Contacts of ligand DME 998A in PDB entry 1MAA
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 DME 998A
in PDB entry 1MAA (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
----------------------------------------------------------
72A TYR* 3.4 38.1 - - - -
74A ASP* 3.6 13.7 - - - -
76A LEU* 6.1 0.7 - - - -
86A TRP* 3.4 63.9 - - - -
120A GLY 4.1 12.6 - - - -
121A GLY* 3.6 15.9 - - - -
122A GLY 3.5 21.3 - - - +
124A TYR* 3.4 29.6 - - + +
125A SER* 5.3 3.4 - - - +
133A TYR* 4.4 2.7 - - - -
202A GLU* 3.9 15.7 - - - -
203A SER* 3.7 22.9 - - - +
286A TRP* 3.2 59.9 - - - -
295A PHE* 6.0 2.5 - - + +
297A PHE* 3.7 26.7 - - + -
337A TYR* 3.7 44.0 - - + +
338A PHE* 3.6 36.6 - - + -
341A TYR* 3.3 60.3 - - + +
447A HIS* 3.6 44.6 - - + -
448A GLY* 5.0 0.2 - - - -
451A ILE* 5.9 0.7 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand DME 998A
and protein in PDB entry 1MAA
(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
------------------------------------------------------------------------
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand DME 998A
in PDB entry 1MAA (back
to top of page)
Total number of contacts is 101
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 C2 VI TRP 286A CZ2 V 3.9 13.7
2 C2 VI TRP 286A CH2 V 4.2 2.5
2 C2 VI TYR 124A OH I 4.5 0.7
2 C2 VI TRP 286A CZ3 V 4.7 1.8
2 C2 VI TRP 286A CE3 V 4.9 0.2
3 C3 IV TYR 341A CD2 V 3.3 7.0
3 C3 IV TYR 341A CE2 V 3.8 0.4
3 C3 IV TYR 341A CG V 4.0 0.4
3 C3 IV TYR 124A OH I 4.1 1.1*
3 C3 IV TYR 341A CB IV 4.3 2.0
3 C3 IV TYR 341A O II 5.4 0.2*
4 C4 IV TYR 124A OH I 3.5 7.9*
4 C4 IV TYR 124A CZ V 4.1 2.2
4 C4 IV TYR 124A CE2 V 4.2 2.9
4 C4 IV PHE 297A CE1 V 4.3 7.0
4 C4 IV PHE 295A N III 6.0 1.8*
5 C5 IV TYR 341A CD2 V 3.7 14.4
5 C5 IV TYR 341A CG V 3.9 5.2
5 C5 IV TYR 341A CE2 V 4.0 3.8
5 C5 IV TYR 124A OH I 4.0 0.9*
5 C5 IV TYR 341A CD1 V 4.3 2.0
5 C5 IV TYR 337A CE2 V 4.3 0.9
5 C5 IV TYR 341A CB IV 4.4 1.6
5 C5 IV TYR 341A CZ V 4.4 0.2
5 C5 IV PHE 338A CD2 V 4.6 1.8
5 C5 IV PHE 295A N III 6.1 0.4*
6 C6 IV PHE 338A CE2 V 3.6 18.6
6 C6 IV PHE 338A CD2 V 3.6 4.5
6 C6 IV TYR 337A CE2 V 3.8 5.4
6 C6 IV TYR 337A CD2 V 4.3 0.2
6 C6 IV PHE 297A CE1 V 4.4 1.6
7 C7 IV TYR 124A OH I 3.4 9.4*
7 C7 IV TYR 337A CE2 V 3.7 8.7
7 C7 IV TYR 337A OH I 4.5 2.5*
8 C8 IV PHE 338A CE2 V 3.7 11.4
8 C8 IV PHE 297A CZ V 3.7 16.4
8 C8 IV PHE 297A CE1 V 3.9 1.8
8 C8 IV TYR 124A CE2 V 4.2 0.7
8 C8 IV PHE 338A CZ V 4.3 0.2
8 C8 IV SER 203A OG I 5.0 0.4*
8 C8 IV PHE 295A CE1 V 6.1 0.2
9 C9 IV GLY 122A N III 3.5 21.3*
9 C9 IV GLY 121A C VI 3.6 5.6
9 C9 IV GLY 121A CA VI 3.7 0.7
9 C9 IV SER 203A OG I 4.1 2.0*
9 C9 IV TYR 124A CE2 V 4.5 0.9
9 C9 IV TYR 124A OH I 4.5 0.7*
9 C9 IV SER 125A OG I 5.3 0.2*
10 C10 IV HIS 447A CD2 V 3.7 12.3
10 C10 IV SER 203A OG I 3.8 1.8*
10 C10 IV TYR 337A CE2 V 4.4 1.3
11 C11 VI SER 203A OG I 3.7 12.1
11 C11 VI SER 203A CB VI 3.9 6.5
11 C11 VI GLY 121A CA VI 3.9 7.2
13 C13 VI TYR 341A CD2 V 4.0 8.5
13 C13 VI TYR 341A O II 4.6 10.5
13 C13 VI TYR 341A C VI 5.3 0.7
13 C13 VI TYR 341A CA VII 5.4 0.2
14 C14 VI TYR 72A OH I 3.4 19.5
14 C14 VI TYR 72A CZ V 3.6 5.6
14 C14 VI TYR 72A CE1 V 3.6 6.1
14 C14 VI ASP 74A OD1 II 3.6 13.7
14 C14 VI TYR 341A CD2 V 4.0 2.9
14 C14 VI TYR 341A CE2 V 4.0 0.2
14 C14 VI TYR 72A CD1 V 4.5 0.2
14 C14 VI TYR 124A OH I 5.0 1.8
14 C14 VI LEU 76A CB IV 6.1 0.7
15 C15 VI TRP 286A NE1 III 3.2 28.0
15 C15 VI TRP 286A CE2 V 3.4 2.9
