Contacts of ligand DAL 887C in PDB entry 2APH
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 DAL 887C
in PDB entry 2APH (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 GLN* 6.0 3.8 - - - +
266A TYR* 3.8 1.4 - - - -
267A GLY* 3.1 18.2 + - - -
269A ASN* 3.6 17.0 + - + +
341B HIS* 3.7 13.0 - - - +
886C LYS* 1.3 75.1 - - - +
888C DAL 1.3 60.8 + - - +
889C NH2 4.7 3.1 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand DAL 887C
and protein in PDB entry 2APH
(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 N I ASN 269A ND2 III 3.6 3.6
5 O II DAL 888C N I 2.3 0.3
5 O II GLY 267A N III 3.1 17.3
5 O II ASN 269A ND2 III 3.6 7.8
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand DAL 887C
in PDB entry 2APH (back
to top of page)
Total number of contacts is 31
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 N I LYS 886C C VI 1.3 56.6
1 N I LYS 886C CA VII 2.4 4.8
1 N I LYS 886C CB IV 3.1 3.6*
1 N I ASN 269A ND2 III 3.6 3.6
2 CA VI DAL 888C N I 2.4 4.0
2 CA VI LYS 886C C VI 2.5 3.4
2 CA VI LYS 886C O II 2.8 0.4
2 CA VI HIS 341B O II 3.7 6.7
2 CA VI HIS 341B OXT II 4.3 0.2
2 CA VI LYS 886C CG IV 5.0 0.2
3 CB IV DAL 888C N I 3.4 0.9*
3 CB IV HIS 341B O II 4.1 6.1*
3 CB IV NH2 889C N I 4.7 3.1*
3 CB IV ASN 269A ND2 III 4.8 2.2*
3 CB IV ASN 269A CB IV 5.6 2.9
3 CB IV GLN 261A NE2 III 6.0 3.8*
4 C VIII DAL 888C N I 1.3 43.7
4 C VIII DAL 888C CA VI 2.5 2.7
4 C VIII LYS 886C C VI 3.1 3.8
4 C VIII LYS 886C O II 3.1 0.4*
4 C VIII DAL 888C C VIII 3.2 1.8*
4 C VIII TYR 266A CD2 V 4.2 0.2
5 O II DAL 888C N I 2.3 0.3
5 O II DAL 888C CA VI 2.8 6.8
5 O II GLY 267A N III 3.1 17.3
5 O II DAL 888C C VIII 3.4 0.5*
5 O II LYS 886C C VI 3.4 1.9
5 O II ASN 269A ND2 III 3.6 7.8
5 O II TYR 266A CA VII 3.8 1.2
5 O II GLY 267A CA VI 4.0 0.9
5 O II ASN 269A CB IV 5.0 0.5*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand DAL 887C
in PDB entry 2APH (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 222
Actual value (Å2) 146
Normalised complementarity 0.66
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand DAL 887C
in PDB entry 2APH (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 | N
| I |
0.66 |
0.66
|
0.58 |
0.66
|
0.69 |
0.69
|
0.62 |
0.69
|
| 2 | CA
| VI |
0.66 |
0.59
|
0.66 |
0.56
|
0.66 |
0.66
|
0.66 |
0.59
|
| 3 | CB
| IV |
0.78 |
0.72
|
0.72 |
0.66
|
0.80 |
0.80
|
0.75 |
0.75
|
| 4 | C
| VIII |
0.68 |
0.66
|
0.68 |
0.28
|
0.68 |
0.68
|
0.68 |
0.66
|
| 5 | O
| II |
0.66 |
0.66
|
0.43 |
0.44
|
0.67 |
0.67
|
0.43 |
0.66
|
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 GMA 885
2. Oxygen ("hydroxy" or "carbonyl")
4 O1 8 O
3. Nitrogen ("hydrophilic")
1 N 9 N2
Ligand DAL 887
2. Oxygen ("hydroxy" or "carbonyl")
5 O
3. Nitrogen ("hydrophilic")
1 N
Ligand DAL 888
2. Oxygen ("hydroxy" or "carbonyl")
5 O
3. Nitrogen ("hydrophilic")
1 N
Ligand NH2 889
3. Nitrogen ("hydrophilic")
1 N
Ligand GMA 996
2. Oxygen ("hydroxy" or "carbonyl")
4 O1 8 O
3. Nitrogen ("hydrophilic")
1 N 9 N2
Ligand DAL 998
2. Oxygen ("hydroxy" or "carbonyl")
5 O
3. Nitrogen ("hydrophilic")
1 N
Ligand DAL 999
2. Oxygen ("hydroxy" or "carbonyl")
5 O
3. Nitrogen ("hydrophilic")
1 N
Ligand NH2 1000
3. Nitrogen ("hydrophilic")
1 N
Ligand AMU 901
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
12 O1 14 O4 16 O6 17 O7 18 O10
3. Nitrogen ("hydrophilic")
19 N2
Ligand AMU 1101
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
12 O1 14 O4 16 O6 17 O7 18 O10
3. Nitrogen ("hydrophilic")
19 N2
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il