Contacts of ligand DME 997C 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 997C
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
----------------------------------------------------------
261A GLY* 2.9 38.6 - - - -
72C TYR* 3.1 36.8 - - - -
74C ASP* 4.1 10.8 - - - -
76C LEU* 6.3 0.2 - - - -
86C TRP* 3.6 67.1 - - - -
120C GLY* 4.1 2.5 - - - -
121C GLY* 3.4 23.6 - - - -
122C GLY* 3.2 26.5 - - - +
124C TYR* 2.9 65.3 - - + +
125C SER* 5.4 2.2 - - - -
133C TYR* 3.9 11.0 - - - -
202C GLU* 3.7 13.9 - - - -
203C SER* 3.1 33.7 - - - +
286C TRP* 2.6 34.5 - - + -
294C ILE* 6.5 0.2 - - - -
295C PHE* 5.6 3.6 - - + +
297C PHE* 3.9 19.7 - - + -
337C TYR* 3.3 39.7 - - + +
338C PHE* 3.1 39.9 - - + -
341C TYR* 2.8 48.9 - - + +
447C HIS* 3.7 32.8 - - + -
448C GLY* 4.4 2.7 - - - -
451C ILE* 4.8 0.9 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand DME 997C
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 997C
in PDB entry 1MAA (back
to top of page)
Total number of contacts is 104
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 TYR 341C CD2 V 2.8 20.2
2 C2 VI GLY 261A O II 3.6 4.9
2 C2 VI TYR 341C CG V 3.6 0.2
2 C2 VI TYR 341C CB IV 4.0 0.7
3 C3 IV TYR 341C CD2 V 3.5 4.3
3 C3 IV TYR 341C CG V 3.8 3.4
3 C3 IV TYR 341C CB IV 4.1 2.7
3 C3 IV TRP 286C CH2 V 4.7 1.3
3 C3 IV PHE 297C CE1 V 5.1 2.2
3 C3 IV PHE 338C CD2 V 5.3 0.9
3 C3 IV PHE 295C N III 5.8 3.1*
3 C3 IV ILE 294C CA VII 6.5 0.2
4 C4 IV TYR 124C OH I 3.1 1.6*
4 C4 IV TYR 341C CD2 V 3.9 7.9
4 C4 IV TYR 341C CE2 V 3.9 4.7
4 C4 IV TYR 341C CG V 4.2 0.7
4 C4 IV TYR 341C CZ V 4.2 1.3
4 C4 IV TYR 337C CE1 V 4.3 0.2
4 C4 IV TYR 341C OH I 4.8 0.2*
4 C4 IV TYR 337C OH I 5.3 0.2*
4 C4 IV ASP 74C CG VI 6.1 0.2
5 C5 IV TYR 124C OH I 3.5 0.7*
5 C5 IV PHE 338C CE2 V 3.7 10.8
5 C5 IV PHE 338C CD2 V 3.8 5.4
5 C5 IV TYR 337C CE1 V 4.1 0.7
5 C5 IV PHE 297C CE1 V 4.3 7.4
5 C5 IV TYR 341C CG V 5.0 0.4
5 C5 IV PHE 295C N III 5.7 0.2*
6 C6 IV TYR 337C CE1 V 3.3 22.9
6 C6 IV TYR 124C OH I 3.4 3.1*
6 C6 IV PHE 338C CE2 V 3.6 0.4
6 C6 IV TYR 337C CZ V 4.3 0.2
6 C6 IV TYR 337C OH I 4.5 0.9*
7 C7 IV PHE 338C CE2 V 3.1 21.8
7 C7 IV PHE 338C CZ V 3.7 0.7
7 C7 IV TYR 337C CE1 V 4.2 0.2
7 C7 IV PHE 297C CZ V 4.3 0.7
7 C7 IV PHE 295C CE1 V 5.6 0.2
8 C8 IV GLY 122C N III 3.6 10.3*
8 C8 IV TYR 124C OH I 3.6 10.3*
8 C8 IV TYR 124C CE1 V 3.8 5.2
8 C8 IV PHE 297C CZ V 3.9 8.7
9 C9 IV SER 203C OG I 3.1 18.2*
9 C9 IV GLY 122C N III 3.2 15.9*
9 C9 IV GLY 121C CA VI 3.4 2.2
9 C9 IV GLY 122C CA VI 4.1 0.2
9 C9 IV HIS 447C CD2 V 4.5 0.2
9 C9 IV PHE 297C CZ V 4.9 0.7
10 C10 IV SER 203C OG I 3.7 0.4*
10 C10 IV HIS 447C CD2 V 4.0 3.6
10 C10 IV TYR 337C CE1 V 4.9 0.7
11 C11 VI SER 203C OG I 3.6 10.3
11 C11 VI GLY 121C N III 3.7 1.8
11 C11 VI SER 203C CB VI 3.7 4.7
11 C11 VI HIS 447C CD2 V 3.8 5.4
11 C11 VI GLU 202C OE1 II 4.0 0.4
13 C13 VI TYR 72C OH I 3.1 28.3
13 C13 VI GLY 261A CA VI 3.4 10.3
13 C13 VI TYR 72C CE1 V 3.4 6.1
13 C13 VI GLY 261A O II 3.6 2.5
13 C13 VI GLY 261A C VI 3.6 0.4
13 C13 VI ASP 74C OD1 II 4.1 8.5
