Contacts of ligand PLM 402A in PDB entry 1M66
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 PLM 402A
in PDB entry 1M66 (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
----------------------------------------------------------
216A GLY* 4.0 21.1 - - - +
219A VAL* 4.1 20.4 - - + -
220A ALA* 4.1 11.0 - - + +
223A LEU* 4.7 4.3 - - + -
225A MET* 3.9 24.9 - - + -
229A ALA* 3.6 27.8 - - + +
232A ALA* 4.1 21.5 - - + +
233A LEU* 3.7 34.3 - - + +
236A ARG* 3.6 45.7 + - + +
320A PRO* 3.8 32.5 - - + +
321A LEU* 4.5 20.6 - - + -
324A GLN* 4.0 12.3 - - + -
325A ILE* 3.3 39.7 - - + +
328A ILE* 3.0 35.7 - - + -
335A PRO 5.2 0.9 - - - +
338A ALA* 4.7 6.3 - - + -
339A LEU* 4.1 34.1 - - + +
342A LEU* 3.3 59.0 + - + +
343A LEU* 4.4 23.3 - - + -
345A CYS* 3.8 26.2 - - - +
348A GLN* 3.8 13.7 + - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand PLM 402A
and protein in PDB entry 1M66
(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
------------------------------------------------------------------------
2 O1 I LEU 342A O II 3.6 7.1
3 O2 I GLN 348A OE1 II 3.8 11.4
3 O2 I ARG 236A NH2 III 4.3 10.6
3 O2 I ARG 236A NE III 4.7 0.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand PLM 402A
in PDB entry 1M66 (back
to top of page)
Total number of contacts is 100
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 VI CYS 345A SG VI 3.9 8.3
1 C1 VI PRO 320A CB IV 4.2 8.7
1 C1 VI GLN 348A OE1 II 4.4 1.8
2 O1 I LEU 342A O II 3.6 7.1
2 O1 I CYS 345A SG VI 3.8 5.5
2 O1 I PRO 320A CB IV 3.8 12.6*
2 O1 I PRO 320A CG IV 4.0 1.9*
2 O1 I LEU 342A CD2 IV 4.2 1.9*
2 O1 I CYS 345A CB IV 4.2 3.8*
2 O1 I LEU 342A CA VII 4.9 0.2
3 O2 I GLN 348A OE1 II 3.8 11.4
3 O2 I PRO 320A CG IV 4.2 8.3*
3 O2 I ARG 236A NH2 III 4.3 10.6
3 O2 I ARG 236A NE III 4.7 0.2
4 C2 IV LEU 342A O II 3.3 16.8*
4 C2 IV CYS 345A SG VI 3.8 8.5
4 C2 IV LEU 342A C VI 4.2 0.4
4 C2 IV LEU 342A CD2 IV 4.3 1.3
4 C2 IV GLN 348A OE1 II 5.1 0.4*
4 C2 IV LEU 343A CD2 IV 5.2 1.8
5 C3 IV ARG 236A NE III 4.5 10.5*
5 C3 IV ARG 236A CG IV 4.6 0.4
5 C3 IV LEU 342A CD2 IV 4.7 2.0
5 C3 IV ARG 236A CB IV 4.8 1.6
5 C3 IV ARG 236A CD VII 5.0 0.2
5 C3 IV PRO 320A CB IV 5.4 0.9
5 C3 IV LEU 321A CG IV 5.5 1.8
6 C4 IV LEU 342A CD1 IV 4.2 15.9
6 C4 IV LEU 343A CD2 IV 4.4 10.3
6 C4 IV LEU 342A CD2 IV 4.5 0.2
6 C4 IV LEU 321A CD2 IV 5.1 0.2
7 C5 IV ARG 236A CG IV 3.6 17.3
7 C5 IV ARG 236A CB IV 4.0 2.7
7 C5 IV ARG 236A CD VII 4.7 0.2
7 C5 IV LEU 321A CD1 IV 4.8 4.5
7 C5 IV LEU 321A CD2 IV 4.8 0.2
8 C6 IV ARG 236A CG IV 4.4 2.0
8 C6 IV LEU 343A CD2 IV 4.5 11.0
8 C6 IV ALA 232A CB IV 4.8 3.6
9 C7 IV ALA 232A CB IV 4.1 14.8
9 C7 IV LEU 233A N III 4.2 4.9*
9 C7 IV ALA 232A C VI 4.2 1.8
9 C7 IV ALA 232A O II 4.3 0.4*
9 C7 IV LEU 233A CA VII 4.3 2.2
9 C7 IV LEU 321A CD2 IV 4.6 2.2
10 C8 IV LEU 321A CD2 IV 4.5 4.7
10 C8 IV LEU 342A CD1 IV 4.9 2.9
10 C8 IV LEU 339A CD2 IV 4.9 3.8
10 C8 IV LEU 343A CD2 IV 5.6 0.2
10 C8 IV MET 225A CE IV 6.0 0.2
11 C9 IV ALA 229A O II 3.6 17.7*
11 C9 IV LEU 233A CB IV 3.7 10.5
11 C9 IV LEU 233A CD1 IV 4.4 0.2
11 C9 IV ALA 229A C VI 4.4 0.2
11 C9 IV ALA 232A CB IV 4.6 0.9
11 C9 IV ALA 229A CB IV 4.7 0.7
11 C9 IV ALA 229A CA VII 4.8 0.2
12 CA IV MET 225A SD VIII 3.9 18.2
12 CA IV ALA 229A O II 4.0 6.5*
12 CA IV ALA 220A CB IV 4.1 6.5
12 CA IV ALA 229A CB IV 4.3 2.5
