Contacts of ligand CM5 502B in PDB entry 5UAP
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 CM5 502B
in PDB entry 5UAP (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
----------------------------------------------------------
39B LEU* 4.3 42.5 - - + +
40B LEU* 4.0 20.9 - - + -
43B LEU* 4.2 19.3 - - + -
72B PRO* 6.4 2.0 - - - -
216B LEU* 4.1 18.8 - - + -
220B PHE* 4.0 55.0 - - + -
222B GLY 5.7 1.0 - - - -
223B PHE* 3.6 63.4 + - + +
224B LEU* 4.0 20.4 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand CM5 502B
and protein in PDB entry 5UAP
(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
------------------------------------------------------------------------
12 O12 I PHE 223B N III 5.3 1.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand CM5 502B
in PDB entry 5UAP (back
to top of page)
Total number of contacts is 53
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 C7 IV PHE 220B CE2 V 4.1 11.4
1 C7 IV LEU 43B CD2 IV 4.2 8.3
1 C7 IV PHE 220B CZ V 4.4 0.2
1 C7 IV LEU 40B CD2 IV 4.5 4.0
2 C8 IV LEU 43B CD2 IV 4.4 11.0
2 C8 IV PHE 220B CE2 V 4.7 1.6
2 C8 IV LEU 216B CD2 IV 5.1 1.1
2 C8 IV LEU 216B CD1 IV 5.3 1.8
3 C9 IV LEU 216B CD2 IV 4.4 8.5
3 C9 IV LEU 224B CD2 IV 5.0 0.9
3 C9 IV PHE 223B CE2 V 5.4 0.9
4 C10 IV LEU 224B CD2 IV 4.0 19.5
4 C10 IV PHE 220B CD2 V 4.0 11.9
4 C10 IV LEU 216B CD2 IV 4.1 7.4
5 C11 IV PHE 223B CD2 V 3.6 18.8
5 C11 IV PHE 223B CE2 V 3.9 1.3
5 C11 IV PHE 220B CG V 4.1 7.2
5 C11 IV PHE 220B CB IV 4.2 0.2
6 C6 IV PHE 223B CE2 V 4.7 1.1
6 C6 IV PHE 223B CZ V 5.3 0.2
7 C5 IV LEU 40B CD2 IV 4.0 13.2
7 C5 IV PHE 220B CD1 V 4.2 5.4
8 C4 IV PHE 223B CG V 3.8 11.2
8 C4 IV PHE 223B CD1 V 4.0 2.0
8 C4 IV PHE 223B CB IV 4.1 0.2
8 C4 IV PHE 223B CE1 V 4.4 2.5
8 C4 IV PHE 220B CD1 V 4.6 0.2
8 C4 IV PHE 223B CZ V 4.7 0.2
9 C3 IV PHE 220B CD1 V 4.2 11.9
9 C3 IV PHE 223B CB IV 4.3 0.4
9 C3 IV PHE 220B CE1 V 4.4 2.2
9 C3 IV LEU 39B O II 4.7 2.7*
9 C3 IV LEU 40B CD2 IV 4.7 3.6
9 C3 IV LEU 39B CB IV 4.8 3.1
9 C3 IV LEU 39B CD1 IV 5.3 1.1
10 C2 IV PHE 223B CD1 V 4.0 15.5
10 C2 IV PHE 223B CB IV 4.0 2.2
10 C2 IV LEU 39B CB IV 5.0 0.9
10 C2 IV LEU 39B CD1 IV 5.1 3.6
11 C1 VI LEU 39B CD2 IV 4.3 20.0
11 C1 VI LEU 39B CB IV 4.5 2.2
11 C1 VI LEU 39B O II 4.7 4.3
11 C1 VI PHE 223B CB IV 4.7 2.7
11 C1 VI LEU 39B CA VII 4.8 0.2
11 C1 VI LEU 39B CD1 IV 4.9 0.2
11 C1 VI PHE 220B CD1 V 5.3 2.7
11 C1 VI PHE 223B N III 5.5 0.7
11 C1 VI PRO 72B CD IV 6.4 2.0
12 O12 I LEU 39B CD2 IV 4.5 4.2*
12 O12 I PHE 223B CB IV 4.9 1.9*
12 O12 I PHE 223B CD1 V 5.2 0.2
12 O12 I PHE 223B N III 5.3 1.2
12 O12 I GLY 222B C VI 5.7 1.0
------------------------------------------------------------------------
Table V
Complementarity values for the ligand CM5 502B
in PDB entry 5UAP (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 392
Actual value (Å2) 225
Normalised complementarity 0.58
