Contacts of ligand SO4 338P in PDB entry 3DBV
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 SO4 338P
in PDB entry 3DBV (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
----------------------------------------------------------
149P CYS* 5.5 3.1 - - - -
176P HIS* 5.9 0.7 - - - -
179P THR* 2.8 35.5 + - - +
180P ASN* 5.0 0.5 + - - +
181P ASP* 4.0 14.2 + - - +
195P ARG* 3.3 16.3 + - - -
231P ARG* 3.1 22.7 + - - -
336P NAD 3.1 60.4 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand SO4 338P
and protein in PDB entry 3DBV
(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 THR 179P OG1 I 2.8 19.4
2 O1 I ARG 231P NH2 III 3.1 19.2
2 O1 I ARG 195P NH1 III 3.3 6.9
3 O2 I NAD 336P O2D I 3.1 8.8
3 O2 I NAD 336P N1N I 3.8 0.9
3 O2 I ARG 231P NH2 III 4.4 2.6
4 O3 I NAD 336P O2D I 3.2 8.0
4 O3 I THR 179P OG1 I 3.6 7.6
4 O3 I NAD 336P O1N I 4.2 7.3
4 O3 I NAD 336P O5D II 4.4 0.3
4 O3 I ASP 181P N III 4.6 1.4
4 O3 I ASN 180P N III 5.0 0.2
4 O3 I NAD 336P O3 II 5.3 0.3
5 O4 I NAD 336P O2D I 3.1 9.2
5 O4 I ARG 195P NH1 III 4.0 8.5
5 O4 I ARG 195P NH2 III 5.0 0.7
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand SO4 338P
in PDB entry 3DBV (back
to top of page)
Total number of contacts is 38
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 S VI NAD 336P O2D I 3.3 1.8
1 S VI THR 179P OG1 I 3.7 1.6
1 S VI ARG 231P NH2 III 4.3 0.9
1 S VI ARG 195P NH1 III 4.3 0.2
1 S VI THR 179P CB VI 4.4 0.4
1 S VI ASP 181P CB IV 4.4 0.9
2 O1 I THR 179P OG1 I 2.8 19.4
2 O1 I ARG 231P NH2 III 3.1 19.2
2 O1 I ARG 195P NH1 III 3.3 6.9
2 O1 I THR 179P CB VI 3.7 0.2
2 O1 I ASP 181P CB IV 4.0 0.2*
3 O2 I NAD 336P O2D I 3.1 8.8
3 O2 I NAD 336P C2N V 3.7 14.0
3 O2 I NAD 336P N1N I 3.8 0.9
3 O2 I NAD 336P C3N V 4.2 2.1
3 O2 I ARG 231P NH2 III 4.4 2.6
3 O2 I NAD 336P C6N V 4.4 1.7
3 O2 I THR 179P CG2 IV 4.5 2.8*
3 O2 I NAD 336P C4N V 4.8 0.3
3 O2 I NAD 336P C5N V 4.9 0.2
3 O2 I CYS 149P SG VI 5.5 3.1
3 O2 I HIS 176P CE1 V 5.9 0.7
4 O3 I NAD 336P O2D I 3.2 8.0
4 O3 I THR 179P OG1 I 3.6 7.6
4 O3 I NAD 336P C2D VI 3.6 5.4
4 O3 I THR 179P CB VI 4.0 3.5
4 O3 I ASP 181P CB IV 4.1 7.3*
4 O3 I NAD 336P O1N I 4.2 7.3
4 O3 I NAD 336P O5D II 4.4 0.3
4 O3 I ASP 181P N III 4.6 1.4
4 O3 I ASN 180P N III 5.0 0.2
4 O3 I NAD 336P O3 II 5.3 0.3
4 O3 I ASN 180P CB IV 5.8 0.3*
5 O4 I NAD 336P O2D I 3.1 9.2
5 O4 I ARG 195P NH1 III 4.0 8.5
5 O4 I ASP 181P CB IV 4.4 3.6*
5 O4 I ASP 181P CG VI 4.8 0.9
5 O4 I ARG 195P NH2 III 5.0 0.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand SO4 338P
in PDB entry 3DBV (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 192
Actual value (Å2) 125
Normalised complementarity 0.65
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand SO4 338P
in PDB entry 3DBV (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 | S
| VI |
0.64 |
0.64
|
0.63 |
0.60
|
0.65 |
0.65
|
0.64 |
0.65
|
| 2 | O1
| I |
0.65 |
0.65
|
0.38 |
0.18
|
0.65 |
0.65
|
0.38 |
0.65
|
| 3 | O2
| I |
0.65 |
0.65
|
0.62 |
0.55
|
0.68 |
0.68
|
0.65 |
0.68
|
| 4 | O3
| I |
0.65 |
0.64
|
0.63 |
0.47
|
0.73 |
0.73
|
0.71 |
0.72
|
| 5 | O4
| I |
0.65 |
0.65
|
0.55 |
0.50
|
0.69 |
0.69
|
0.59 |
0.69
|
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 NAD 336
1. Carbon (in rings)
6 C4B 12 C1B 10 C2B 8 C3B 14 C8A 16 C5A
22 C4A 16 C5A 17 C6A 20 C2A 22 C4A 29 C4D
35 C1D 33 C2D 31 C3D 37 C2N 38 C3N 42 C4N
43 C5N 44 C6N
2. Oxygen ("hydroxy" or "carbonyl")
9 O3B 11 O2B 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Ligand NAD 336
1. Carbon (in rings)
6 C4B 12 C1B 10 C2B 8 C3B 14 C8A 16 C5A
22 C4A 16 C5A 17 C6A 20 C2A 22 C4A 29 C4D
35 C1D 33 C2D 31 C3D 37 C2N 38 C3N 42 C4N
43 C5N 44 C6N
2. Oxygen ("hydroxy" or "carbonyl")
9 O3B 11 O2B 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Ligand NAD 336
1. Carbon (in rings)
6 C4B 12 C1B 10 C2B 8 C3B 14 C8A 16 C5A
22 C4A 16 C5A 17 C6A 20 C2A 22 C4A 29 C4D
35 C1D 33 C2D 31 C3D 37 C2N 38 C3N 42 C4N
43 C5N 44 C6N
2. Oxygen ("hydroxy" or "carbonyl")
9 O3B 11 O2B 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Ligand NAD 336
1. Carbon (in rings)
6 C4B 12 C1B 10 C2B 8 C3B 14 C8A 16 C5A
22 C4A 16 C5A 17 C6A 20 C2A 22 C4A 29 C4D
35 C1D 33 C2D 31 C3D 37 C2N 38 C3N 42 C4N
43 C5N 44 C6N
2. Oxygen ("hydroxy" or "carbonyl")
9 O3B 11 O2B 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il