C9' VI C 9A O2 II 3.9 1.1
20 O1 II C 21B C5' VIII 3.8 2.3*
20 O1 II T 7A C4' VIII 3.9 1.6*
20 O1 II T 7A O3' II 4.9 0.2*
21 O1' II T 19B C4' VIII 4.0 1.2*
21 O1' II T 8A C4' VIII 4.3 2.1*
21 O1' II C 9A C5' VIII 4.3 0.5*
21 O1' II T 8A O3' II 4.6 0.3*
21 O1' II T 19B O3' II 4.6 0.3*
22 N1 I A 5A N3 II 2.8 27.5
22 N1 I A 6A O4' II 2.9 7.1
22 N1 I A 5A C2 V 2.9 3.6
22 N1 I C 21B O2 II 3.3 4.4
22 N1 I A 6A C4' VIII 3.6 1.2
22 N1 I A 6A C5' VIII 4.2 1.6
22 N1 I G 4A N2 III 4.3 2.4
22 N1 I A 5A C1' I 4.7 0.4
23 N2 I C 21B O2 II 4.1 3.6
23 N2 I A 6A O4' II 4.1 0.8
23 N2 I A 6A C4' VIII 4.2 4.9
23 N2 I C 21B C1' I 4.3 3.6
23 N2 I C 21B C4' VIII 4.4 0.8
23 N2 I G 22B C5' VIII 4.5 13.3
23 N2 I A 6A C5' VIII 4.8 1.4
23 N2 I G 22B O4' II 4.8 1.2
23 N2 I G 22B C4' VIII 5.0 0.4
24 N1' I A 18B O4' II 2.7 17.8
24 N1' I A 17B N3 II 2.9 19.4
24 N1' I A 17B C2 V 3.0 2.2
24 N1' I C 9A O2 II 3.5 4.4
24 N1' I A 18B C4' VIII 3.6 0.8
24 N1' I G 16B N2 III 4.4 2.2
24 N1' I A 18B C5' VIII 4.4 0.8
24 N1' I A 17B C1' I 4.9 0.2
25 N2' I C 9A O4' II 3.9 2.6
25 N2' I A 18B C4' VIII 4.0 8.1
25 N2' I G 10A C5' VIII 4.1 20.0
25 N2' I C 9A O2 II 4.5 0.4
25 N2' I A 18B O3' II 4.7 0.8
25 N2' I G 10A C4' VIII 4.8 0.8
25 N2' I A 18B C5' VIII 4.9 0.6
25 N2' I G 10A OP1 I 5.0 0.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand PNT 25B
in PDB entry 1D64 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 622
Actual value (Å2) 364
Normalised complementarity 0.59
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand PNT 25B
in PDB entry 1D64 (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
| V |
0.59 |
0.56
|
0.59 |
0.59
|
0.59 |
0.59
|
0.59 |
0.56
|
| 2 | C2
| V |
0.59 |
0.52
|
0.59 |
0.52
|
0.59 |
0.59
|
0.59 |
0.52
|
| 3 | C3
| V |
0.59 |
0.50
|
0.59 |
0.50
|
0.59 |
0.59
|
0.59 |
0.50
|
| 4 | C4
| V |
0.59 |
0.57
|
0.59 |
0.57
|
0.59 |
0.59
|
0.59 |
0.57
|
| 5 | C5
| V |
0.59 |
0.53
|
0.59 |
0.58
|
0.59 |
0.59
|
0.59 |
0.53
|
| 6 | C6
| V |
0.59 |
0.51
|
0.59 |
0.59
|
0.59 |
0.59
|
0.59 |
0.51
|
| 7 | C7
| VIII |
0.64 |
0.59
|
0.64 |
0.58
|
0.64 |
0.64
|
0.64 |
0.59
|
| 8 | C8
| IV |
0.59 |
0.51
|
0.59 |
0.59
|
0.59 |
0.59
|
0.59 |
0.51
|
| 9 | C9
| VI |
0.59 |
0.55
|
0.59 |
0.55
|
0.59 |
0.59
|
0.59 |
0.55
|
| 10 | C10
| IV |
0.66 |
0.59
|
0.66 |
0.59
|
0.66 |
0.66
|
0.66 |
0.59
|
| 11 | C1'
| V |
0.59 |
0.56
|
0.59 |
0.57
|
0.59 |
0.59
|
0.59 |
0.56
|
| 12 | C2'
| V |
0.59 |
0.52
|
0.59 |
0.52
|
0.59 |
0.59
|
0.59 |
0.52
|
| 13 | C3'
| V |
0.59 |
0.50
|
0.59 |
0.50
|
0.59 |
0.59
|
0.59 |
0.50
|
| 14 | C4'
| V |
0.59 |
0.57
|
0.59 |
0.57
|
0.59 |
0.59
|
0.59 |
0.57
|
| 15 | C5'
| V |
0.59 |
0.53
|
0.59 |
0.56
|
0.59 |
0.59
|
0.59 |
0.53
|
| 16 | C6'
| V |
0.59 |
0.52
|
0.59 |
0.59
|
0.59 |
0.59
|
0.59 |
0.52
|
| 17 | C7'
| VIII |
0.65 |
0.59
|
0.65 |
0.58
|
0.65 |
0.65
|
0.65 |
0.59
|
| 18 | C8'
| IV |
0.59 |
0.51
|
0.59 |
0.59
|
0.59 |
0.59
|
0.59 |
0.51
|
| 19 | C9'
| VI |
0.59 |
0.55
|
0.59 |
0.55
|
0.59 |
0.59
|
0.59 |
0.55
|
| 20 | O1
| II |
0.60 |
0.59
|
0.60 |
0.60
|
0.60 |
0.60
|
0.60 |
0.59
|
| 21 | O1'
| II |
0.60 |
0.59
|
0.60 |
0.60
|
0.60 |
0.60
|
0.60 |
0.59
|
| 22 | N1
| I |
0.59 |
0.45
|
0.58 |
0.45
|
0.59 |
0.59
|
0.58 |
0.45
|
| 23 | N2
| I |
0.59 |
0.50
|
0.59 |
0.56
|
0.59 |
0.59
|
0.59 |
0.50
|
| 24 | N1'
| I |
0.59 |
0.45
|
0.58 |
0.44
|
0.59 |
0.59
|
0.58 |
0.45
|
| 25 | N2'
| I |
0.59 |
0.48
|
0.59 |
0.57
|
0.59 |
0.59
|
0.59 |
0.48
|
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 PNT 25
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5 6 C6
11 C1' 12 C2' 13 C3' 14 C4' 15 C5' 16 C6'
3. Nitrogen ("hydrophilic")
22 N1 23 N2 24 N1' 25 N2'
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il