Contacts of ligand B22 301A in PDB entry 2FOU
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 B22 301A
in PDB entry 2FOU (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
----------------------------------------------------------
1A MET* 5.2 14.0 - - + +
92A GLN* 4.1 14.8 - - - +
94A HIS* 3.2 11.5 + + - -
96A HIS* 3.3 4.0 + - - -
119A HIS* 3.4 12.3 + - - +
121A VAL* 3.8 25.9 - - + +
131A PHE* 3.4 48.3 - + + -
132A GLY* 4.0 22.5 + - - -
135A VAL* 3.8 19.4 - - + +
136A GLN* 6.1 1.0 + - - +
143A VAL* 3.8 14.2 - - + +
198A LEU* 3.3 50.2 - - + +
199A THR* 2.9 38.4 + - - -
200A THR* 3.4 30.2 - - + +
201A PRO 5.1 0.9 - - - -
202A PRO* 3.4 34.7 - - + +
204A LEU* 4.3 6.5 - - + +
207A VAL* 5.3 0.2 - - - +
209A TRP* 3.6 13.1 - - - -
262A ZN 1.9 39.9 - - - -
351A GOL 3.9 24.7 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand B22 301A
and protein in PDB entry 2FOU
(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 THR 199A N III 2.9 21.1
3 O2 I HIS 119A ND1 I 3.4 5.5
4 N1 I THR 199A OG1 I 2.9 17.2
4 N1 I HIS 94A NE2 I 3.2 0.6
4 N1 I HIS 96A NE2 I 3.3 1.8
4 N1 I HIS 119A ND1 I 3.4 0.4
22 N17 I GLY 132A O II 5.1 1.0
22 N17 I GLN 136A NE2 III 6.1 0.8
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand B22 301A
in PDB entry 2FOU (back
to top of page)
Total number of contacts is 89
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 S VI HIS 119A ND1 I 4.0 1.1
1 S VI TRP 209A CZ2 V 4.4 0.7
1 S VI VAL 143A CG2 IV 4.9 0.2
2 O1 I THR 199A N III 2.9 21.1
2 O1 I LEU 198A CA VII 3.3 7.8
2 O1 I TRP 209A CZ2 V 3.6 12.5
2 O1 I LEU 198A CD2 IV 4.1 1.0*
2 O1 I VAL 143A CG2 IV 4.9 0.7*
2 O1 I VAL 207A CG2 IV 5.3 0.2*
3 O2 I ZN 262A ZN VI 3.0 7.4
3 O2 I HIS 94A CE1 V 3.3 6.2
3 O2 I HIS 119A ND1 I 3.4 5.5
3 O2 I HIS 119A CB IV 3.7 4.9*
3 O2 I HIS 119A CG V 3.8 0.3
3 O2 I VAL 143A CG1 IV 3.8 11.6*
3 O2 I VAL 121A CG2 IV 3.9 0.3*
3 O2 I VAL 143A CG2 IV 4.0 0.5*
4 N1 I ZN 262A ZN VI 1.9 32.5
4 N1 I THR 199A OG1 I 2.9 17.2
4 N1 I HIS 94A NE2 I 3.2 0.6
4 N1 I HIS 96A NE2 I 3.3 1.8
4 N1 I HIS 119A ND1 I 3.4 0.4
4 N1 I HIS 96A CE1 V 3.8 2.2
4 N1 I THR 200A CG2 IV 4.5 0.8*
5 C1 V LEU 198A CD2 IV 3.9 1.6
5 C1 V GOL 351A C1 VI 4.0 2.7
6 C2 V THR 200A OG1 I 3.4 13.5
6 C2 V GOL 351A C1 VI 3.9 7.6
6 C2 V LEU 198A CD2 IV 4.0 3.4
6 C2 V LEU 198A CD1 IV 4.2 1.6
7 C3 V THR 200A OG1 I 3.4 12.8
7 C3 V LEU 198A CD2 IV 4.0 4.0
7 C3 V LEU 198A CB IV 4.1 3.6
7 C3 V THR 200A CG2 IV 4.2 2.9
7 C3 V GOL 351A C1 VI 4.3 2.9
7 C3 V THR 200A N III 4.3 0.2
8 C4 V LEU 198A CD2 IV 3.8 1.1
8 C4 V HIS 94A CE1 V 4.0 2.2
9 C5 V LEU 198A CD2 IV 3.8 6.5
9 C5 V VAL 121A CG2 IV 3.8 13.7
9 C5 V HIS 94A CE1 V 4.0 2.5
9 C5 V VAL 121A CG1 IV 4.2 2.2
9 C5 V VAL 143A CG2 IV 5.1 1.1
10 C6 V LEU 198A CD2 IV 3.8 5.4
10 C6 V GLN 92A NE2 III 4.1 12.6
10 C6 V VAL 121A CG1 IV 4.3 9.6
10 C6 V PHE 131A CZ V 4.6 4.0
11 C7 IV GOL 351A O1 I 4.2 10.3*
11 C7 IV PHE 131A CZ V 4.3 7.6
11 C7 IV GOL 351A C1 VI 4.4 1.1
11 C7 IV PHE 131A CE2 V 4.5 0.2
11 C7 IV GLN 92A NE2 III 4.8 2.2*
12 C8 VI LEU 198A CD1 IV 3.7 8.5
12 C8 VI PRO 202A CD IV 4.3 5.8
12 C8 VI PHE 131A CE2 V 4.5 1.6
12 C8 VI PHE 131A CZ V 4.6 0.2
12 C8 VI PRO 201A O II 5.1 0.9
13 N9 I PHE 131A CE2 V 3.9 2.2
14 C10 VI PHE 131A CE2 V 4.0 2.2
14 C10 VI PRO 202A CD IV 4.3 4.0
14 C10 VI MET 1A CB IV 6.2 0.2
15 O10 II PRO 202A CG IV 3.4 15.9*
15 O10 II LEU 198A CD1 IV 3.6 5.7*
15 O10 II LEU 204A CD1 IV 4.3 1.7*
