Contacts of ligand M3L 36C in PDB entry 5CIU
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 M3L 36C
in PDB entry 5CIU (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
----------------------------------------------------------
231B GLY 5.8 0.2 - - - -
233B ILE* 3.8 24.8 - - + +
236B PHE* 3.8 41.1 - - - -
237B SER 5.2 0.4 - - - -
239B TRP* 3.5 74.7 - - - -
263B TRP* 3.3 54.3 - - + +
266B ASP* 3.8 24.9 - - - +
268B LYS* 3.7 11.1 - - + +
269B PHE 2.9 9.9 + - - -
270B SER* 3.4 18.1 + - - +
35C VAL* 1.3 78.9 - - - +
37C LYS* 1.3 65.0 + - - +
38C PRO* 4.3 2.6 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand M3L 36C
and protein in PDB entry 5CIU
(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
------------------------------------------------------------------------
1 N I PHE 269B O II 2.9 9.9
9 O II LYS 37C N III 2.2 0.5
9 O II SER 270B OG I 3.9 4.9
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand M3L 36C
in PDB entry 5CIU (back
to top of page)
Total number of contacts is 74
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 N I VAL 35C C VI 1.3 57.0
1 N I VAL 35C CA VII 2.4 4.6
1 N I PHE 269B O II 2.9 9.9
1 N I LYS 268B CD IV 3.7 1.8*
1 N I LYS 268B CB IV 3.8 0.8*
2 CA VI LYS 37C N III 2.4 3.6
2 CA VI VAL 35C C VI 2.4 4.0
2 CA VI VAL 35C O II 2.8 1.1
2 CA VI LYS 268B CD IV 3.7 5.4
3 CB IV SER 270B OG I 3.4 13.2*
3 CB IV TRP 263B NE1 III 3.5 4.9*
3 CB IV TRP 263B CD1 V 3.6 4.0
3 CB IV LYS 268B CB IV 4.0 2.0
3 CB IV ILE 233B CD1 IV 4.4 0.2
4 CG IV LYS 37C N III 3.4 2.7*
4 CG IV ASP 266B OD2 II 4.0 10.5*
4 CG IV LYS 37C O II 4.2 2.5*
4 CG IV ILE 233B CD1 IV 4.3 0.7
4 CG IV LYS 268B CD IV 4.5 1.1
5 CD IV TRP 263B NE1 III 3.3 10.8*
5 CD IV TRP 263B CD1 V 3.4 0.9
5 CD IV ILE 233B CD1 IV 3.8 6.3
6 CE VI ILE 233B CD1 IV 4.2 4.0
6 CE VI PHE 236B CE2 V 4.2 9.2
6 CE VI PHE 236B CZ V 4.3 1.1
6 CE VI ASP 266B OD2 II 4.3 2.0
6 CE VI LYS 37C O II 4.8 0.4
8 C VIII LYS 37C N III 1.3 44.0
8 C VIII LYS 37C CA VII 2.4 2.5
8 C VIII VAL 35C C VI 3.2 2.9
8 C VIII VAL 35C O II 3.2 0.2*
8 C VIII LYS 37C C VI 3.4 0.4
8 C VIII LYS 37C CB IV 3.5 0.4
8 C VIII LYS 37C CG IV 3.6 0.7
8 C VIII ILE 233B CD1 IV 4.7 0.2
9 O II LYS 37C N III 2.2 0.5
9 O II LYS 37C CA VII 2.8 6.6
9 O II LYS 37C C VI 3.7 0.5
9 O II VAL 35C C VI 3.7 0.5
9 O II VAL 35C CG1 IV 3.9 8.5*
9 O II SER 270B OG I 3.9 4.9
9 O II LYS 37C CG IV 4.0 0.2*
9 O II ILE 233B CD1 IV 4.2 6.4*
9 O II PRO 38C CD IV 4.3 2.6*
