Contacts of ligand PTI1547A in PDB entry 1UOM
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 PTI1547A
in PDB entry 1UOM (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
----------------------------------------------------------
343A MET* 3.6 35.9 - - + -
346A LEU* 3.7 53.4 - - + -
347A THR* 3.5 40.2 - - - -
349A LEU* 4.0 12.3 - - + -
350A ALA* 3.6 25.8 - - + -
351A ASP* 2.9 36.5 + - + +
353A GLU* 2.7 41.2 + - - -
354A LEU* 4.0 20.4 - - + -
383A TRP* 3.6 56.5 - + + -
384A LEU* 3.7 20.9 - - + -
387A LEU* 3.5 35.0 + - + +
388A MET* 3.7 37.0 - - + -
391A LEU* 3.9 23.6 - - + -
394A ARG* 3.0 17.3 + - - -
404A PHE* 4.4 9.2 - + - -
421A MET* 4.4 20.0 - - + -
424A ILE* 3.6 31.0 - - + -
425A PHE* 5.1 3.6 - + - -
428A LEU* 4.3 13.2 - - + -
521A GLY* 3.4 34.8 - - - -
524A HIS* 3.7 24.2 - + - -
525A LEU* 3.4 41.4 - - + +
536A LEU* 3.8 16.6 - - + -
539A LEU* 3.6 32.5 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand PTI1547A
and protein in PDB entry 1UOM
(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
------------------------------------------------------------------------
4 N1 I ASP 351A OD1 II 2.9 3.8
26 O53 I GLU 353A OE2 II 2.7 13.5
26 O53 I GLU 353A OE1 II 2.8 10.9
26 O53 I ARG 394A NH2 III 3.0 13.5
26 O53 I LEU 387A O II 3.7 5.9
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand PTI1547A
in PDB entry 1UOM (back
to top of page)
Total number of contacts is 124
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 VI ASP 351A OD1 II 3.5 1.3
1 C3 VI TRP 383A CH2 V 3.6 16.4
1 C3 VI TRP 383A CZ3 V 3.9 0.4
1 C3 VI TRP 383A CZ2 V 4.2 2.2
1 C3 VI LEU 536A CD1 IV 5.2 0.4
1 C3 VI ALA 350A CB IV 5.5 0.2
2 C6 IV ASP 351A OD1 II 3.5 6.7*
2 C6 IV LEU 354A CD2 IV 4.0 14.8
2 C6 IV TRP 383A CZ3 V 4.2 10.5
2 C6 IV TRP 383A CH2 V 4.2 0.4
2 C6 IV ASP 351A CG VI 4.3 0.7
2 C6 IV LEU 536A CD1 IV 4.4 2.9
2 C6 IV TRP 383A CE3 V 4.6 0.2
2 C6 IV ASP 351A CA VII 4.7 2.7
2 C6 IV LEU 354A CG IV 5.0 0.2
2 C6 IV LEU 354A CB IV 5.1 0.9
2 C6 IV ASP 351A N III 5.1 0.4*
2 C6 IV ALA 350A C VI 5.4 0.2
3 C9 IV LEU 539A CD2 IV 3.6 21.5
3 C9 IV LEU 536A CD1 IV 3.8 13.2
3 C9 IV LEU 354A CD2 IV 4.0 4.5
4 N1 I ASP 351A OD1 II 2.9 3.8
5 C12 IV ASP 351A OD1 II 3.6 6.3*
5 C12 IV ASP 351A CG VI 3.8 6.3
5 C12 IV ASP 351A OD2 II 3.8 0.9*
5 C12 IV LEU 539A CD2 IV 4.0 11.0
5 C12 IV ASP 351A CB IV 4.7 0.2
6 C15 VI ASP 351A OD1 II 3.6 2.0
6 C15 VI ASP 351A OD2 II 3.9 3.8
6 C15 VI THR 347A CG2 IV 5.3 0.4
7 C18 VI THR 347A CG2 IV 4.2 3.4
7 C18 VI LEU 525A CD2 IV 4.4 5.8
7 C18 VI LEU 525A CG IV 4.6 1.8
8 C21 VIII THR 347A CG2 IV 3.5 18.4
8 C21 VIII ASP 351A OD1 II 3.9 1.3*
8 C21 VIII THR 347A OG1 I 4.0 1.8
8 C21 VIII LEU 525A CD2 IV 4.1 4.0
8 C21 VIII LEU 525A CD1 IV 4.1 4.0
8 C21 VIII LEU 525A CG IV 4.2 0.2
9 O24 II LEU 525A CD2 IV 3.4 1.7*
10 C25 V LEU 525A CD2 IV 3.7 4.7
10 C25 V ALA 350A CB IV 3.8 4.7
11 C26 V THR 347A CA VII 3.5 16.2
11 C26 V MET 343A CE IV 3.6 10.8
