Contacts of ligand NAG 2D in PDB entry 4BTW
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 NAG 2D
in PDB entry 4BTW (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
----------------------------------------------------------
448B TYR 4.4 1.0 - - - +
449B SER* 3.9 5.6 - - - +
450B HIS* 3.6 49.6 + - + +
726B ARG* 4.2 10.8 - - + -
727B GLY* 5.2 0.2 - - - -
728B ASP* 3.1 36.1 + - - +
1D NAG 1.5 89.2 + - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand NAG 2D
and protein in PDB entry 4BTW
(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 N2 I ASP 728B OD2 II 3.9 4.4
9 N2 I NAG 1D O6 I 4.0 1.0
10 O3 I ASP 728B OD2 II 5.3 0.7
12 O5 II NAG 1D O4 I 2.4 0.9
12 O5 II NAG 1D O3 I 2.8 6.1
13 O6 I NAG 1D O3 I 3.6 7.1
14 O7 II NAG 1D O4 I 3.2 4.3
14 O7 II HIS 450B N III 3.6 12.6
14 O7 II HIS 450B ND1 I 4.6 0.5
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand NAG 2D
in PDB entry 4BTW (back
to top of page)
Total number of contacts is 44
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 VIII NAG 1D O4 I 1.5 33.9
1 C1 VIII NAG 1D C4 VI 2.4 8.3
1 C1 VIII NAG 1D O3 I 3.3 0.4
1 C1 VIII NAG 1D C5 VIII 3.6 1.1*
1 C1 VIII NAG 1D C6 VI 3.7 2.5
2 C2 VI NAG 1D O4 I 2.4 2.0
3 C3 VI ASP 728B OD2 II 5.4 0.4
6 C6 VI NAG 1D O3 I 4.2 1.6
7 C7 VI NAG 1D O4 I 3.3 4.0
7 C7 VI NAG 1D O6 I 3.6 2.9
7 C7 VI ASP 728B OD2 II 4.0 0.2
7 C7 VI HIS 450B CB IV 4.9 0.7
7 C7 VI HIS 450B CG V 5.2 0.2
7 C7 VI HIS 450B CD2 V 5.5 0.7
7 C7 VI ASP 728B CB IV 5.6 0.2
8 C8 IV ASP 728B OD2 II 3.1 23.3*
8 C8 IV NAG 1D O6 I 3.7 11.4*
8 C8 IV HIS 450B N III 3.9 13.7*
8 C8 IV HIS 450B O II 4.1 9.9*
8 C8 IV ASP 728B CG VI 4.2 0.4
8 C8 IV ARG 726B CD VII 4.2 10.5
8 C8 IV SER 449B OG I 4.3 0.2*
8 C8 IV HIS 450B CB IV 4.5 3.1
8 C8 IV ARG 726B CB IV 4.8 0.2
8 C8 IV ASP 728B N III 4.8 2.7*
8 C8 IV GLY 727B CA VI 5.2 0.2
9 N2 I ASP 728B OD2 II 3.9 4.4
9 N2 I NAG 1D O6 I 4.0 1.0
9 N2 I NAG 1D C6 VI 4.3 0.4
10 O3 I ASP 728B OD2 II 5.3 0.7
10 O3 I ASP 728B CB IV 5.6 3.6*
12 O5 II NAG 1D O4 I 2.4 0.9
12 O5 II NAG 1D O3 I 2.8 6.1
12 O5 II NAG 1D C4 VI 2.9 1.2
13 O6 I NAG 1D O3 I 3.6 7.1
14 O7 II NAG 1D O4 I 3.2 4.3
14 O7 II HIS 450B N III 3.6 12.6
14 O7 II SER 449B CA VII 3.9 5.4
14 O7 II HIS 450B CG V 4.3 6.4
14 O7 II TYR 448B O II 4.4 0.9*
14 O7 II HIS 450B ND1 I 4.6 0.5
14 O7 II HIS 450B CD2 V 4.7 1.2
14 O7 II TYR 448B C VI 5.0 0.2
14 O7 II HIS 450B CE1 V 5.1 0.5
------------------------------------------------------------------------
Table V
Complementarity values for the ligand NAG 2D
in PDB entry 4BTW (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 376
Actual value (Å2) 58
Normalised complementarity 0.16
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand NAG 2D
