Contacts of ligand AX7 290A in PDB entry 3KQS
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 AX7 290A
in PDB entry 3KQS (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
----------------------------------------------------------
35A TYR* 2.7 33.3 + - - -
39A ASN* 3.5 39.1 + - + +
40A TYR* 2.9 24.5 + + - -
44A ARG* 3.4 36.1 - - - -
53A VAL* 3.6 42.8 - - + -
57A LYS* 3.3 21.8 - - - -
182A PHE* 3.5 48.3 + + - +
216A ALA* 5.4 2.2 - - - +
219A GLU* 5.0 5.7 + - - -
222A TYR* 5.2 7.5 - - - +
258A MET* 4.2 19.3 - - + -
267A ASP* 4.3 6.9 + - - -
269A VAL* 4.5 7.6 - - + +
272A VAL* 4.4 1.6 - - + -
2001A SAH 4.6 1.8 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand AX7 290A
and protein in PDB entry 3KQS
(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 NAF I TYR 40A OH I 2.9 20.0
1 NAF I ASN 39A OD1 II 3.7 1.8
8 NAG I ASN 39A OD1 II 3.5 3.8
8 NAG I ASP 267A OD2 II 4.3 6.9
8 NAG I GLU 219A OE1 II 5.0 5.3
8 NAG I GLU 219A OE2 II 5.5 0.4
10 NAA I TYR 35A OH I 2.7 24.0
10 NAA I PHE 182A O II 4.9 0.4
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand AX7 290A
in PDB entry 3KQS (back
to top of page)
Total number of contacts is 66
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 NAF I TYR 40A OH I 2.9 20.0
1 NAF I PHE 182A CE1 V 3.5 2.4
1 NAF I TYR 40A CZ V 3.5 3.2
1 NAF I ASN 39A OD1 II 3.7 1.8
1 NAF I ASN 39A CB IV 3.8 0.4*
2 CAI V PHE 182A CZ V 3.6 4.0
2 CAI V ASN 39A OD1 II 3.7 3.8
2 CAI V ASN 39A CB IV 3.9 0.2
3 CAD V LYS 57A NZ III 3.3 20.4
3 CAD V ASN 39A O II 3.9 15.0
3 CAD V PHE 182A CZ V 4.1 0.7
3 CAD V TYR 40A CE2 V 4.1 1.3
3 CAD V ASN 39A CB IV 4.2 0.2
4 CAB V VAL 53A CG1 IV 3.6 22.4
4 CAB V VAL 53A CG2 IV 3.8 6.1
4 CAB V LYS 57A NZ III 3.9 1.3
4 CAB V ARG 44A CD VII 4.2 6.3
4 CAB V ASN 39A O II 4.3 2.5
4 CAB V PHE 182A CZ V 4.6 0.4
5 CAC V ARG 44A NH1 III 3.9 7.4
5 CAC V ARG 44A CD VII 4.0 5.4
5 CAC V VAL 53A CG2 IV 4.0 12.3
5 CAC V VAL 53A CG1 IV 4.1 2.0
5 CAC V ARG 44A CZ VI 4.1 1.6
5 CAC V ARG 44A NE III 4.2 0.2
5 CAC V MET 258A SD VIII 4.2 9.0
5 CAC V MET 258A CE IV 4.2 1.1
5 CAC V VAL 272A CG2 IV 4.4 1.1
6 CAE V ARG 44A NH1 III 3.4 13.9
6 CAE V ARG 44A CZ VI 4.0 1.3
6 CAE V PHE 182A CZ V 4.4 3.8
6 CAE V PHE 182A CE2 V 4.4 1.8
6 CAE V MET 258A CE IV 4.4 9.2
6 CAE V VAL 269A CG1 IV 4.5 6.3
6 CAE V VAL 272A CG2 IV 4.5 0.4
6 CAE V VAL 269A CG2 IV 4.9 1.1
7 CAJ V ASN 39A OD1 II 3.6 4.3
7 CAJ V PHE 182A CZ V 3.8 3.6
8 NAG I ASN 39A OD1 II 3.5 3.8
8 NAG I PHE 182A CE2 V 3.7 6.3
8 NAG I PHE 182A CD2 V 3.8 1.0
8 NAG I ASP 267A OD2 II 4.3 6.9
8 NAG I GLU 219A OE1 II 5.0 5.3
8 NAG I ALA 216A CB IV 5.4 2.2*
