Contacts of ligand LDA 112A in PDB entry 4DDJ
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 LDA 112A
in PDB entry 4DDJ (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
----------------------------------------------------------
61A ILE* 4.4 32.6 - - + +
62A ILE* 4.0 27.1 - - + -
65A GLU* 3.8 35.2 + - + +
66A MET* 3.9 21.3 - - + -
68A ARG* 5.3 2.8 + - - -
102A LDA 4.1 8.1 - - + -
109A LDA 4.5 7.9 - - + -
111A LDA 3.5 73.8 + - + -
113A LDA 3.7 22.0 - - + -
116A LDA 3.4 90.6 - - + +
118A LDA 4.1 52.7 - - + -
119A LDA 2.9 47.3 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand LDA 112A
and protein in PDB entry 4DDJ
(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 LDA 111A O1 I 4.2 0.3
2 O1 I GLU 65A OE1 II 4.8 0.7
2 O1 I ARG 68A NH2 III 5.3 2.8
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand LDA 112A
in PDB entry 4DDJ (back
to top of page)
Total number of contacts is 73
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
------------------------------------------------------------------------
2 O1 I LDA 111A CM1 VI 3.5 13.5
2 O1 I LDA 111A O1 I 4.2 0.3
2 O1 I GLU 65A OE1 II 4.8 0.7
2 O1 I ARG 68A NH2 III 5.3 2.8
2 O1 I ILE 61A CG2 IV 5.3 0.5*
3 CM1 VI ILE 61A CG2 IV 4.9 9.6
3 CM1 VI LDA 118A C7 IV 5.3 6.1
3 CM1 VI LDA 118A C6 IV 5.6 2.2
3 CM1 VI ILE 61A CG1 IV 5.8 2.0
3 CM1 VI ILE 61A CD1 IV 5.9 0.4
3 CM1 VI LDA 118A C4 IV 6.3 1.1
4 CM2 VI LDA 116A O1 I 3.4 17.3
4 CM2 VI LDA 116A CM2 VI 3.7 12.6
4 CM2 VI LDA 111A CM1 VI 3.8 13.7
4 CM2 VI LDA 111A C1 VI 4.0 0.2
5 C1 VI GLU 65A OE1 II 4.2 9.9
5 C1 VI ILE 61A CG2 IV 4.7 4.9
5 C1 VI LDA 111A O1 I 4.8 1.1
6 C2 IV LDA 116A O1 I 3.9 9.6*
6 C2 IV LDA 116A C5 IV 4.6 4.3
6 C2 IV LDA 111A C5 IV 4.6 2.9
6 C2 IV LDA 116A CM2 VI 5.1 0.9
7 C3 IV LDA 116A C7 IV 4.0 14.8
7 C3 IV LDA 116A C5 IV 4.5 0.4
7 C3 IV LDA 118A C8 IV 5.1 9.2
7 C3 IV LDA 118A C7 IV 5.3 0.2
8 C4 IV GLU 65A OE1 II 4.3 6.3*
8 C4 IV ILE 61A CG2 IV 4.4 7.0
8 C4 IV LDA 111A C5 IV 4.6 1.8
8 C4 IV GLU 65A CB IV 4.7 0.2
8 C4 IV LDA 118A C8 IV 5.3 0.4
9 C5 IV LDA 111A C7 IV 4.1 14.8
9 C5 IV LDA 116A C7 IV 4.1 7.2
9 C5 IV LDA 116A C9 IV 4.2 3.4
9 C5 IV ILE 61A CG2 IV 5.0 0.2
9 C5 IV LDA 118A C8 IV 5.3 3.4
9 C5 IV LDA 118A C10 IV 5.4 0.4
10 C6 IV GLU 65A CB IV 3.8 17.5
10 C6 IV GLU 65A CG IV 3.9 0.7
10 C6 IV ILE 61A CG2 IV 4.6 7.9
10 C6 IV ILE 62A CA VII 4.6 0.9
11 C7 IV ILE 62A CG1 IV 4.0 11.4
11 C7 IV LDA 118A C10 IV 4.7 9.6
11 C7 IV LDA 118A C12 IV 4.8 0.2
11 C7 IV LDA 116A C9 IV 4.9 1.8
11 C7 IV LDA 118A C9 IV 5.2 0.2
12 C8 IV MET 66A CE IV 3.9 16.4
12 C8 IV ILE 62A CG2 IV 4.1 6.7
12 C8 IV LDA 111A C9 IV 4.4 2.7
12 C8 IV ILE 62A CA VII 4.5 0.2
13 C9 IV LDA 111A C9 IV 4.2 16.6
13 C9 IV LDA 111A C11 IV 4.3 2.9
13 C9 IV LDA 116A C10 IV 4.5 7.2
13 C9 IV LDA 116A C12 IV 4.5 0.2
14 C10 IV LDA 118A C12 IV 4.1 19.5
14 C10 IV ILE 62A CG1 IV 4.3 5.6
14 C10 IV LDA 116A C12 IV 4.6 4.9
14 C10 IV LDA 102A C12 IV 4.6 0.7
14 C10 IV LDA 109A C12 IV 4.8 0.2
15 C11 IV LDA 119A C12 IV 3.5 13.0
15 C11 IV LDA 119A C11 IV 3.7 0.9
15 C11 IV LDA 102A C12 IV 4.1 7.4
15 C11 IV LDA 109A C12 IV 4.5 7.2
15 C11 IV LDA 109A C11 IV 4.7 0.4
