Contacts of ligand 0MC 201A in PDB entry 4DRN
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 0MC 201A
in PDB entry 4DRN (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
----------------------------------------------------------
57A TYR* 3.4 43.2 - - + +
67A PHE* 3.5 36.3 + - + -
68A ASP* 2.8 35.0 + - - +
73A ARG* 5.9 0.4 - - - +
77A PHE* 3.5 64.3 - + + -
78A VAL 6.0 0.4 - - - -
79A PHE* 5.7 2.7 - - + -
84A GLY* 3.2 34.1 - - - +
85A GLN* 3.1 45.1 - - + -
86A VAL* 3.3 37.8 - - + +
87A ILE* 2.9 49.9 + - + +
88A LYS* 4.8 9.0 + - - +
90A TRP* 3.4 58.3 - - + +
112A ALA 3.7 17.7 - - - +
113A TYR* 2.7 80.1 + + + +
118A SER* 3.7 31.4 - - - +
121A LYS* 4.6 18.4 + - + -
122A ILE* 3.5 26.9 - - + -
130A PHE* 4.1 7.7 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand 0MC 201A
and protein in PDB entry 4DRN
(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
------------------------------------------------------------------------
9 OAI I ASP 68A OD2 II 2.8 14.0
9 OAI I PHE 67A O II 4.8 0.9
9 OAI I LYS 121A NZ III 5.2 2.3
13 OAF II TYR 113A OH I 2.7 14.0
21 O II ILE 87A N III 2.9 25.3
22 OBF II TYR 113A OH I 3.3 1.0
31 OBC II LYS 88A N III 4.8 0.3
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand 0MC 201A
in PDB entry 4DRN (back
to top of page)
Total number of contacts is 124
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 CAA IV ILE 122A CD1 IV 3.5 23.3
1 CAA IV SER 118A OG I 3.7 18.6*
1 CAA IV SER 118A CB VI 3.8 3.4
1 CAA IV ILE 122A CG1 IV 3.9 3.6
1 CAA IV SER 118A O II 4.2 4.7*
1 CAA IV TYR 113A OH I 4.4 1.1*
1 CAA IV LYS 121A CB IV 4.6 8.1
1 CAA IV LYS 121A CD IV 4.9 1.6
2 CAQ IV PHE 67A CD1 V 3.9 14.4
2 CAQ IV LYS 121A CD IV 4.9 5.2
3 CBQ IV TYR 113A OH I 3.9 3.6*
4 CAX IV SER 118A OG I 4.7 4.7*
4 CAX IV TYR 113A OH I 4.7 0.2*
4 CAX IV LYS 121A CD IV 5.9 1.3
6 CAU IV ASP 68A OD2 II 4.7 0.9*
7 CBB IV ASP 68A OD2 II 4.0 3.8*
7 CBB IV TYR 57A OH I 4.2 1.6*
7 CBB IV PHE 77A CE1 V 5.5 0.9
7 CBB IV ARG 73A NH2 III 5.9 0.4*
9 OAI I ASP 68A OD2 II 2.8 14.0
9 OAI I ASP 68A CG VI 3.4 5.4
9 OAI I ASP 68A CB IV 3.5 0.7*
9 OAI I PHE 67A O II 4.8 0.9
9 OAI I LYS 121A NZ III 5.2 2.3
10 CBJ VIII PHE 67A CE1 V 4.0 0.4
11 OAG II ASP 68A OD2 II 3.3 9.7*
11 OAG II TYR 57A CE1 V 3.4 11.8
11 OAG II PHE 67A CE1 V 3.5 12.5
11 OAG II ASP 68A CB IV 3.5 0.5*
11 OAG II PHE 130A CE1 V 4.4 0.2
12 CBI VI PHE 67A CE1 V 4.4 2.2
12 CBI VI PHE 130A CZ V 4.4 0.9
13 OAF II TYR 113A OH I 2.7 14.0
13 OAF II TYR 113A CZ V 3.6 2.9
13 OAF II TYR 113A CE2 V 3.6 4.2
13 OAF II PHE 67A CE1 V 4.0 5.9
13 OAF II PHE 130A CZ V 4.1 1.9
15 CBA VI TYR 57A OH I 3.6 4.7
15 CBA VI PHE 77A CE1 V 4.0 7.6
16 CAT IV TYR 57A CZ V 3.6 21.3
16 CAT IV PHE 77A CZ V 3.7 9.4
16 CAT IV TYR 57A CE2 V 3.7 3.1
16 CAT IV TRP 90A CH2 V 3.8 5.2
16 CAT IV TRP 90A CZ2 V 3.8 0.9
16 CAT IV TYR 57A CE1 V 4.0 0.7
17 CAR IV TRP 90A CE2 V 3.5 11.7
17 CAR IV TRP 90A CD2 V 3.6 4.7
17 CAR IV TRP 90A CZ2 V 3.6 0.7
17 CAR IV TRP 90A CE3 V 3.6 4.7