15 O10 II PHE 131A CE2 V 4.6 0.3
15 O10 II VAL 135A CG1 IV 4.9 1.0*
16 C11 V PHE 131A CE2 V 3.9 2.0
17 C12 V PHE 131A CE2 V 3.4 15.5
17 C12 V PHE 131A CD2 V 3.6 0.7
18 C13 V PHE 131A CD2 V 3.9 11.7
18 C13 V GLY 132A CA VI 4.1 5.6
18 C13 V GLY 132A N III 4.6 0.2
19 C14 V GLY 132A CA VI 4.0 15.7
19 C14 V VAL 135A CG2 IV 4.1 0.2
20 C15 V VAL 135A CG2 IV 3.8 3.4
21 C16 V VAL 135A CG2 IV 3.9 7.4
21 C16 V PRO 202A CG IV 4.6 8.5
21 C16 V LEU 204A CD1 IV 4.6 0.4
21 C16 V MET 1A CB IV 6.0 2.0
21 C16 V MET 1A SD VIII 6.2 0.4
21 C16 V MET 1A CE IV 6.2 0.2
22 N17 I VAL 135A CG2 IV 4.0 7.3*
22 N17 I LEU 204A CD1 IV 4.9 4.4*
22 N17 I GLY 132A O II 5.1 1.0
22 N17 I MET 1A CE IV 5.2 10.9*
22 N17 I PRO 202A CG IV 5.7 0.4*
22 N17 I MET 1A SD VIII 5.7 0.2
22 N17 I GLN 136A NE2 III 6.1 0.8
22 N17 I GLN 136A CG IV 6.4 0.2*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand B22 301A
in PDB entry 2FOU (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 550
Actual value (Å2) 266
Normalised complementarity 0.48
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand B22 301A
in PDB entry 2FOU (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 | S
| VI |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 2 | O1
| I |
0.48 |
0.48
|
0.38 |
0.41
|
0.49 |
0.49
|
0.39 |
0.49
|
| 3 | O2
| I |
0.48 |
0.48
|
0.48 |
0.53
|
0.55 |
0.55
|
0.55 |
0.55
|
| 4 | N1
| I |
0.48 |
0.48
|
0.48 |
0.41
|
0.49 |
0.49
|
0.49 |
0.49
|
| 5 | C1
| V |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 6 | C2
| V |
0.47 |
0.47
|
0.47 |
0.43
|
0.48 |
0.48
|
0.48 |
0.48
|
| 7 | C3
| V |
0.45 |
0.45
|
0.44 |
0.44
|
0.48 |
0.48
|
0.48 |
0.48
|
| 8 | C4
| V |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 9 | C5
| V |
0.40 |
0.40
|
0.40 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 10 | C6
| V |
0.43 |
0.43
|
0.38 |
0.44
|
0.48 |
0.48
|
0.44 |
0.48
|
| 11 | C7
| IV |
0.53 |
0.53
|
0.52 |
0.48
|
0.53 |
0.53
|
0.52 |
0.53
|
| 12 | C8
| VI |
0.43 |
0.43
|
0.43 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 13 | N9
| I |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 14 | C10
| VI |
0.47 |
0.47
|
0.47 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 15 | O10
| II |
0.48 |
0.48
|
0.48 |
0.57
|
0.57 |
0.57
|
0.57 |
0.57
|
| 16 | C11
| V |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 17 | C12
| V |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 18 | C13
| V |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 19 | C14
| V |
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 20 | C15
| V |
0.47 |
0.47
|
0.47 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 21 | C16
| V |
0.42 |
0.41
|
0.42 |
0.48
|
0.48 |
0.48
|
0.48 |
0.48
|
| 22 | N17
| I |
0.48 |
0.48
|
0.48 |
0.56
|
0.57 |
0.57
|
0.57 |
0.56
|
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 CMH 206
2. Oxygen ("hydroxy" or "carbonyl")
4 O
3. Nitrogen ("hydrophilic")
1 N
Ligand B22 301
1. Carbon (in rings)
5 C1 6 C2 7 C3 8 C4 9 C5 10 C6
16 C11 17 C12 18 C13 19 C14 20 C15 21 C16
2. Oxygen ("hydroxy" or "carbonyl")
15 O10
3. Nitrogen ("hydrophilic")
4 N1 13 N9 22 N17
Ligand B22 303
1. Carbon (in rings)
5 C1 6 C2 7 C3 8 C4 9 C5 10 C6
16 C11 17 C12 18 C13 19 C14 20 C15 21 C16
2. Oxygen ("hydroxy" or "carbonyl")
15 O10 24 O18 29 OXA 30 OXB 33 OXC 34 OXD
3. Nitrogen ("hydrophilic")
4 N1 13 N9 22 N17 26 N20
Ligand GOL 351
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