13 C13 VI TYR 341C CD2 V 4.1 1.6
13 C13 VI LEU 76C CB IV 6.3 0.2
14 C14 VI TYR 124C OH I 2.9 24.5
14 C14 VI TYR 124C CZ V 3.1 11.7
14 C14 VI TYR 124C CE2 V 3.3 6.7
14 C14 VI TRP 286C CZ2 V 3.3 2.5
14 C14 VI TRP 286C CH2 V 3.4 0.2
14 C14 VI TYR 72C CE1 V 4.1 2.5
14 C14 VI TYR 341C CE2 V 4.9 0.7
14 C14 VI ASP 74C OD1 II 5.3 0.4
14 C14 VI ASP 74C CG VI 5.5 1.3
14 C14 VI ASP 74C CB IV 5.7 0.2
15 C15 VI TRP 286C CH2 V 2.6 26.7
15 C15 VI GLY 261A CA VI 2.9 19.7
15 C15 VI TRP 286C CZ2 V 3.0 0.2
15 C15 VI TRP 286C CZ3 V 3.0 3.6
15 C15 VI GLY 261A O II 3.6 0.7
16 C16 VI TRP 86C CE3 V 3.6 15.7
16 C16 VI TRP 86C CZ3 V 3.6 4.7
16 C16 VI GLU 202C OE1 II 3.7 13.5
16 C16 VI GLY 121C N III 3.8 10.1
16 C16 VI TYR 133C OH I 3.9 11.0
16 C16 VI GLY 120C CA VI 4.1 2.2
16 C16 VI GLY 120C N III 4.7 0.2
16 C16 VI ILE 451C CD1 IV 4.8 0.9
17 C17 VI HIS 447C O II 3.7 23.1
17 C17 VI TRP 86C CE2 V 3.7 20.4
17 C17 VI TRP 86C CZ2 V 3.8 1.8
17 C17 VI TRP 86C CH2 V 4.0 0.7
17 C17 VI TRP 86C NE1 III 4.3 0.9
17 C17 VI GLY 448C CA VI 4.4 2.7
17 C17 VI TRP 86C CD1 V 4.6 0.4
17 C17 VI TYR 337C CZ V 4.6 7.4
17 C17 VI HIS 447C CD2 V 4.7 0.4
18 C18 VI TRP 86C CD2 V 4.0 11.7
18 C18 VI TRP 86C CG V 4.0 4.9
18 C18 VI TRP 86C CE3 V 4.0 0.7
18 C18 VI GLY 121C CA VI 4.1 9.4
18 C18 VI TRP 86C CB IV 4.2 5.2
18 C18 VI TYR 337C OH I 4.4 6.3
18 C18 VI SER 125C OG I 5.4 2.2
18 C18 VI TYR 124C OH I 5.6 1.6
------------------------------------------------------------------------
Table V
Complementarity values for the ligand DME 997C
in PDB entry 1MAA (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 558
Actual value (Å2) 424
Normalised complementarity 0.76
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand DME 997C
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 |
0.76 |
0.74
|
0.76 |
0.74
|
0.76 |
0.76
|
0.76 |
0.74
|
| 3 | C3
| IV |
0.76 |
0.76
|
0.75 |
0.76
|
0.77 |
0.77
|
0.76 |
0.77
|
| 4 | C4
| IV |
0.77 |
0.77
|
0.77 |
0.76
|
0.77 |
0.77
|
0.77 |
0.77
|
| 5 | C5
| IV |
0.76 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 6 | C6
| IV |
0.77 |
0.77
|
0.77 |
0.76
|
0.77 |
0.77
|
0.77 |
0.77
|
| 7 | C7
| IV |
0.76 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 8 | C8
| IV |
0.83 |
0.83
|
0.80 |
0.76
|
0.83 |
0.83
|
0.80 |
0.83
|
| 9 | C9
| IV |
0.88 |
0.88
|
0.82 |
0.76
|
0.88 |
0.88
|
0.82 |
0.88
|
| 10 | C10
| IV |
0.76 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 11 | C11
| VI |
0.76 |
0.76
|
0.75 |
0.71
|
0.76 |
0.76
|
0.75 |
0.76
|
| 13 | C13
| VI |
0.76 |
0.72
|
0.76 |
0.62
|
0.76 |
0.76
|
0.76 |
0.72
|
| 14 | C14
| VI |
0.76 |
0.76
|
0.76 |
0.67
|
0.76 |
0.76
|
0.76 |
0.76
|
| 15 | C15
| VI |
0.76 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 16 | C16
| VI |
0.76 |
0.71
|
0.72 |
0.64
|
0.76 |
0.76
|
0.72 |
0.71
|
| 17 | C17
| VI |
0.76 |
0.68
|
0.76 |
0.67
|
0.76 |
0.76
|
0.76 |
0.68
|
| 18 | C18
| VI |
0.74 |
0.74
|
0.74 |
0.72
|
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 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