11 C26 V LEU 525A CD1 IV 3.8 0.4
11 C26 V LEU 346A O II 4.0 0.2
12 C28 V MET 343A CE IV 3.6 17.0
12 C28 V LEU 346A CB IV 3.7 12.6
12 C28 V LEU 346A C VI 3.7 3.1
12 C28 V LEU 346A O II 3.7 0.2
14 C31 V LEU 384A CD1 IV 3.7 10.5
14 C31 V ALA 350A CB IV 3.8 1.8
14 C31 V LEU 387A CD1 IV 4.3 1.3
15 C33 V TRP 383A CH2 V 3.6 22.4
15 C33 V TRP 383A CZ3 V 3.6 3.8
15 C33 V ALA 350A CB IV 3.6 4.5
15 C33 V LEU 525A CD2 IV 3.7 4.9
15 C33 V LEU 384A CD1 IV 4.1 0.2
16 C35 V LEU 346A CG IV 4.2 7.0
18 C38 V MET 388A CE IV 4.2 11.4
18 C38 V LEU 428A CD1 IV 4.3 13.0
18 C38 V LEU 391A CD2 IV 4.4 2.7
18 C38 V PHE 404A CE1 V 4.5 2.9
18 C38 V PHE 404A CZ V 5.3 0.2
19 C41 V MET 388A CG IV 3.7 23.6
19 C41 V LEU 391A CD2 IV 3.9 9.0
19 C41 V LEU 384A CD1 IV 4.5 2.0
19 C41 V LEU 428A CD1 IV 4.9 0.2
20 C44 V LEU 391A CD2 IV 4.1 2.7
20 C44 V LEU 387A CB IV 4.4 0.7
21 C45 V PHE 404A CE1 V 4.4 2.2
22 C46 V ALA 350A CB IV 3.6 6.7
22 C46 V LEU 346A O II 3.7 9.0
22 C46 V LEU 346A C VI 4.4 1.6
22 C46 V LEU 346A CB IV 4.5 2.7
22 C46 V LEU 346A CG IV 4.5 2.0
22 C46 V PHE 404A CD1 V 4.6 1.3
22 C46 V LEU 346A CA VII 4.6 0.4
23 C48 V GLU 353A OE2 II 3.0 15.5
23 C48 V ALA 350A CB IV 3.8 7.6
23 C48 V LEU 349A CD2 IV 4.0 12.3
23 C48 V PHE 404A CD1 V 4.7 0.9
24 C50 V GLU 353A OE2 II 3.2 0.4
24 C50 V GLU 353A CD VI 4.0 0.4
24 C50 V LEU 387A CB IV 4.0 4.9
24 C50 V ARG 394A NH2 III 4.0 3.8
24 C50 V LEU 391A CB IV 4.8 0.2
24 C50 V PHE 404A CD1 V 4.8 1.6
25 C51 V LEU 387A O II 3.5 16.2
25 C51 V LEU 387A CB IV 3.7 4.9
25 C51 V LEU 391A CD2 IV 4.0 9.0
26 O53 I GLU 353A OE2 II 2.7 13.5
26 O53 I GLU 353A OE1 II 2.8 10.9
26 O53 I ARG 394A NH2 III 3.0 13.5
26 O53 I GLU 353A CD VI 3.1 0.3
26 O53 I LEU 387A O II 3.7 5.9
26 O53 I LEU 387A CD2 IV 4.1 1.0*
27 C55 V ILE 424A CG2 IV 4.9 0.4
28 C56 V LEU 346A CD2 IV 4.2 14.6
28 C56 V ILE 424A CG2 IV 4.6 4.5
28 C56 V MET 343A CE IV 4.6 0.2
28 C56 V MET 421A CG IV 5.0 2.0
28 C56 V PHE 425A CE2 V 5.1 3.6
29 C58 V ILE 424A CD1 IV 4.0 8.7
29 C58 V HIS 524A ND1 I 4.3 4.3
29 C58 V MET 421A CG IV 4.4 16.6
29 C58 V MET 343A CE IV 4.4 7.6
29 C58 V MET 421A CE IV 4.4 1.3
29 C58 V ILE 424A CG2 IV 4.5 0.7
30 C60 V ILE 424A CD1 IV 3.6 16.4
30 C60 V HIS 524A ND1 I 3.7 19.5
30 C60 V HIS 524A CG V 3.9 0.4
30 C60 V LEU 525A CD1 IV 4.3 3.1
30 C60 V MET 343A CE IV 4.6 0.2
31 C62 V GLY 521A O II 3.4 22.9
31 C62 V GLY 521A CA VI 3.7 6.3
31 C62 V LEU 525A CD1 IV 3.8 9.6
31 C62 V ILE 424A CD1 IV 4.2 0.2
31 C62 V LEU 525A CB IV 4.5 0.2
32 C64 V LEU 525A CD1 IV 4.3 0.7
32 C64 V GLY 521A CA VI 4.4 5.6
32 C64 V LEU 384A CD1 IV 4.4 7.6
32 C64 V LEU 384A CD2 IV 4.7 0.4
32 C64 V MET 388A CE IV 4.8 2.0
------------------------------------------------------------------------
Table V
Complementarity values for the ligand PTI1547A
in PDB entry 1UOM (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 712
Actual value (Å2) 645
Normalised complementarity 0.91
