Contacts of ligand ASD1224K in PDB entry 2VCV
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 ASD1224K
in PDB entry 2VCV (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
----------------------------------------------------------
9K TYR* 4.2 1.6 - - - +
10K PHE* 3.7 38.8 - - + -
14K GLY* 4.7 9.0 - - - +
15K ARG* 4.5 13.0 - - + +
107K LEU* 3.7 60.6 - - + +
108K LEU* 4.3 17.9 - - + -
110K PRO* 3.2 27.8 - - + +
111K LEU* 4.1 44.6 - - + -
208K ALA* 3.7 27.8 - - + +
209K ASP 5.0 0.2 - - - +
212K ALA* 3.9 6.3 - - + +
213K LEU* 3.6 34.0 - - + +
216K ALA* 3.5 27.6 - - + -
220K PHE* 3.8 14.9 - - + +
222K PHE* 4.0 43.0 - - + +
1223K GSH 3.6 66.2 + - + +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand ASD1224K
and protein in PDB entry 2VCV
(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
------------------------------------------------------------------------
20 O1 II GSH 1223K N3 I 3.9 13.2
20 O1 II GSH 1223K OE1 I 4.0 3.3
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand ASD1224K
in PDB entry 2VCV (back
to top of page)
Total number of contacts is 84
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 IV LEU 111K CD1 IV 4.3 13.7
1 C1 IV LEU 108K CD2 IV 4.3 3.6
1 C1 IV PHE 222K CG V 4.6 4.9
3 C11 IV LEU 111K CD1 IV 4.1 11.7
3 C11 IV LEU 107K O II 4.3 4.9*
3 C11 IV LEU 111K CD2 IV 4.3 0.2
3 C11 IV LEU 108K CD2 IV 4.3 2.9
4 C12 IV LEU 107K O II 4.0 7.4*
4 C12 IV LEU 111K CG IV 4.1 13.7
4 C12 IV LEU 111K CD2 IV 4.1 4.5
4 C12 IV PRO 110K CB IV 4.4 2.7
4 C12 IV LEU 213K CD1 IV 4.5 0.2
6 C14 IV ALA 216K CB IV 4.1 2.7
6 C14 IV PHE 222K CZ V 4.3 2.5
7 C15 IV ALA 216K CB IV 3.5 12.1
7 C15 IV PHE 10K CZ V 3.7 14.8
7 C15 IV PHE 10K CE2 V 4.1 1.6
7 C15 IV ALA 212K O II 4.3 0.2*
8 C16 IV LEU 213K CA VII 3.8 17.5
8 C16 IV ALA 208K CB IV 3.8 14.1
8 C16 IV LEU 213K N III 3.8 3.4*
8 C16 IV ALA 212K O II 3.9 2.5*
8 C16 IV ALA 212K C VI 3.9 1.1
8 C16 IV ALA 212K CB IV 4.4 2.5
8 C16 IV PHE 10K CE2 V 5.0 1.1
9 C17 VIII ALA 208K CB IV 3.9 2.2
9 C17 VIII LEU 213K CB IV 4.2 3.1
9 C17 VIII LEU 213K CD1 IV 4.2 0.2
10 C18 IV LEU 107K O II 3.7 14.4*
10 C18 IV LEU 107K CD1 IV 3.8 15.0
10 C18 IV ALA 208K CB IV 4.5 7.6
10 C18 IV GLY 14K CA VI 4.7 6.7
10 C18 IV PRO 110K CG IV 4.8 0.7
10 C18 IV GLY 14K N III 5.0 1.3*
11 C19 IV GSH 1223K SG2 VI 4.0 10.8
11 C19 IV LEU 108K CD2 IV 4.4 8.5
11 C19 IV LEU 107K CD1 IV 4.5 13.9
11 C19 IV LEU 107K CD2 IV 4.5 4.9
11 C19 IV ARG 15K NE III 4.5 4.9*
11 C19 IV ARG 15K CG IV 4.7 1.6
11 C19 IV TYR 9K OH I 4.9 1.3*
11 C19 IV GLY 14K CA VI 5.4 0.2
12 C2 IV PHE 222K CG V 4.8 1.8
12 C2 IV GSH 1223K OE1 I 4.8 3.6*
12 C2 IV PHE 222K CB IV 4.9 1.8
12 C2 IV LEU 108K CD2 IV 5.0 2.9
12 C2 IV ARG 15K NH2 III 5.0 6.5*
12 C2 IV GSH 1223K SG2 VI 5.0 0.2
12 C2 IV LEU 111K CD1 IV 5.2 0.9
13 C3 VIII GSH 1223K CA2 VI 4.1 4.5
13 C3 VIII PHE 222K CD2 V 4.3 4.7
13 C3 VIII GSH 1223K OE1 I 4.4 1.8
13 C3 VIII PHE 222K CG V 4.4 0.2
14 C4 IV GSH 1223K CB2 IV 3.6 15.0
14 C4 IV GSH 1223K CA2 VI 3.8 0.2
14 C4 IV PHE 222K CD2 V 4.1 8.3
14 C4 IV PHE 220K CG V 4.4 4.5
15 C5 IV GSH 1223K SG2 VI 3.7 0.2
15 C5 IV PHE 222K CE2 V 4.3 0.4
16 C6 IV GSH 1223K SG2 VI 3.6 12.6
16 C6 IV PHE 10K CE1 V 3.8 10.5