15 C11 IV LDA 116A C12 IV 4.9 6.1
15 C11 IV LDA 111A C12 IV 5.0 2.7
16 C12 IV LDA 119A C11 IV 2.9 31.2
16 C12 IV LDA 119A C12 IV 3.2 2.2
16 C12 IV LDA 113A C12 IV 3.7 21.3
16 C12 IV MET 66A CE IV 4.1 4.9
16 C12 IV ILE 62A CG2 IV 4.1 2.2
16 C12 IV LDA 113A C10 IV 4.6 0.7
16 C12 IV LDA 111A C12 IV 4.9 0.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand LDA 112A
in PDB entry 4DDJ (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 508
Actual value (Å2) 388
Normalised complementarity 0.76
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand LDA 112A
in PDB entry 4DDJ (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 |
|---|
| 2 | O1
| I |
0.76 |
0.76
|
0.75 |
0.75
|
0.77 |
0.77
|
0.76 |
0.76
|
| 3 | CM1
| VI |
0.68 |
0.68
|
0.68 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 4 | CM2
| VI |
0.76 |
0.76
|
0.76 |
0.70
|
0.76 |
0.76
|
0.76 |
0.76
|
| 5 | C1
| VI |
0.74 |
0.71
|
0.74 |
0.72
|
0.76 |
0.76
|
0.76 |
0.73
|
| 6 | C2
| IV |
0.77 |
0.77
|
0.77 |
0.76
|
0.80 |
0.80
|
0.80 |
0.80
|
| 7 | C3
| IV |
0.67 |
0.67
|
0.67 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 8 | C4
| IV |
0.75 |
0.73
|
0.75 |
0.76
|
0.79 |
0.79
|
0.79 |
0.76
|
| 9 | C5
| IV |
0.65 |
0.65
|
0.65 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 10 | C6
| IV |
0.66 |
0.66
|
0.66 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 11 | C7
| IV |
0.67 |
0.67
|
0.67 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 12 | C8
| IV |
0.66 |
0.66
|
0.66 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 13 | C9
| IV |
0.66 |
0.66
|
0.66 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 14 | C10
| IV |
0.64 |
0.64
|
0.64 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 15 | C11
| IV |
0.62 |
0.62
|
0.62 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 16 | C12
| IV |
0.52 |
0.52
|
0.52 |
0.76
|
0.76 |
0.76
|
0.76 |
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 LDA 101
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 102
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 103
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 104
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 105
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 106
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 107
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 108
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 109
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 110
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 111
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 112
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 113
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 114
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 115
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 116
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 117
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 118
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 119
3. Nitrogen ("hydrophilic")
1 N1
Ligand LDA 120
3. Nitrogen ("hydrophilic")
1 N1
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il