Contacts of ligand MTA4001A in PDB entry 2IPX
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.
(In PDB entry 2IPX some ATOMs are from nucleic
acids or have "unusual" 3-letter residue code. The
analysis does not take into account these atoms.)
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 MTA4001A
in PDB entry 2IPX (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
----------------------------------------------------------
166A TYR* 5.8 1.3 - - - +
168A GLY* 3.4 30.8 - - - +
170A ALA* 3.5 31.9 - - + +
191A VAL* 4.2 6.6 + - + -
192A GLU* 2.6 52.8 + - - +
193A PHE* 3.3 68.5 + + + -
194A SER* 4.1 6.1 - - - -
197A SER* 4.5 4.2 + - - -
216A GLU 3.5 9.9 - - - -
217A ASP* 2.6 27.4 + - - -
218A ALA* 2.9 34.8 + - + +
219A ARG* 3.4 25.7 + - - +
237A ASP* 3.3 36.3 - - - +
238A VAL* 3.4 43.0 - - + +
239A ALA* 4.6 9.2 - - + -
240A GLN* 3.5 26.4 + - - +
246A ILE* 4.5 3.0 - - + +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand MTA4001A
and protein in PDB entry 2IPX
(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
------------------------------------------------------------------------
7 O2' I GLU 192A OE2 II 2.6 17.7
9 O3' I GLU 192A OE1 II 2.6 15.2
9 O3' I SER 197A OG I 4.5 4.2
13 N7 I GLN 240A NE2 III 3.7 1.0
16 N6 I ASP 217A OD1 II 2.6 23.4
16 N6 I ARG 219A NH1 III 3.4 17.8
16 N6 I ALA 218A N III 3.7 1.4
16 N6 I ARG 219A N III 4.2 0.6
17 N1 I ALA 218A N III 2.9 17.2
17 N1 I ASP 217A OD1 II 3.6 0.6
19 N3 I PHE 193A N III 3.3 8.3
19 N3 I VAL 191A O II 4.3 2.6
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand MTA4001A
in PDB entry 2IPX (back
to top of page)
Total number of contacts is 81
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 CS IV GLY 168A O II 3.7 15.5*
1 CS IV ALA 170A CB IV 3.8 16.8
1 CS IV ASP 237A OD2 II 3.8 19.3*
1 CS IV TYR 166A OH I 5.8 1.3*
2 S5' VI ASP 237A O II 4.0 0.9
2 S5' VI ALA 170A CB IV 4.5 1.3
2 S5' VI ASP 237A OD2 II 4.7 0.9
2 S5' VI ASP 237A CG VI 5.1 0.7
2 S5' VI ASP 237A OD1 II 5.3 0.4
2 S5' VI ALA 239A CB IV 5.4 1.8
3 C5' IV ASP 237A O II 3.3 12.6*
3 C5' IV VAL 238A O II 4.0 9.0*
3 C5' IV VAL 238A C VI 4.1 1.6
3 C5' IV ALA 239A CB IV 4.6 7.4
4 C4' VIII GLU 192A OE1 II 3.7 3.4*
4 C4' VIII ASP 237A O II 3.9 1.6*
4 C4' VIII GLY 168A CA VI 3.9 3.8
5 O4' II GLY 168A CA VI 3.4 8.0
5 O4' II VAL 238A CA VII 3.6 3.3
6 C2' VI PHE 193A CE2 V 4.0 0.9
7 O2' I GLU 192A OE2 II 2.6 17.7
7 O2' I PHE 193A CE2 V 3.3 12.3
7 O2' I SER 194A CB VI 4.1 5.9
9 O3' I GLU 192A OE1 II 2.6 15.2
9 O3' I GLU 192A CD VI 3.2 3.1
9 O3' I ALA 170A CA VII 3.5 11.1
9 O3' I ALA 170A CB IV 3.6 2.6*
9 O3' I SER 197A OG I 4.5 4.2
9 O3' I SER 194A CB VI 5.2 0.2
10 C1' VI GLU 192A OE1 II 3.3 5.4
10 C1' VI GLY 168A CA VI 4.0 0.9
12 C8 V VAL 238A O II 3.4 17.3
12 C8 V PHE 193A CE2 V 3.5 6.5
12 C8 V GLN 240A NE2 III 3.7 9.4
12 C8 V VAL 238A CB IV 4.1 0.9
13 N7 I PHE 193A CZ V 3.5 6.9
13 N7 I GLN 240A CG IV 3.5 15.2*
13 N7 I GLN 240A NE2 III 3.7 1.0
13 N7 I GLN 240A CD VI 3.8 0.8
13 N7 I PHE 193A CE1 V 4.1 0.2
14 C5 V PHE 193A CE2 V 3.5 4.0
14 C5 V VAL 238A CB IV 4.4 4.5
15 C6 V ASP 217A OD1 II 3.5 0.4
15 C6 V ALA 218A N III 3.7 0.2
15 C6 V PHE 193A CD1 V 3.8 4.7
15 C6 V ALA 218A CB IV 4.1 3.4