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand CM5 502B
in PDB entry 5UAP (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 | C7
| IV |
0.51 |
0.51
|
0.51 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 2 | C8
| IV |
0.50 |
0.50
|
0.50 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 3 | C9
| IV |
0.53 |
0.53
|
0.53 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 4 | C10
| IV |
0.44 |
0.44
|
0.44 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 5 | C11
| IV |
0.57 |
0.57
|
0.57 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 6 | C6
| IV |
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 7 | C5
| IV |
0.51 |
0.51
|
0.51 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 8 | C4
| IV |
0.57 |
0.57
|
0.57 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 9 | C3
| IV |
0.55 |
0.53
|
0.55 |
0.58
|
0.59 |
0.59
|
0.59 |
0.58
|
| 10 | C2
| IV |
0.54 |
0.54
|
0.54 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 11 | C1
| VI |
0.44 |
0.42
|
0.43 |
0.55
|
0.58 |
0.58
|
0.57 |
0.55
|
| 12 | O12
| I |
0.58 |
0.58
|
0.57 |
0.60
|
0.61 |
0.61
|
0.60 |
0.61
|
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 HEM 501
1. Carbon (in rings)
5 C1A 6 C2A 7 C3A 8 C4A 15 C1B 16 C2B
17 C3B 18 C4B 22 C1C 23 C2C 24 C3C 25 C4C
29 C1D 30 C2D 31 C3D 32 C4D
2. Oxygen ("hydroxy" or "carbonyl")
13 O1A 14 O2A 37 O1D 38 O2D
3. Nitrogen ("hydrophilic")
39 NA 40 NB 41 NC 42 ND
Ligand CM5 502
1. Carbon (in rings)
1 C7 2 C8 3 C9 4 C10 5 C11 6 C6
2. Oxygen ("hydroxy" or "carbonyl")
12 O12
Ligand CM5 503
1. Carbon (in rings)
1 C7 2 C8 3 C9 4 C10 5 C11 6 C6
13 C13 14 C18 16 C17 22 C16 19 C15 24 C24
26 C26 29 C27 31 C28 33 C29
2. Oxygen ("hydroxy" or "carbonyl")
15 O22 17 O21 21 O20 28 O31 30 O32 32 O33
34 O34
Ligand CM5 504
1. Carbon (in rings)
1 C7 2 C8 3 C9 4 C10 5 C11 6 C6
2. Oxygen ("hydroxy" or "carbonyl")
12 O12
Ligand 82S 505
1. Carbon (in rings)
1 C2 2 C3 3 C4 4 C5 5 C6 11 C1
1 C2 2 C3 3 C4 6 C7 11 C1 3 C4
4 C5 5 C6 11 C1 6 C7
Ligand HEM 501
1. Carbon (in rings)
5 C1A 6 C2A 7 C3A 8 C4A 15 C1B 16 C2B
17 C3B 18 C4B 22 C1C 23 C2C 24 C3C 25 C4C
29 C1D 30 C2D 31 C3D 32 C4D
2. Oxygen ("hydroxy" or "carbonyl")
13 O1A 14 O2A 37 O1D 38 O2D
3. Nitrogen ("hydrophilic")
39 NA 40 NB 41 NC 42 ND
Ligand CM5 502
1. Carbon (in rings)
1 C7 2 C8 3 C9 4 C10 5 C11 6 C6
2. Oxygen ("hydroxy" or "carbonyl")
12 O12
Ligand CM5 503
1. Carbon (in rings)
1 C7 2 C8 3 C9 4 C10 5 C11 6 C6
13 C13 14 C18 16 C17 22 C16 19 C15 24 C24
26 C26 29 C27 31 C28 33 C29
2. Oxygen ("hydroxy" or "carbonyl")
15 O22 17 O21 21 O20 28 O31 30 O32 32 O33
34 O34
Ligand CM5 504
1. Carbon (in rings)
1 C7 2 C8 3 C9 4 C10 5 C11 6 C6
2. Oxygen ("hydroxy" or "carbonyl")
12 O12
Ligand 82S 505
1. Carbon (in rings)
1 C2 2 C3 3 C4 4 C5 5 C6 11 C1
1 C2 2 C3 3 C4 6 C7 11 C1 3 C4
4 C5 5 C6 11 C1 6 C7
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il