Contacts of ligand 211 390X in PDB entry 3H7C
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.
(In PDB entry 3H7C some ATOMs are from nucleic
acids or have "unusual" 3-letter residue code. The
analysis does not take into account these atoms.)
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 211 390X
in PDB entry 3H7C (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
----------------------------------------------------------
35X ASN* 3.0 18.7 + - - -
89X ASP* 3.9 7.0 - - - -
91X TRP* 3.3 52.7 - - - -
94X ASP* 3.3 16.1 + - - -
125X TRP* 3.4 30.7 + - - -
132X CYS* 3.7 28.5 + - - +
133X TYR* 4.0 5.4 - - - -
218X ASP* 5.2 0.9 - - - -
220X ASP* 3.6 28.1 - - - +
221X THR* 3.1 41.7 - - - +
224X HIS* 4.7 0.7 + - - -
301X ARG* 2.8 53.2 + - - -
360X ALA 3.1 16.2 + - - -
361X GLY* 3.5 28.2 + - - -
362X GLY* 3.9 2.0 - - - -
366X CYS* 4.8 5.1 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand 211 390X
and protein in PDB entry 3H7C
(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
------------------------------------------------------------------------
1 O1 I ARG 301X NH2 III 2.8 30.7
1 O1 I ASN 35X ND2 III 3.0 9.5
1 O1 I ASN 35X OD1 II 3.6 0.2
1 O1 I CYS 132X O II 5.1 0.7
2 O2 I ARG 301X NH2 III 3.2 20.8
2 O2 I ALA 360X O II 3.5 3.1
2 O2 I ARG 301X NH1 III 3.8 1.7
5 O3 I ASP 94X OD2 II 3.3 12.3
5 O3 I TRP 125X NE1 III 3.4 1.6
5 O3 I GLY 361X O II 4.4 0.5
5 O3 I HIS 224X ND1 I 4.8 0.5
10 N1 I ALA 360X O II 3.1 1.4
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand 211 390X
in PDB entry 3H7C (back
to top of page)
Total number of contacts is 55
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 O1 I ARG 301X NH2 III 2.8 30.7
1 O1 I ASN 35X ND2 III 3.0 9.5
1 O1 I ASN 35X OD1 II 3.6 0.2
1 O1 I ASN 35X CG VI 3.6 0.5
1 O1 I CYS 132X CB IV 4.0 3.5*
1 O1 I TYR 133X CD1 V 4.8 0.7
1 O1 I CYS 132X O II 5.1 0.7
2 O2 I ARG 301X NH2 III 3.2 20.8
2 O2 I ALA 360X O II 3.5 3.1
2 O2 I ASP 220X CB IV 3.6 10.4*
2 O2 I GLY 361X CA VI 3.7 5.0
2 O2 I ARG 301X NH1 III 3.8 1.7
2 O2 I CYS 132X SG VI 4.2 1.0
3 C1 VI TRP 91X NE1 III 3.3 15.5
3 C1 VI TRP 91X CD1 V 3.5 3.1
3 C1 VI TRP 91X CE2 V 3.5 0.7
3 C1 VI TRP 125X CH2 V 3.6 4.5
4 C2 VI TRP 125X CZ3 V 3.6 16.2
4 C2 VI ASN 35X ND2 III 3.7 8.5
4 C2 VI CYS 132X CB IV 3.8 10.1
4 C2 VI ASP 89X OD2 II 3.9 7.0
4 C2 VI TYR 133X CE1 V 4.0 4.3
4 C2 VI TYR 133X CD1 V 4.3 0.4
5 O3 I THR 221X CG2 IV 3.1 19.8*
5 O3 I ASP 94X OD2 II 3.3 12.3
5 O3 I TRP 125X NE1 III 3.4 1.6
5 O3 I GLY 361X O II 4.4 0.5
5 O3 I HIS 224X CE1 V 4.7 0.2
5 O3 I HIS 224X ND1 I 4.8 0.5
5 O3 I CYS 366X SG VI 5.0 2.4
6 C3 VI CYS 132X SG VI 3.7 12.3
6 C3 VI THR 221X CG2 IV 4.0 3.4
6 C3 VI TRP 125X CD2 V 4.0 3.8
7 C4 VI THR 221X CG2 IV 3.6 18.6
7 C4 VI ASP 220X CB IV 3.7 17.7
7 C4 VI CYS 132X SG VI 4.0 0.9
7 C4 VI GLY 361X O II 4.0 6.3
7 C4 VI GLY 361X CA VI 4.1 0.7
7 C4 VI ASP 218X OD1 II 5.2 0.9
8 C5 VI ALA 360X O II 3.3 11.7
8 C5 VI GLY 361X C VI 3.5 14.6
8 C5 VI TRP 91X CE2 V 3.7 5.2
8 C5 VI TRP 91X CZ2 V 3.8 0.4
8 C5 VI GLY 362X N III 3.9 0.2
9 C6 VI TRP 91X CD2 V 3.4 19.1
9 C6 VI TRP 91X CE3 V 3.6 5.2
9 C6 VI TRP 91X CG V 3.7 3.1
9 C6 VI TRP 125X CZ2 V 3.8 4.7
9 C6 VI TRP 91X CZ3 V 4.0 0.4
9 C6 VI ASP 94X OD2 II 4.0 3.8
9 C6 VI GLY 361X O II 4.4 0.9
9 C6 VI GLY 361X C VI 4.6 0.2
9 C6 VI GLY 362X CA VI 4.8 1.8
9 C6 VI CYS 366X CB IV 4.8 2.7
10 N1 I ALA 360X O II 3.1 1.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand 211 390X
in PDB entry 3H7C (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 314
Actual value (Å2) 268
Normalised complementarity 0.85
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand 211 390X
in PDB entry 3H7C (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 | O1
| I |
0.85 |
0.85
|
0.60 |
0.61
|
0.87 |
0.87
|
0.62 |
0.87
|
| 2 | O2
| I |
0.85 |
0.83
|
0.71 |
0.76
|
0.92 |
0.92
|
0.77 |
0.90
|
| 3 | C1
| VI |
0.85 |
0.85
|
0.75 |
0.75
|
0.85 |
0.85
|
0.75 |
0.85
|
| 4 | C2
| VI |
0.79 |
0.74
|
0.73 |
0.75
|
0.85 |
0.85
|
0.80 |
0.81
|
| 5 | O3
| I |
0.85 |
0.77
|
0.84 |
0.88
|
0.98 |
0.98
|
0.97 |
0.90
|
| 6 | C3
| VI |
0.83 |
0.83
|
0.83 |
0.85
|
0.85 |
0.85
|
0.85 |
0.85
|
| 7 | C4
| VI |
0.62 |
0.58
|
0.62 |
0.81
|
0.85 |
0.85
|
0.85 |
0.81
|
| 8 | C5
| VI |
0.85 |
0.78
|
0.85 |
0.78
|
0.85 |
0.85
|
0.85 |
0.78
|
| 9 | C6
| VI |
0.83 |
0.81
|
0.83 |
0.82
|
0.85 |
0.85
|
0.85 |
0.82
|
| 10 | N1
| I |
0.85 |
0.84
|
0.85 |
0.84
|
0.85 |
0.85
|
0.85 |
0.84
|
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 211 390
2. Oxygen ("hydroxy" or "carbonyl")
1 O1 2 O2 5 O3
3. Nitrogen ("hydrophilic")
10 N1
Ligand 1PE 391
2. Oxygen ("hydroxy" or "carbonyl")
1 OH2
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il