16 C6 IV PHE 220K CE2 V 3.8 8.5
16 C6 IV PHE 220K CD2 V 3.9 0.2
16 C6 IV TYR 9K OH I 4.2 0.2*
17 C7 IV PHE 10K CE1 V 3.7 9.2
17 C7 IV ALA 216K CB IV 3.8 12.8
17 C7 IV PHE 222K CE2 V 4.0 3.1
17 C7 IV PHE 220K CD2 V 4.2 0.4
18 C8 IV PHE 10K CZ V 4.4 1.6
18 C8 IV GLY 14K CA VI 5.2 0.7
19 C9 IV PHE 222K CZ V 4.1 5.2
20 O1 II GSH 1223K N3 I 3.9 13.2
20 O1 II GSH 1223K CA2 VI 4.0 0.3
20 O1 II GSH 1223K OE1 I 4.0 3.3
20 O1 II PHE 222K CB IV 4.2 9.7*
20 O1 II PHE 222K CD2 V 4.4 0.3
20 O1 II PHE 220K CB IV 4.8 1.2*
20 O1 II GSH 1223K CA3 VI 4.9 0.2
20 O1 II GSH 1223K O31 II 5.2 0.3*
21 O2 II PRO 110K CB IV 3.2 22.3*
21 O2 II PRO 110K CG IV 3.3 2.1*
21 O2 II LEU 213K CB IV 3.6 9.5*
21 O2 II ALA 208K CB IV 3.7 3.8*
21 O2 II ASP 209K O II 5.0 0.2*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand ASD1224K
in PDB entry 2VCV (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 465
Actual value (Å2) 233
Normalised complementarity 0.50
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand ASD1224K
in PDB entry 2VCV (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
| IV |
0.43 |
0.43
|
0.43 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 3 | C11
| IV |
0.46 |
0.44
|
0.46 |
0.50
|
0.52 |
0.52
|
0.52 |
0.50
|
| 4 | C12
| IV |
0.44 |
0.41
|
0.44 |
0.50
|
0.53 |
0.53
|
0.53 |
0.50
|
| 6 | C14
| IV |
0.49 |
0.49
|
0.49 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 7 | C15
| IV |
0.45 |
0.45
|
0.45 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 8 | C16
| IV |
0.46 |
0.44
|
0.37 |
0.50
|
0.53 |
0.53
|
0.44 |
0.52
|
| 9 | C17
| VIII |
0.48 |
0.48
|
0.48 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 10 | C18
| IV |
0.47 |
0.41
|
0.46 |
0.50
|
0.57 |
0.57
|
0.56 |
0.51
|
| 11 | C19
| IV |
0.40 |
0.40
|
0.38 |
0.50
|
0.53 |
0.53
|
0.51 |
0.53
|
| 12 | C2
| IV |
0.52 |
0.52
|
0.49 |
0.50
|
0.54 |
0.54
|
0.52 |
0.54
|
| 13 | C3
| VIII |
0.50 |
0.50
|
0.50 |
0.49
|
0.50 |
0.50
|
0.50 |
0.50
|
| 14 | C4
| IV |
0.44 |
0.44
|
0.44 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 15 | C5
| IV |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 16 | C6
| IV |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 17 | C7
| IV |
0.45 |
0.45
|
0.45 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 18 | C8
| IV |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 19 | C9
| IV |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 20 | O1
| II |
0.50 |
0.50
|
0.50 |
0.48
|
0.55 |
0.55
|
0.55 |
0.55
|
| 21 | O2
| II |
0.50 |
0.50
|
0.50 |
0.66
|
0.66 |
0.66
|
0.66 |
0.66
|
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 GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand GSH 1223
2. Oxygen ("hydroxy" or "carbonyl")
4 O11 5 O12 9 OE1 13 O2 19 O31 20 O32
3. Nitrogen ("hydrophilic")
1 N1 10 N2 16 N3
Ligand ASD 1224
1. Carbon (in rings)
1 C1 2 C10 15 C5 14 C4 13 C3 12 C2
2 C10 15 C5 16 C6 17 C7 18 C8 19 C9
3 C11 4 C12 5 C13 6 C14 18 C8 19 C9
5 C13 6 C14 7 C15 8 C16 9 C17
2. Oxygen ("hydroxy" or "carbonyl")
20 O1 21 O2
Please E-mail any questions and/or suggestions
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Vladimir.Sobolev@weizmann.ac.il