Contacts of ligand MYR1001A in PDB entry 2BXN
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 MYR1001A
in PDB entry 2BXN (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
----------------------------------------------------------
115A LEU* 4.5 29.9 - - + +
116A VAL 4.9 1.1 - - - +
117A ARG* 2.9 60.9 + - + +
123A MET* 3.7 32.8 - - + -
134A PHE* 4.8 1.8 - - + -
135A LEU* 4.4 20.9 - - + +
138A TYR* 3.4 61.7 - - + +
139A LEU* 3.9 38.6 - - + +
142A ILE* 4.4 23.1 - - + -
154A LEU* 4.7 5.8 - - + +
157A PHE* 4.5 4.5 - - + -
158A ALA* 3.8 24.5 - - + +
161A TYR* 3.5 73.8 + - + +
165A PHE* 3.9 15.5 - - + -
182A LEU* 4.5 16.1 - - + +
186A ARG* 4.1 21.2 + - + +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand MYR1001A
and protein in PDB entry 2BXN
(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 II ARG 117A NH2 III 2.9 23.6
2 O1 II ARG 117A NE III 3.3 2.4
2 O1 II TYR 161A OH I 4.6 2.3
3 O2 II ARG 117A NE III 3.9 6.1
3 O2 II ARG 117A NH2 III 3.9 1.7
3 O2 II ARG 117A N III 4.7 0.2
3 O2 II ARG 186A NH1 III 5.0 2.4
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand MYR1001A
in PDB entry 2BXN (back
to top of page)
Total number of contacts is 102
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 VI ARG 117A NH2 III 3.8 2.5
1 C1 VI ARG 117A NE III 3.9 3.4
1 C1 VI ARG 186A CB IV 4.6 8.5
1 C1 VI ARG 186A CD VII 5.4 0.2
2 O1 II ARG 117A NH2 III 2.9 23.6
2 O1 II ARG 117A NE III 3.3 2.4
2 O1 II ARG 186A CB IV 4.1 7.6*
2 O1 II LEU 182A O II 4.5 2.1*
2 O1 II TYR 161A OH I 4.6 2.3
2 O1 II LEU 182A CB IV 5.0 1.2*
2 O1 II TYR 161A CE1 V 5.3 0.2
3 O2 II ARG 117A NE III 3.9 6.1
3 O2 II ARG 117A NH2 III 3.9 1.7
3 O2 II ARG 117A CB IV 4.1 6.1*
3 O2 II LEU 115A O II 4.5 8.1*
3 O2 II ARG 117A N III 4.7 0.2
3 O2 II ARG 186A NH1 III 5.0 2.4
3 O2 II ARG 186A CG IV 5.0 0.2*
3 O2 II ARG 186A CD VII 5.4 0.7
4 C2 IV LEU 115A CD2 IV 4.7 10.1
4 C2 IV TYR 161A OH I 5.0 3.6*
4 C2 IV LEU 115A CG IV 5.1 0.9
4 C2 IV LEU 115A O II 5.1 2.0*
4 C2 IV ARG 186A CB IV 5.2 1.6
4 C2 IV LEU 115A CB IV 5.2 0.7
4 C2 IV ILE 142A CD1 IV 5.3 3.4
5 C3 IV TYR 138A CE1 V 4.3 10.8
5 C3 IV LEU 115A CD2 IV 4.7 4.7
5 C3 IV ARG 117A CB IV 4.7 8.7
5 C3 IV ARG 117A CA VII 4.7 4.3
5 C3 IV LEU 115A CG IV 4.9 2.2
5 C3 IV VAL 116A O II 4.9 1.1*
5 C3 IV ARG 117A N III 5.0 0.7*
6 C4 IV TYR 138A CE1 V 4.2 4.5
6 C4 IV TYR 138A CD1 V 4.3 2.2
6 C4 IV TYR 161A CE1 V 4.7 4.3
6 C4 IV TYR 161A OH I 4.8 1.3*
6 C4 IV TYR 161A CZ V 4.9 0.2
6 C4 IV LEU 115A CD2 IV 5.2 1.1
6 C4 IV ILE 142A CD1 IV 5.2 3.1
7 C5 IV MET 123A CE IV 3.9 13.9
7 C5 IV TYR 138A CE1 V 4.4 0.2
7 C5 IV LEU 182A CD2 IV 4.5 11.0
7 C5 IV MET 123A SD VIII 4.9 0.9
7 C5 IV LEU 182A CD1 IV 5.0 1.8
7 C5 IV ARG 117A CG IV 5.2 1.3
8 C6 IV MET 123A CE IV 3.7 17.9
8 C6 IV TYR 138A CD1 V 4.0 9.2
8 C6 IV TYR 138A CG V 4.0 1.3
8 C6 IV TYR 138A CD2 V 4.1 1.1
8 C6 IV PHE 165A CZ V 4.3 2.2
8 C6 IV PHE 134A CZ V 4.9 0.2
9 C7 IV TYR 161A CD1 V 3.5 20.6
9 C7 IV PHE 165A CE2 V 3.9 7.2
10 C8 IV TYR 138A CB IV 3.6 9.6
10 C8 IV TYR 138A CG V 3.7 0.7
10 C8 IV TYR 138A CD2 V 4.0 1.8
10 C8 IV TYR 161A CD1 V 4.2 1.6
10 C8 IV TYR 161A CG V 4.3 0.4
10 C8 IV PHE 165A CE2 V 4.4 6.1
10 C8 IV TYR 161A CB IV 4.5 0.7
10 C8 IV LEU 135A CD2 IV 4.6 6.7
10 C8 IV PHE 134A CE2 V 4.8 1.6
11 C9 IV TYR 138A CB IV 3.4 11.2
11 C9 IV TYR 138A CG V 4.0 0.4
11 C9 IV TYR 161A CG V 4.1 2.5
11 C9 IV TYR 161A CD2 V 4.2 0.4
11 C9 IV TYR 138A CD1 V 4.4 1.1