8 NAG I GLU 219A OE2 II 5.5 0.4
8 NAG I VAL 269A CG2 IV 5.7 0.2*
8 NAG I TYR 222A CB IV 6.4 0.2*
9 CAH V PHE 182A CG V 3.6 7.4
9 CAH V TYR 35A OH I 3.7 0.7
9 CAH V ASN 39A OD1 II 3.7 6.7
9 CAH V ASN 39A CG VI 3.9 0.2
10 NAA I TYR 35A OH I 2.7 24.0
10 NAA I PHE 182A CG V 3.5 12.1
10 NAA I PHE 182A CB IV 3.5 4.0*
10 NAA I TYR 35A CZ V 3.6 4.2
10 NAA I TYR 35A CE1 V 3.6 4.6
10 NAA I PHE 182A CD2 V 3.9 0.4
10 NAA I ASN 39A CG VI 4.5 0.2
10 NAA I SAH 2001A CG IV 4.6 0.4*
10 NAA I SAH 2001A SD VI 4.6 1.4
10 NAA I PHE 182A O II 4.9 0.4
10 NAA I TYR 222A CE1 V 5.2 3.6
10 NAA I TYR 222A CD1 V 5.3 2.2
10 NAA I TYR 222A CZ V 5.5 0.8
10 NAA I TYR 222A CG V 5.7 0.4
10 NAA I TYR 222A CD2 V 6.0 0.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand AX7 290A
in PDB entry 3KQS (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 305
Actual value (Å2) 283
Normalised complementarity 0.93
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand AX7 290A
in PDB entry 3KQS (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 | NAF
| I |
0.93 |
0.92
|
0.93 |
0.79
|
0.93 |
0.93
|
0.93 |
0.92
|
| 2 | CAI
| V |
0.93 |
0.90
|
0.93 |
0.91
|
0.93 |
0.93
|
0.93 |
0.91
|
| 3 | CAD
| V |
0.93 |
0.83
|
0.80 |
0.70
|
0.93 |
0.93
|
0.80 |
0.83
|
| 4 | CAB
| V |
0.74 |
0.73
|
0.69 |
0.91
|
0.93 |
0.93
|
0.88 |
0.91
|
| 5 | CAC
| V |
0.82 |
0.76
|
0.74 |
0.88
|
0.93 |
0.93
|
0.85 |
0.87
|
| 6 | CAE
| V |
0.82 |
0.82
|
0.73 |
0.84
|
0.93 |
0.93
|
0.84 |
0.93
|
| 7 | CAJ
| V |
0.93 |
0.90
|
0.93 |
0.90
|
0.93 |
0.93
|
0.93 |
0.90
|
| 8 | NAG
| I |
0.93 |
0.82
|
0.93 |
0.84
|
0.95 |
0.95
|
0.95 |
0.84
|
| 9 | CAH
| V |
0.93 |
0.89
|
0.93 |
0.88
|
0.93 |
0.93
|
0.93 |
0.89
|
| 10 | NAA
| I |
0.93 |
0.93
|
0.93 |
0.80
|
0.96 |
0.96
|
0.96 |
0.96
|
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 SAH 2001
1. Carbon (in rings)
10 C4' 16 C1' 14 C2' 12 C3' 18 C8 20 C5
26 C4 20 C5 21 C6 24 C2 26 C4
2. Oxygen ("hydroxy" or "carbonyl")
7 O 8 OXT 13 O3' 15 O2'
3. Nitrogen ("hydrophilic")
1 N 17 N9 19 N7 22 N6 23 N1 25 N3
Ligand AX7 290
1. Carbon (in rings)
2 CAI 7 CAJ 9 CAH 2 CAI 3 CAD 4 CAB
5 CAC 6 CAE 7 CAJ
3. Nitrogen ("hydrophilic")
1 NAF 8 NAG 10 NAA
Ligand SAH 2002
1. Carbon (in rings)
10 C4' 16 C1' 14 C2' 12 C3' 18 C8 20 C5
26 C4 20 C5 21 C6 24 C2 26 C4
2. Oxygen ("hydroxy" or "carbonyl")
7 O 8 OXT 13 O3' 15 O2'
3. Nitrogen ("hydrophilic")
1 N 17 N9 19 N7 22 N6 23 N1 25 N3
Ligand AX7 290
1. Carbon (in rings)
2 CAI 7 CAJ 9 CAH 2 CAI 3 CAD 4 CAB
5 CAC 6 CAE 7 CAJ
3. Nitrogen ("hydrophilic")
1 NAF 8 NAG 10 NAA
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il