17 CAR IV TRP 90A CZ3 V 3.7 0.9
17 CAR IV PHE 77A CZ V 3.7 9.2
17 CAR IV PHE 77A CE2 V 3.7 0.7
17 CAR IV VAL 86A CG1 IV 4.2 2.5
18 CB IV TRP 90A CE2 V 3.4 18.2
18 CB IV TRP 90A NE1 III 3.5 4.9*
18 CB IV TRP 90A CD2 V 3.6 2.5
18 CB IV TRP 90A CD1 V 3.8 3.4
18 CB IV TRP 90A CG V 3.8 0.4
18 CB IV TRP 90A CZ2 V 3.9 0.2
18 CB IV PHE 130A CZ V 4.2 3.4
18 CB IV ILE 87A CG1 IV 4.2 1.1
19 CA VI TYR 113A OH I 3.7 0.9
19 CA VI ILE 87A CG1 IV 4.3 4.9
19 CA VI PHE 130A CZ V 4.4 1.3
19 CA VI ILE 87A CD1 IV 4.5 0.2
20 C VI TYR 113A OH I 3.5 3.6
20 C VI ILE 87A CG2 IV 4.3 1.1
21 O II ILE 87A N III 2.9 25.3
21 O II VAL 86A CA VII 3.4 3.8
21 O II ILE 87A CG2 IV 3.6 1.0*
22 OBF II TYR 113A OH I 3.3 1.0
24 CAZ IV TYR 113A OH I 3.4 14.1*
24 CAZ IV TYR 113A CE1 V 4.3 2.2
25 CAV IV TYR 113A CE1 V 4.9 0.4
27 CAO V ILE 87A CG2 IV 4.0 3.4
27 CAO V TYR 113A CE1 V 4.2 2.7
28 CAM V GLN 85A O II 3.5 16.8
28 CAM V GLN 85A C VI 3.9 0.4
28 CAM V GLN 85A CA VII 4.9 0.2
29 CAN V VAL 86A C VI 3.5 10.5
29 CAN V VAL 86A O II 3.6 0.2
29 CAN V GLY 84A O II 3.6 9.9
29 CAN V VAL 86A N III 3.7 0.2
30 CBN V VAL 86A O II 3.7 3.8
30 CBN V VAL 86A C VI 3.7 0.7
30 CBN V ILE 87A N III 3.9 0.2
31 OBC II VAL 86A O II 3.5 0.3*
31 OBC II VAL 86A C VI 4.0 0.2
31 OBC II ILE 87A CA VII 4.0 1.9
31 OBC II LYS 88A N III 4.8 0.3
31 OBC II LYS 88A CG IV 5.6 0.2*
32 CAB VIII GLY 84A O II 3.2 16.8*
32 CAB VIII VAL 86A O II 3.3 12.6*
32 CAB VIII GLY 84A C VI 3.8 2.7
32 CAB VIII GLY 84A CA VI 4.0 4.7
32 CAB VIII ILE 87A CA VII 4.7 0.9
32 CAB VIII ILE 87A C VI 5.1 0.9
32 CAB VIII LYS 88A N III 5.1 1.3
32 CAB VIII LYS 88A CG IV 5.5 6.3
32 CAB VIII LYS 88A NZ III 6.3 0.9
33 CBO V ILE 87A CG2 IV 3.8 4.7
34 OBD II ILE 87A CG2 IV 3.7 1.7*
34 OBD II ALA 112A O II 4.2 0.7*
34 OBD II ILE 87A CA VII 4.4 0.2
35 CAC VIII TYR 113A CD1 V 3.6 26.0
35 CAC VIII ALA 112A O II 3.7 17.0*
35 CAC VIII ILE 87A CG2 IV 3.8 2.2
35 CAC VIII TYR 113A CA VII 4.4 2.7
35 CAC VIII TYR 113A C VI 5.4 0.2
36 CBM V PHE 77A CZ V 4.4 0.4
38 CAL V GLN 85A O II 3.1 17.3
38 CAL V PHE 77A CZ V 3.9 6.3
38 CAL V VAL 86A CG1 IV 4.0 1.3
39 CAJ V GLN 85A O II 3.4 8.7
39 CAJ V PHE 77A CZ V 3.5 11.2
39 CAJ V VAL 86A CG1 IV 4.4 1.6
39 CAJ V GLN 85A CB IV 5.5 1.6
39 CAJ V PHE 79A CB IV 5.7 2.7
39 CAJ V VAL 78A O II 6.0 0.4
40 CAK V PHE 77A CZ V 3.7 7.9
40 CAK V PHE 77A CE1 V 3.8 0.9
41 CBL V PHE 77A CE1 V 4.1 4.5
42 OBE II PHE 77A CE1 V 4.5 0.2
43 CAW VIII PHE 77A CE1 V 4.7 5.2
------------------------------------------------------------------------
Table V
Complementarity values for the ligand 0MC 201A
in PDB entry 4DRN (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 886
Actual value (Å2) 358
Normalised complementarity 0.40
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand 0MC 201A
in PDB entry 4DRN (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 | CAA
| IV |
0.38 |
0.37
|
0.38 |
0.40
|
0.46 |
0.46
|
0.46 |
0.45
|
| 2 | CAQ
| IV |
0.39 |
0.39
|
0.39 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 3 | CBQ