11 C9 IV TYR 161A CE2 V 4.5 1.1
11 C9 IV TYR 138A C VI 4.6 0.2
11 C9 IV TYR 138A O II 4.8 0.2*
11 C9 IV ILE 142A CG1 IV 4.9 3.8
11 C9 IV ILE 142A CD1 IV 5.2 0.4
12 C10 IV TYR 138A CB IV 3.9 4.9
12 C10 IV TYR 161A CD2 V 4.1 4.7
12 C10 IV TYR 161A CB IV 4.1 5.8
12 C10 IV LEU 135A CD2 IV 4.4 11.9
12 C10 IV LEU 135A O II 4.4 2.0*
12 C10 IV ALA 158A CA VII 4.7 1.8
12 C10 IV ALA 158A CB IV 4.9 0.7
13 C11 IV LEU 139A CA VII 3.9 26.5
13 C11 IV LEU 139A N III 3.9 0.2*
13 C11 IV LEU 139A CD1 IV 4.0 4.0
13 C11 IV TYR 138A C VI 4.2 1.1
13 C11 IV LEU 139A CB IV 4.3 1.3
13 C11 IV ALA 158A CB IV 4.3 3.6
13 C11 IV TYR 138A O II 4.3 0.9*
13 C11 IV ILE 142A CG1 IV 4.4 0.9
13 C11 IV LEU 135A O II 4.5 0.2*
14 C12 IV TYR 161A CD2 V 3.6 20.2
14 C12 IV ALA 158A CA VII 3.8 13.9
14 C12 IV TYR 161A CE2 V 3.9 3.8
14 C12 IV ALA 158A N III 4.0 3.4*
14 C12 IV ALA 158A CB IV 4.2 1.1
14 C12 IV LEU 139A CD1 IV 4.3 6.5
14 C12 IV PHE 157A C VI 4.5 1.1
14 C12 IV ILE 142A CG1 IV 4.5 10.1
14 C12 IV LEU 154A O II 4.7 2.5*
14 C12 IV PHE 157A CB IV 4.8 3.4
14 C12 IV ILE 142A CB IV 5.2 0.7
14 C12 IV LEU 154A CD1 IV 5.3 3.4
14 C12 IV ILE 142A CG2 IV 5.4 0.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand MYR1001A
in PDB entry 2BXN (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 461
Actual value (Å2) 345
Normalised complementarity 0.75
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand MYR1001A
in PDB entry 2BXN (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
| VI |
0.71 |
0.71
|
0.69 |
0.72
|
0.75 |
0.75
|
0.72 |
0.75
|
| 2 | O1
| II |
0.76 |
0.75
|
0.64 |
0.66
|
0.80 |
0.80
|
0.68 |
0.79
|
| 3 | O2
| II |
0.78 |
0.75
|
0.74 |
0.73
|
0.81 |
0.81
|
0.76 |
0.78
|
| 4 | C2
| IV |
0.70 |
0.69
|
0.70 |
0.75
|
0.77 |
0.77
|
0.77 |
0.76
|
| 5 | C3
| IV |
0.69 |
0.68
|
0.67 |
0.75
|
0.76 |
0.76
|
0.73 |
0.75
|
| 6 | C4
| IV |
0.74 |
0.74
|
0.74 |
0.75
|
0.75 |
0.75
|
0.75 |
0.75
|
| 7 | C5
| IV |
0.63 |
0.62
|
0.63 |
0.75
|
0.75 |
0.75
|
0.75 |
0.74
|
| 8 | C6
| IV |
0.67 |
0.67
|
0.67 |
0.75
|
0.75 |
0.75
|
0.75 |
0.75
|
| 9 | C7
| IV |
0.75 |
0.75
|
0.75 |
0.75
|
0.75 |
0.75
|
0.75 |
0.75
|
| 10 | C8
| IV |
0.67 |
0.67
|
0.67 |
0.75
|
0.75 |
0.75
|
0.75 |
0.75
|
| 11 | C9
| IV |
0.68 |
0.68
|
0.68 |
0.75
|
0.75 |
0.75
|
0.75 |
0.75
|
| 12 | C10
| IV |
0.66 |
0.65
|
0.65 |
0.75
|
0.76 |
0.76
|
0.75 |
0.75
|
| 13 | C11
| IV |
0.71 |
0.71
|
0.60 |
0.75
|
0.75 |
0.75
|
0.64 |
0.75
|
| 14 | C12
| IV |
0.66 |
0.65
|
0.59 |
0.75
|
0.77 |
0.77
|
0.70 |
0.76
|
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 MYR 1001
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2
Ligand MYR 1002
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2
Ligand MYR 1003
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2
Ligand MYR 1004
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2
Ligand MYR 1005
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2
Ligand MYR 1006
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 3 O2
Ligand IDB 2001
1. Carbon (in rings)
8 C1 9 C2 10 C3 11 C4 12 C5 13 C6
26 C12 27 C13 28 C14 29 C15 30 C16 31 C17
2. Oxygen ("hydroxy" or "carbonyl")
4 O1 5 O2 6 O3 22 O4 23 O5 24 O6
3. Nitrogen ("hydrophilic")
7 N1 25 N2
Ligand IDB 2002
1. Carbon (in rings)
8 C1 9 C2 10 C3 11 C4 12 C5 13 C6
2. Oxygen ("hydroxy" or "carbonyl")
4 O1 5 O2 6 O3
3. Nitrogen ("hydrophilic")
7 N1
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il