15 C6 V VAL 238A CG1 IV 5.0 0.7
15 C6 V VAL 238A CB IV 5.2 0.4
15 C6 V ILE 246A CD1 IV 5.2 0.2
16 N6 I ASP 217A OD1 II 2.6 23.4
16 N6 I ARG 219A NH1 III 3.4 17.8
16 N6 I ASP 217A CG VI 3.6 0.6
16 N6 I ALA 218A N III 3.7 1.4
16 N6 I PHE 193A CD1 V 4.0 2.0
16 N6 I ARG 219A CG IV 4.0 6.1*
16 N6 I ARG 219A CZ VI 4.1 1.2
16 N6 I ARG 219A N III 4.2 0.6
16 N6 I ALA 218A CB IV 4.3 0.8*
16 N6 I ILE 246A CD1 IV 4.5 2.8*
17 N1 I ALA 218A N III 2.9 17.2
17 N1 I ALA 218A CB IV 3.4 0.8*
17 N1 I ASP 217A OD1 II 3.6 0.6
17 N1 I ASP 217A CA VII 3.6 2.4
17 N1 I PHE 193A CG V 3.7 0.2
18 C2 V PHE 193A N III 3.3 17.7
18 C2 V GLU 216A O II 3.5 9.9
18 C2 V PHE 193A CB IV 3.6 0.4
18 C2 V ALA 218A N III 3.7 2.7
18 C2 V ALA 218A CB IV 3.9 8.3
18 C2 V GLU 192A C VI 4.0 1.8
18 C2 V GLU 192A CA VII 4.1 2.7
18 C2 V VAL 191A CG1 IV 4.2 3.4
18 C2 V VAL 191A O II 4.5 0.7
18 C2 V VAL 238A CG1 IV 4.9 1.1
18 C2 V GLY 168A N III 5.0 0.2
19 N3 I PHE 193A N III 3.3 8.3
19 N3 I GLU 192A CA VII 3.9 3.6
19 N3 I VAL 191A O II 4.3 2.6
19 N3 I GLY 168A CA VI 4.4 2.4
20 C4 V PHE 193A CD2 V 3.3 4.3
20 C4 V VAL 238A CG1 IV 4.2 4.3
------------------------------------------------------------------------
Table V
Complementarity values for the ligand MTA4001A
in PDB entry 2IPX (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 492
Actual value (Å2) 236
Normalised complementarity 0.48
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand MTA4001A
in PDB entry 2IPX (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 | CS
| IV |
0.56 |
0.42
|
0.56 |
0.48
|
0.63 |
0.63
|
0.63 |
0.48
|
| 2 | S5'
| VI |
0.47 |
0.46
|
0.47 |
0.47
|
0.48 |
0.48
|
0.48 |
0.47
|
| 3 | C5'
| IV |
0.54 |
0.45
|
0.54 |
0.48
|
0.57 |
0.57
|
0.57 |
0.48
|
| 4 | C4'
| VIII |
0.50 |
0.48
|
0.50 |
0.48
|
0.50 |
0.50
|
0.50 |
0.48
|
| 5 | O4'
| II |
0.48 |
0.48
|
0.47 |
0.48
|
0.48 |
0.48
|
0.47 |
0.48
|
| 6 | C2'
| VI |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 7 | O2'
| I |
0.48 |
0.41
|
0.48 |
0.41
|
0.48 |
0.48
|
0.48 |
0.41
|
| 9 | O3'
| I |
0.48 |
0.42
|
0.43 |
0.41
|
0.49 |
0.49
|
0.44 |
0.43
|
| 10 | C1'
| VI |
0.48 |
0.46
|
0.48 |
0.46
|
0.48 |
0.48
|
0.48 |
0.46
|
| 12 | C8
| V |
0.48 |
0.41
|
0.44 |
0.37
|
0.48 |
0.48
|
0.44 |
0.41
|
| 13 | N7
| I |
0.48 |
0.48
|
0.47 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 14 | C5
| V |
0.46 |
0.46
|
0.46 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 15 | C6
| V |
0.46 |
0.46
|
0.46 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 16 | N6
| I |
0.48 |
0.38
|
0.40 |
0.34
|
0.52 |
0.52
|
0.44 |
0.42
|
| 17 | N1
| I |
0.48 |
0.48
|
0.40 |
0.41
|
0.48 |
0.48
|
0.40 |
0.48
|
| 18 | C2
| V |
0.43 |
0.38
|
0.33 |
0.35
|
0.48 |
0.48
|
0.38 |
0.44
|
| 19 | N3
| I |
0.48 |
0.47
|
0.43 |
0.43
|
0.48 |
0.48
|
0.43 |
0.47
|
| 20 | C4
| V |
0.46 |
0.46
|
0.46 |
0.48
|
0.48 |
0.48
|
0.48 |
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 MTA 4001
1. Carbon (in rings)
4 C4' 10 C1' 6 C2' 8 C3' 12 C8 14 C5
20 C4 14 C5 15 C6 18 C2 20 C4
2. Oxygen ("hydroxy" or "carbonyl")
7 O2' 9 O3'
3. Nitrogen ("hydrophilic")
11 N9 13 N7 16 N6 17 N1 19 N3
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il