| IV |
0.41 |
0.41
|
0.41 |
0.40
|
0.41 |
0.41
|
0.41 |
0.41
|
| 4 | CAX
| IV |
0.41 |
0.41
|
0.41 |
0.40
|
0.42 |
0.42
|
0.42 |
0.42
|
| 6 | CAU
| IV |
0.41 |
0.40
|
0.41 |
0.40
|
0.41 |
0.41
|
0.41 |
0.40
|
| 7 | CBB
| IV |
0.42 |
0.41
|
0.42 |
0.40
|
0.42 |
0.42
|
0.42 |
0.41
|
| 9 | OAI
| I |
0.40 |
0.37
|
0.40 |
0.37
|
0.41 |
0.41
|
0.40 |
0.37
|
| 10 | CBJ
| VIII |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 11 | OAG
| II |
0.43 |
0.40
|
0.43 |
0.41
|
0.43 |
0.43
|
0.43 |
0.41
|
| 12 | CBI
| VI |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 13 | OAF
| II |
0.40 |
0.40
|
0.40 |
0.37
|
0.40 |
0.40
|
0.40 |
0.40
|
| 15 | CBA
| VI |
0.40 |
0.40
|
0.40 |
0.39
|
0.40 |
0.40
|
0.40 |
0.40
|
| 16 | CAT
| IV |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 17 | CAR
| IV |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 18 | CB
| IV |
0.41 |
0.41
|
0.40 |
0.40
|
0.42 |
0.42
|
0.40 |
0.42
|
| 19 | CA
| VI |
0.39 |
0.39
|
0.39 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 20 | C
| VI |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 21 | O
| II |
0.40 |
0.40
|
0.34 |
0.35
|
0.41 |
0.41
|
0.34 |
0.41
|
| 22 | OBF
| II |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 24 | CAZ
| IV |
0.44 |
0.44
|
0.44 |
0.40
|
0.44 |
0.44
|
0.44 |
0.44
|
| 25 | CAV
| IV |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 27 | CAO
| V |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 28 | CAM
| V |
0.40 |
0.37
|
0.40 |
0.37
|
0.40 |
0.40
|
0.40 |
0.37
|
| 29 | CAN
| V |
0.40 |
0.38
|
0.40 |
0.38
|
0.40 |
0.40
|
0.40 |
0.38
|
| 30 | CBN
| V |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 31 | OBC
| II |
0.41 |
0.40
|
0.40 |
0.40
|
0.41 |
0.41
|
0.40 |
0.40
|
| 32 | CAB
| VIII |
0.46 |
0.39
|
0.45 |
0.40
|
0.47 |
0.47
|
0.46 |
0.40
|
| 33 | CBO
| V |
0.39 |
0.39
|
0.39 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 34 | OBD
| II |
0.41 |
0.40
|
0.41 |
0.41
|
0.41 |
0.41
|
0.41 |
0.41
|
| 35 | CAC
| VIII |
0.44 |
0.40
|
0.43 |
0.40
|
0.44 |
0.44
|
0.44 |
0.40
|
| 36 | CBM
| V |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 38 | CAL
| V |
0.40 |
0.36
|
0.40 |
0.37
|
0.40 |
0.40
|
0.40 |
0.37
|
| 39 | CAJ
| V |
0.39 |
0.37
|
0.39 |
0.38
|
0.40 |
0.40
|
0.40 |
0.38
|
| 40 | CAK
| V |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 41 | CBL
| V |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 42 | OBE
| II |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
| 43 | CAW
| VIII |
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
0.40 |
0.40
|
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 0MC 201
1. Carbon (in rings)
3 CBQ 4 CAX 5 CAS 6 CAU 7 CBB 8 CBT
15 CBA 16 CAT 17 CAR 18 CB 19 CA 26 CBK
27 CAO 33 CBO 30 CBN 29 CAN 28 CAM 36 CBM
37 CAP 41 CBL 40 CAK 39 CAJ 38 CAL
2. Oxygen ("hydroxy" or "carbonyl")
9 OAI 11 OAG 13 OAF 21 O 45 OAH 46 OAD
3. Nitrogen ("hydrophilic")
14 N
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il