10 CM1 VI TRP 239B CG V 3.6 18.8
10 CM1 VI TRP 239B CD2 V 3.7 0.2
10 CM1 VI TRP 239B CD1 V 3.8 4.7
10 CM1 VI PHE 236B CG V 3.8 14.1
10 CM1 VI PHE 236B CB IV 4.0 1.8
10 CM1 VI TRP 239B CB IV 4.1 2.5
10 CM1 VI PHE 236B CD2 V 4.2 0.9
10 CM1 VI TRP 263B CD2 V 4.4 4.7
10 CM1 VI ILE 233B CD1 IV 4.4 4.5
10 CM1 VI ILE 233B CG1 IV 4.5 2.5
10 CM1 VI TRP 263B CE3 V 4.5 0.7
10 CM1 VI TRP 263B CZ3 V 4.6 1.1
10 CM1 VI TRP 263B CH2 V 4.7 0.2
10 CM1 VI SER 237B O II 5.2 0.4
10 CM1 VI GLY 231B O II 5.8 0.2
11 CM2 VI TRP 263B CG V 3.5 20.0
11 CM2 VI TRP 239B CE3 V 3.6 15.3
11 CM2 VI TRP 263B CB IV 3.7 5.8
11 CM2 VI TRP 263B CD2 V 3.7 1.1
11 CM2 VI ASP 266B OD1 II 3.8 9.2
11 CM2 VI ASP 266B OD2 II 4.1 0.2
11 CM2 VI TRP 239B CZ3 V 4.2 0.7
11 CM2 VI ASP 266B CG VI 4.2 0.4
12 CM3 VI TRP 239B CE2 V 3.5 19.7
12 CM3 VI TRP 239B CZ2 V 3.5 7.4
12 CM3 VI TRP 239B CH2 V 3.5 4.7
12 CM3 VI TRP 239B CZ3 V 3.6 0.7
12 CM3 VI PHE 236B CE1 V 3.8 13.9
12 CM3 VI ASP 266B OD2 II 5.0 1.8
12 CM3 VI ASP 266B CG VI 5.4 0.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand M3L 36C
in PDB entry 5CIU (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 397
Actual value (Å2) 275
Normalised complementarity 0.69
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand M3L 36C
in PDB entry 5CIU (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 | N
| I |
0.69 |
0.64
|
0.67 |
0.66
|
0.71 |
0.71
|
0.68 |
0.66
|
| 2 | CA
| VI |
0.67 |
0.66
|
0.65 |
0.67
|
0.69 |
0.69
|
0.68 |
0.69
|
| 3 | CB
| IV |
0.77 |
0.77
|
0.75 |
0.69
|
0.78 |
0.78
|
0.76 |
0.78
|
| 4 | CG
| IV |
0.76 |
0.70
|
0.75 |
0.69
|
0.77 |
0.77
|
0.76 |
0.71
|
| 5 | CD
| IV |
0.72 |
0.72
|
0.66 |
0.69
|
0.75 |
0.75
|
0.69 |
0.75
|
| 6 | CE
| VI |
0.67 |
0.66
|
0.67 |
0.68
|
0.69 |
0.69
|
0.69 |
0.68
|
| 8 | C
| VIII |
0.69 |
0.69
|
0.45 |
0.47
|
0.69 |
0.69
|
0.46 |
0.69
|
| 9 | O
| II |
0.69 |
0.69
|
0.66 |
0.76
|
0.78 |
0.78
|
0.75 |
0.78
|
| 10 | CM1
| VI |
0.64 |
0.63
|
0.64 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 11 | CM2
| VI |
0.66 |
0.62
|
0.66 |
0.65
|
0.69 |
0.69
|
0.69 |
0.65
|
| 12 | CM3
| VI |
0.69 |
0.68
|
0.69 |
0.68
|
0.69 |
0.69
|
0.69 |
0.68
|
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 M3L 36
2. Oxygen ("hydroxy" or "carbonyl")
9 O
3. Nitrogen ("hydrophilic")
1 N 7 NZ
Ligand M3L 36
2. Oxygen ("hydroxy" or "carbonyl")
9 O
3. Nitrogen ("hydrophilic")
1 N 7 NZ
Ligand GOL 401
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il