Contacts of ligand CME 199X in PDB entry 3EHI
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 CME 199X
in PDB entry 3EHI (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
----------------------------------------------------------
91X PHE* 6.0 0.2 - - - -
139X TRP* 3.7 30.4 + - - +
177X ILE 3.8 1.4 - - - +
178X ILE* 3.2 4.5 - - - +
179X MET* 2.8 71.5 + - + +
180X CME 4.0 2.5 - - - -
181X ALA* 3.3 19.7 - - - +
197X ALA* 3.6 33.0 - - - +
198X LEU* 1.3 75.6 - - - -
200X GLN* 1.3 57.8 + - - +
201X PHE* 3.8 21.8 - - + -
210X CYS* 4.2 8.5 - - - -
211X GLN 3.2 7.4 - - - +
212X LEU* 4.2 4.7 - - - -
230X TYR* 2.5 64.5 + - - -
233X LEU* 4.3 3.8 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand CME 199X
and protein in PDB entry 3EHI
(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 MET 179X O II 2.8 6.5
8 OH I TYR 230X OH I 2.5 23.7
8 OH I TRP 139X NE1 III 3.7 4.7
10 O II GLN 200X N III 2.2 0.7
10 O II MET 179X N III 2.9 23.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand CME 199X
in PDB entry 3EHI (back
to top of page)
Total number of contacts is 61
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 LEU 198X C VI 1.3 57.8
1 N I LEU 198X CA VII 2.5 4.4
1 N I MET 179X O II 2.8 6.5
2 CA VI LEU 198X C VI 2.5 7.6
2 CA VI GLN 200X N III 2.5 3.4
2 CA VI LEU 198X O II 2.8 1.6
2 CA VI GLN 211X O II 3.2 6.1
3 CB IV GLN 200X N III 3.4 0.2*
3 CB IV PHE 201X CE2 V 3.8 17.7
3 CB IV MET 179X O II 4.0 0.7*
3 CB IV PHE 201X CZ V 4.2 0.9
3 CB IV GLN 211X O II 4.2 1.3*
3 CB IV CYS 210X SG VI 4.2 2.9
3 CB IV MET 179X N III 4.7 0.4*
4 SG VI TYR 230X CE1 V 3.2 20.4
4 SG VI TYR 230X CD1 V 3.4 6.7
4 SG VI LEU 198X C VI 4.1 0.7
4 SG VI LEU 212X CD1 IV 4.2 4.3
4 SG VI CYS 210X SG VI 4.4 5.6
4 SG VI PHE 201X CE2 V 4.7 1.3
4 SG VI PHE 201X CZ V 4.7 0.9
5 SD VI TYR 230X CE1 V 3.4 8.1
5 SD VI TRP 139X CZ2 V 3.9 11.4
5 SD VI TYR 230X CD1 V 4.1 0.2
5 SD VI MET 179X CE IV 4.1 14.4
5 SD VI LEU 233X CD2 IV 4.3 3.8
6 CE IV MET 179X O II 3.2 20.0*
6 CE IV TRP 139X NE1 III 3.7 13.2*
6 CE IV MET 179X C VI 3.7 6.1
6 CE IV CME 180X C VIII 4.0 2.5
6 CE IV MET 179X CB IV 4.3 0.2
7 CZ VI TYR 230X OH I 3.5 4.7
7 CZ VI ALA 197X O II 3.6 20.2
7 CZ VI ALA 181X CB IV 3.6 6.5
7 CZ VI ALA 197X CB IV 3.8 10.3
7 CZ VI ALA 197X C VI 3.9 1.8
7 CZ VI TYR 230X CE1 V 4.0 0.2
7 CZ VI LEU 198X C VI 4.3 0.2
7 CZ VI LEU 212X CD1 IV 4.4 0.4
8 OH I TYR 230X OH I 2.5 23.7
8 OH I ALA 181X CB IV 3.3 13.2*
8 OH I TYR 230X CZ V 3.3 0.2
8 OH I TYR 230X CE1 V 3.5 0.2
8 OH I TRP 139X NE1 III 3.7 4.7
8 OH I TRP 139X CZ2 V 3.7 1.0
8 OH I ALA 197X CB IV 4.2 0.7*
8 OH I PHE 91X CE1 V 6.0 0.2
9 C VIII GLN 200X N III 1.3 42.8
9 C VIII GLN 200X CA VII 2.5 2.9
9 C VIII LEU 198X C VI 3.4 1.3
9 C VIII GLN 200X C VI 3.4 0.4
9 C VIII GLN 200X CB IV 3.6 0.9
9 C VIII LEU 198X CD1 IV 4.0 2.0
9 C VIII PHE 201X N III 4.2 0.2
10 O II GLN 200X N III 2.2 0.7
10 O II GLN 200X CA VII 2.8 6.4
10 O II MET 179X N III 2.9 23.2
10 O II ILE 178X CA VII 3.2 4.2
10 O II ILE 177X O II 3.8 1.4*
10 O II ILE 178X CG2 IV 3.8 0.3*
10 O II PHE 201X CD2 V 4.3 0.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand CME 199X
in PDB entry 3EHI (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 345
Actual value (Å2) 304
Normalised complementarity 0.88
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand CME 199X
in PDB entry 3EHI (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 |
0.88 |
0.84
|
0.86 |
0.84
|
0.88 |
0.88
|
0.86 |
0.84
|
| 2 | CA
| VI |
0.88 |
0.84
|
0.86 |
0.82
|
0.88 |
0.88
|
0.86 |
0.84
|
| 3 | CB
| IV |
0.90 |
0.89
|
0.89 |
0.88
|
0.90 |
0.90
|
0.89 |
0.89
|
| 4 | SG
| VI |
0.86 |
0.86
|
0.86 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
| 5 | SD
| VI |
0.78 |
0.78
|
0.78 |
0.88
|
0.88 |
0.88
|
0.88 |
0.88
|
| 6 | CE
| IV |
1.07 |
0.94
|
1.00 |
0.88
|
1.07 |
1.07
|
1.00 |
0.94
|
| 7 | CZ
| VI |
0.78 |
0.66
|
0.78 |
0.74
|
0.88 |
0.88
|
0.88 |
0.76
|
| 8 | OH
| I |
0.88 |
0.88
|
0.85 |
0.80
|
0.96 |
0.96
|
0.93 |
0.96
|
| 9 | C
| VIII |
0.86 |
0.86
|
0.60 |
0.63
|
0.88 |
0.88
|
0.62 |
0.88
|
| 10 | O
| II |
0.89 |
0.88
|
0.69 |
0.75
|
0.89 |
0.89
|
0.69 |
0.88
|
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 CME 180
2. Oxygen ("hydroxy" or "carbonyl")
8 OH 10 O
3. Nitrogen ("hydrophilic")
1 N
Ligand CME 199
2. Oxygen ("hydroxy" or "carbonyl")
8 OH 10 O
3. Nitrogen ("hydrophilic")
1 N
Ligand EDO 318
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Please E-mail any questions and/or suggestions
concerning this page to
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