in PDB entry 4BTW (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
| VIII |
0.16 |
0.16
|
0.16 |
-0.02
|
0.16 |
0.16
|
0.16 |
0.16
|
| 2 | C2
| VI |
0.16 |
0.16
|
0.16 |
0.14
|
0.16 |
0.16
|
0.16 |
0.16
|
| 3 | C3
| VI |
0.16 |
0.15
|
0.16 |
0.15
|
0.16 |
0.16
|
0.16 |
0.15
|
| 6 | C6
| VI |
0.16 |
0.16
|
0.16 |
0.15
|
0.16 |
0.16
|
0.16 |
0.16
|
| 7 | C7
| VI |
0.15 |
0.15
|
0.15 |
0.12
|
0.16 |
0.16
|
0.16 |
0.15
|
| 8 | C8
| IV |
0.46 |
0.29
|
0.32 |
0.16
|
0.48 |
0.48
|
0.34 |
0.30
|
| 9 | N2
| I |
0.16 |
0.13
|
0.16 |
0.13
|
0.16 |
0.16
|
0.16 |
0.13
|
| 10 | O3
| I |
0.16 |
0.15
|
0.16 |
0.17
|
0.17 |
0.17
|
0.17 |
0.17
|
| 12 | O5
| II |
0.16 |
0.16
|
0.16 |
0.12
|
0.16 |
0.16
|
0.16 |
0.16
|
| 13 | O6
| I |
0.16 |
0.16
|
0.16 |
0.12
|
0.16 |
0.16
|
0.16 |
0.16
|
| 14 | O7
| II |
0.16 |
0.16
|
0.06 |
0.06
|
0.16 |
0.16
|
0.06 |
0.16
|
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 TPQ 471
1. Carbon (in rings)
6 C1 7 C2 9 C3 10 C4 12 C5 14 C6
2. Oxygen ("hydroxy" or "carbonyl")
5 O 8 O2 11 O4 13 O5
3. Nitrogen ("hydrophilic")
1 N
Ligand TPQ 471
1. Carbon (in rings)
6 C1 7 C2 9 C3 10 C4 12 C5 14 C6
2. Oxygen ("hydroxy" or "carbonyl")
5 O 8 O2 11 O4 13 O5
3. Nitrogen ("hydrophilic")
1 N
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 BMA 3
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O3 9 O4 11 O6
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 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 BMA 3
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O3 9 O4 11 O6
Ligand MAN 4
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O3 9 O4 11 O6
Ligand BMA 5
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O3 9 O4 11 O6
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 NAG 1770
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 1771
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 JW7 2000
1. Carbon (in rings)
1 CAL 2 CAJ 3 CAI 4 CAK 5 CAM 6 CAX
8 CAT 9 CAH 10 CAW 20 CAV 13 CAS 14 CAE
15 CAC 16 CAB 17 CAD 18 CAF 21 CAU 23 CAG
2. Oxygen ("hydroxy" or "carbonyl")
11 OAA
3. Nitrogen ("hydrophilic")
7 NAQ 12 NAY 19 NAP 22 NAN 24 NAR 25 NAO
Ligand NAG 1772
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 1773
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 1774
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 1775
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 JW7 2000
1. Carbon (in rings)
1 CAL 2 CAJ 3 CAI 4 CAK 5 CAM 6 CAX
8 CAT 9 CAH 10 CAW 20 CAV 13 CAS 14 CAE
15 CAC 16 CAB 17 CAD 18 CAF 21 CAU 23 CAG
2. Oxygen ("hydroxy" or "carbonyl")
11 OAA
3. Nitrogen ("hydrophilic")
7 NAQ 12 NAY 19 NAP 22 NAN 24 NAR 25 NAO
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il