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand PTI1547A
in PDB entry 1UOM (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
| VI |
0.90 |
0.90
|
0.90 |
0.90
|
0.91 |
0.91
|
0.91 |
0.90
|
| 2 | C6
| IV |
0.87 |
0.85
|
0.86 |
0.91
|
0.93 |
0.93
|
0.92 |
0.91
|
| 3 | C9
| IV |
0.80 |
0.80
|
0.80 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 4 | N1
| I |
0.91 |
0.89
|
0.91 |
0.89
|
0.91 |
0.91
|
0.91 |
0.89
|
| 5 | C12
| IV |
0.89 |
0.87
|
0.89 |
0.91
|
0.93 |
0.93
|
0.93 |
0.91
|
| 6 | C15
| VI |
0.90 |
0.89
|
0.90 |
0.89
|
0.91 |
0.91
|
0.91 |
0.89
|
| 7 | C18
| VI |
0.87 |
0.87
|
0.87 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 8 | C21
| VIII |
0.83 |
0.83
|
0.83 |
0.90
|
0.91 |
0.91
|
0.91 |
0.91
|
| 9 | O24
| II |
0.91 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 10 | C25
| V |
0.88 |
0.88
|
0.88 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 11 | C26
| V |
0.87 |
0.87
|
0.83 |
0.90
|
0.91 |
0.91
|
0.86 |
0.90
|
| 12 | C28
| V |
0.82 |
0.82
|
0.82 |
0.90
|
0.91 |
0.91
|
0.91 |
0.90
|
| 14 | C31
| V |
0.87 |
0.87
|
0.87 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 15 | C33
| V |
0.88 |
0.88
|
0.88 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 16 | C35
| V |
0.89 |
0.89
|
0.89 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 18 | C38
| V |
0.83 |
0.83
|
0.83 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 19 | C41
| V |
0.81 |
0.81
|
0.81 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 20 | C44
| V |
0.90 |
0.90
|
0.90 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 21 | C45
| V |
0.91 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 22 | C46
| V |
0.87 |
0.85
|
0.87 |
0.88
|
0.91 |
0.91
|
0.90 |
0.88
|
| 23 | C48
| V |
0.85 |
0.81
|
0.85 |
0.86
|
0.91 |
0.91
|
0.91 |
0.86
|
| 24 | C50
| V |
0.89 |
0.89
|
0.88 |
0.89
|
0.91 |
0.91
|
0.89 |
0.90
|
| 25 | C51
| V |
0.87 |
0.82
|
0.87 |
0.86
|
0.91 |
0.91
|
0.91 |
0.86
|
| 26 | O53
| I |
0.91 |
0.82
|
0.87 |
0.79
|
0.91 |
0.91
|
0.87 |
0.82
|
| 27 | C55
| V |
0.90 |
0.90
|
0.90 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 28 | C56
| V |
0.85 |
0.85
|
0.85 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
| 29 | C58
| V |
0.81 |
0.81
|
0.81 |
0.89
|
0.91 |
0.91
|
0.91 |
0.91
|
| 30 | C60
| V |
0.85 |
0.85
|
0.85 |
0.85
|
0.91 |
0.91
|
0.91 |
0.91
|
| 31 | C62
| V |
0.88 |
0.81
|
0.88 |
0.84
|
0.91 |
0.91
|
0.91 |
0.84
|
| 32 | C64
| V |
0.88 |
0.88
|
0.88 |
0.91
|
0.91 |
0.91
|
0.91 |
0.91
|
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 PTI 1547
1. Carbon (in rings)
1 C3 2 C6 3 C9 5 C12 6 C15 10 C25
11 C26 12 C28 13 C30 14 C31 15 C33 16 C35
18 C38 19 C41 20 C44 21 C45 20 C44 21 C45
22 C46 23 C48 24 C50 25 C51 27 C55 28 C56
29 C58 30 C60 31 C62 32 C64
2. Oxygen ("hydroxy" or "carbonyl")
26 O53
3. Nitrogen ("hydrophilic")
4 N1 17 N37
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il