15 C15 VI TRP 286A CD1 V 3.5 6.7
15 C15 VI TRP 286A CD2 V 3.7 2.2
15 C15 VI TRP 286A CG V 3.8 1.1
15 C15 VI TYR 72A CZ V 4.0 5.6
15 C15 VI TYR 72A CE2 V 4.2 0.4
15 C15 VI TYR 72A OH I 4.2 0.7
15 C15 VI TRP 286A CE3 V 4.5 0.2
15 C15 VI TRP 286A CB IV 4.8 0.4
16 C16 VI TRP 86A CZ3 V 3.4 27.6
16 C16 VI TRP 86A CE3 V 3.5 1.1
16 C16 VI TRP 86A CH2 V 3.8 1.8
16 C16 VI GLU 202A OE1 II 3.9 14.8
16 C16 VI GLY 120A O II 4.1 9.6
16 C16 VI TYR 133A OH I 4.4 2.7
16 C16 VI GLU 202A CD VI 4.8 0.9
16 C16 VI GLY 448A CA VI 5.0 0.2
16 C16 VI ILE 451A CD1 IV 5.9 0.7
17 C17 VI HIS 447A O II 3.6 23.8
17 C17 VI HIS 447A CD2 V 3.7 8.3
17 C17 VI TYR 337A CE2 V 4.1 12.8
17 C17 VI TYR 337A CZ V 4.2 2.5
17 C17 VI TRP 86A CE2 V 4.3 6.1
17 C17 VI HIS 447A C VI 4.4 0.2
18 C18 VI TRP 86A CD2 V 3.7 16.4
18 C18 VI TRP 86A CG V 3.7 6.3
18 C18 VI TYR 337A OH I 3.8 9.6
18 C18 VI TRP 86A CE3 V 3.9 0.7
18 C18 VI TRP 86A CB IV 4.1 4.0
18 C18 VI GLY 120A O II 4.7 2.9
18 C18 VI GLY 121A CA VI 4.8 2.5
18 C18 VI SER 125A OG I 5.4 3.1
18 C18 VI TYR 124A OH I 5.9 0.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand DME 998A
in PDB entry 1MAA (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 572
Actual value (Å2) 414
Normalised complementarity 0.72
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand DME 998A
in PDB entry 1MAA (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 | C2
| VI |
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 3 | C3
| IV |
0.72 |
0.72
|
0.72 |
0.72
|
0.73 |
0.73
|
0.73 |
0.73
|
| 4 | C4
| IV |
0.76 |
0.76
|
0.75 |
0.72
|
0.76 |
0.76
|
0.75 |
0.76
|
| 5 | C5
| IV |
0.72 |
0.72
|
0.72 |
0.72
|
0.73 |
0.73
|
0.73 |
0.73
|
| 6 | C6
| IV |
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 7 | C7
| IV |
0.77 |
0.77
|
0.77 |
0.72
|
0.77 |
0.77
|
0.77 |
0.77
|
| 8 | C8
| IV |
0.73 |
0.73
|
0.73 |
0.72
|
0.73 |
0.73
|
0.73 |
0.73
|
| 9 | C9
| IV |
0.81 |
0.81
|
0.73 |
0.72
|
0.81 |
0.81
|
0.73 |
0.81
|
| 10 | C10
| IV |
0.73 |
0.73
|
0.73 |
0.72
|
0.73 |
0.73
|
0.73 |
0.73
|
| 11 | C11
| VI |
0.72 |
0.72
|
0.72 |
0.68
|
0.72 |
0.72
|
0.72 |
0.72
|
| 13 | C13
| VI |
0.72 |
0.69
|
0.72 |
0.69
|
0.72 |
0.72
|
0.72 |
0.69
|
| 14 | C14
| VI |
0.72 |
0.67
|
0.72 |
0.60
|
0.72 |
0.72
|
0.72 |
0.68
|
| 15 | C15
| VI |
0.72 |
0.72
|
0.62 |
0.62
|
0.72 |
0.72
|
0.63 |
0.72
|
| 16 | C16
| VI |
0.72 |
0.64
|
0.72 |
0.63
|
0.72 |
0.72
|
0.72 |
0.64
|
| 17 | C17
| VI |
0.72 |
0.64
|
0.72 |
0.64
|
0.72 |
0.72
|
0.72 |
0.64
|
| 18 | C18
| VI |
0.71 |
0.70
|
0.71 |
0.67
|
0.72 |
0.72
|
0.72 |
0.71
|
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 NAG 1
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 2
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand FUL 3
1. Carbon (in rings)
1 C1 2 C2 4 C3 6 C4 8 C5
2. Oxygen ("hydroxy" or "carbonyl")
3 O2 5 O3 7 O4
Ligand NAG 709
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand DME 998
3. Nitrogen ("hydrophilic")
1 N1 12 N12
Ligand GOL 954
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand DME 996
3. Nitrogen ("hydrophilic")
1 N1 12 N12
Ligand GOL 953
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand DME 997
3. Nitrogen ("hydrophilic")
1 N1 12 N12
Ligand GOL 951
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand DME 999
3. Nitrogen ("hydrophilic")
1 N1 12 N12
Ligand GOL 952
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