12 CA IV LEU 233A CB IV 4.5 0.9
12 CA IV MET 225A CE IV 4.6 0.4
13 CB IV LEU 339A CD2 IV 4.1 14.8
13 CB IV MET 225A SD VIII 4.1 6.1
13 CB IV LEU 321A CD2 IV 5.0 0.4
13 CB IV LEU 342A CD1 IV 5.1 0.2
14 CC IV LEU 233A CD1 IV 3.9 13.5
14 CC IV GLY 216A O II 4.1 5.2*
14 CC IV ALA 220A CB IV 4.1 3.1
14 CC IV LEU 321A CD2 IV 4.6 2.0
15 CD IV VAL 219A CG1 IV 4.3 9.9
15 CD IV LEU 339A CG IV 4.5 11.2
15 CD IV LEU 339A CD2 IV 4.7 0.9
15 CD IV ALA 220A N III 4.7 1.3*
15 CD IV LEU 223A CD2 IV 4.7 4.3
15 CD IV LEU 342A CD1 IV 5.0 1.1
16 CE IV GLY 216A O II 4.0 11.9*
16 CE IV VAL 219A CG1 IV 4.1 4.7
16 CE IV GLY 216A CA VI 4.2 4.0
16 CE IV ILE 325A CG1 IV 4.7 1.1
16 CE IV LEU 233A CD1 IV 4.7 2.0
16 CE IV LEU 321A CD2 IV 4.7 3.6
17 CF IV ILE 328A CD1 IV 3.8 6.5
17 CF IV VAL 219A CG1 IV 4.4 1.1
17 CF IV ILE 325A CG1 IV 4.5 0.2
17 CF IV GLN 324A CB IV 4.6 9.0
17 CF IV ALA 338A CB IV 4.7 6.3
17 CF IV LEU 342A CD1 IV 4.7 8.7
17 CF IV LEU 321A CD2 IV 5.0 0.9
17 CF IV LEU 339A N III 5.1 3.4*
17 CF IV PRO 335A O II 5.2 0.9*
18 CG IV ILE 328A CD1 IV 3.0 29.2
18 CG IV ILE 325A CG1 IV 3.3 30.5
18 CG IV ILE 325A CA VII 3.8 4.5
18 CG IV ILE 325A N III 3.8 3.4*
18 CG IV GLN 324A C VI 4.0 2.5
18 CG IV GLN 324A CB IV 4.3 0.9
18 CG IV VAL 219A CG1 IV 4.5 2.2
18 CG IV VAL 219A CG2 IV 4.6 2.5
------------------------------------------------------------------------
Table V
Complementarity values for the ligand PLM 402A
in PDB entry 1M66 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 572
Actual value (Å2) 291
Normalised complementarity 0.51
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand PLM 402A
in PDB entry 1M66 (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
| VI |
0.48 |
0.47
|
0.48 |
0.50
|
0.51 |
0.51
|
0.51 |
0.50
|
| 2 | O1
| I |
0.51 |
0.48
|
0.51 |
0.56
|
0.58 |
0.58
|
0.58 |
0.56
|
| 3 | O2
| I |
0.51 |
0.47
|
0.47 |
0.46
|
0.54 |
0.54
|
0.50 |
0.50
|
| 4 | C2
| IV |
0.56 |
0.50
|
0.56 |
0.51
|
0.57 |
0.57
|
0.57 |
0.51
|
| 5 | C3
| IV |
0.52 |
0.52
|
0.48 |
0.51
|
0.55 |
0.55
|
0.51 |
0.55
|
| 6 | C4
| IV |
0.42 |
0.42
|
0.42 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 7 | C5
| IV |
0.42 |
0.42
|
0.42 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 8 | C6
| IV |
0.45 |
0.45
|
0.45 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 9 | C7
| IV |
0.47 |
0.47
|
0.44 |
0.51
|
0.53 |
0.53
|
0.50 |
0.53
|
| 10 | C8
| IV |
0.47 |
0.47
|
0.47 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 11 | C9
| IV |
0.53 |
0.47
|
0.53 |
0.51
|
0.57 |
0.57
|
0.57 |
0.51
|
| 12 | CA
| IV |
0.50 |
0.41
|
0.50 |
0.51
|
0.53 |
0.53
|
0.53 |
0.45
|
| 13 | CB
| IV |
0.45 |
0.43
|
0.45 |
0.51
|
0.51 |
0.51
|
0.51 |
0.49
|
| 14 | CC
| IV |
0.46 |
0.44
|
0.46 |
0.51
|
0.53 |
0.53
|
0.53 |
0.51
|
| 15 | CD
| IV |
0.42 |
0.42
|
0.41 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 16 | CE
| IV |
0.51 |
0.47
|
0.51 |
0.51
|
0.55 |
0.55
|
0.55 |
0.51
|
| 17 | CF
| IV |
0.41 |
0.41
|
0.40 |
0.51
|
0.52 |
0.52
|
0.51 |
0.52
|
| 18 | CG
| IV |
0.29 |
0.29
|
0.27 |
0.51
|
0.52 |
0.52
|
0.49 |
0.52
|
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 BCP 401
1. Carbon (in rings)
2 C6 4 C2 7 C4 6 C5 6 C5 7 C4
10 C8
3. Nitrogen ("hydrophilic")
3 N1 8 N3 9 N7 11 N9
Ligand PLM 402
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il