Contacts of ligand Y1Z 201A in PDB entry 4NQN
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 Y1Z 201A
in PDB entry 4NQN (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
----------------------------------------------------------
42A HIS 3.4 27.4 - - - +
43A GLY* 3.9 12.8 - - - +
44A PHE* 3.4 64.1 + + + +
45A PHE* 3.5 36.6 - - + -
47A PHE 6.0 1.1 - - - -
49A VAL* 3.8 30.7 - - + +
52A ALA 5.0 2.2 - - - -
53A ILE* 3.3 104.2 - - + -
54A ALA* 3.9 21.8 - - + -
55A PRO* 5.8 0.7 - - + -
57A TYR* 4.5 8.4 + - - +
96A ALA* 3.8 14.7 - - + +
99A TYR* 3.9 14.1 - + - -
100A ASN* 2.9 46.1 + - - -
106A TYR* 3.0 66.3 + + + +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand Y1Z 201A
and protein in PDB entry 4NQN
(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
------------------------------------------------------------------------
3 OBC I TYR 106A OH I 3.0 16.6
33 NAH I PHE 44A O II 3.6 1.0
34 NAM I ASN 100A ND2 III 2.9 21.8
35 NAL I ASN 100A ND2 III 3.5 7.5
35 NAL I TYR 57A OH I 4.8 0.8
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand Y1Z 201A
in PDB entry 4NQN (back
to top of page)
Total number of contacts is 103
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 OBD I PHE 44A CE1 V 4.9 0.3
2 SBB VI PHE 44A CE1 V 4.4 0.7
3 OBC I TYR 106A OH I 3.0 16.6
3 OBC I PHE 44A CE1 V 3.7 7.4
3 OBC I PHE 44A CZ V 4.5 0.5
5 CBF V TYR 106A OH I 3.9 2.7
6 CBG V ILE 53A O II 3.7 11.4
7 CBH V ILE 53A O II 3.6 13.5
7 CBH V ILE 53A CG2 IV 3.9 1.3
7 CBH V ILE 53A CA VII 4.0 3.1
7 CBH V ALA 52A O II 5.0 2.2
8 CBI V ILE 53A CG2 IV 4.1 7.0
8 CBI V ILE 53A CG1 IV 4.1 6.7
8 CBI V ILE 53A CA VII 4.4 0.2
10 CL IV ILE 53A CG1 IV 5.0 1.0
11 NAU I PHE 44A CE1 V 3.8 3.6
12 CAS V PHE 44A CD1 V 3.5 3.1
15 CBA VI ILE 53A CD1 IV 4.2 12.1
18 CAX VIII HIS 42A O II 3.5 11.9*
18 CAX VIII GLY 43A O II 4.7 1.1*
18 CAX VIII GLY 43A CA VI 5.1 0.9
19 CAW VI HIS 42A O II 3.4 15.5
19 CAW VI GLY 43A O II 3.9 8.5
19 CAW VI GLY 43A C VI 4.1 0.7
19 CAW VI PHE 44A CD1 V 4.4 0.4
19 CAW VI PHE 44A CE1 V 4.9 0.2
20 CAQ V PHE 44A O II 4.0 6.3
20 CAQ V PHE 44A CA VII 4.0 1.3
20 CAQ V ILE 53A CD1 IV 4.2 7.2
20 CAQ V GLY 43A O II 4.4 1.6
20 CAQ V PHE 47A O II 6.1 0.7
21 CAP V PHE 44A O II 3.5 9.2
21 CAP V ILE 53A CG2 IV 3.9 7.4
21 CAP V ILE 53A CD1 IV 4.5 1.8
21 CAP V VAL 49A CG2 IV 4.9 5.8
21 CAP V VAL 49A CA VII 5.6 0.7
21 CAP V PHE 47A O II 6.0 0.4
22 CAO V ILE 53A CG2 IV 3.7 0.7
22 CAO V PHE 44A CD1 V 3.9 1.8
23 CAT V PHE 44A CD1 V 3.4 7.0
23 CAT V TYR 106A OH I 3.7 0.9
24 CAG V TYR 106A CE1 V 3.5 2.2
24 CAG V ILE 53A CG2 IV 4.0 0.9
24 CAG V VAL 49A CG2 IV 4.9 0.9
25 CAD V TYR 106A CZ V 3.4 2.9
25 CAD V ILE 53A CG2 IV 3.8 2.2
25 CAD V ALA 54A CB IV 4.6 0.2
26 CAC V ILE 53A CG2 IV 3.3 11.7
26 CAC V TYR 106A OH I 3.4 5.2
27 CAB V ILE 53A O II 3.6 15.3
27 CAB V TYR 106A CE2 V 3.7 6.1
27 CAB V TYR 106A OH I 3.8 1.3
27 CAB V ILE 53A CG2 IV 4.0 0.2
28 CAA V TYR 106A CE2 V 3.6 6.5
28 CAA V ALA 54A CB IV 3.9 8.5
28 CAA V TYR 106A CD2 V 4.0 0.2
28 CAA V ASN 100A OD1 II 4.3 1.3
28 CAA V TYR 99A CE2 V 4.3 4.5
28 CAA V ILE 53A O II 4.3 0.4
28 CAA V ALA 54A CA VII 4.4 0.9
28 CAA V TYR 99A OH I 4.9 0.7
28 CAA V PRO 55A CD IV 5.8 0.7
29 CAF V ASN 100A OD1 II 3.4 15.5
29 CAF V TYR 106A CD2 V 3.5 2.9
29 CAF V ALA 54A CB IV 3.9 8.1
29 CAF V TYR 99A CE2 V 3.9 3.4
30 CAE V TYR 106A CD2 V 3.6 2.5
30 CAE V ALA 54A CB IV 4.3 2.7
31 CAJ V TYR 106A CG V 3.6 4.7
31 CAJ V VAL 49A CG2 IV 4.6 3.1
31 CAJ V ALA 54A CB IV 4.9 1.3
32 NAI I TYR 106A CD1 V 3.7 0.4
32 NAI I VAL 49A CG2 IV 3.9 1.6*
33 NAH I PHE 44A O II 3.6 1.0
33 NAH I TYR 106A CD1 V 3.8 4.2
33 NAH I TYR 106A CE1 V 3.8 0.2
33 NAH I PHE 44A CB IV 3.8 1.0*
33 NAH I VAL 49A CG2 IV 4.2 0.8*
34 NAM I ASN 100A ND2 III 2.9 21.8
34 NAM I TYR 106A CB IV 3.8 0.2*
34 NAM I TYR 99A CD2 V 4.4 5.5
34 NAM I TYR 57A CE1 V 4.5 3.0
35 NAL I ASN 100A ND2 III 3.5 7.5
35 NAL I ALA 96A CB IV 3.8 12.5*
35 NAL I TYR 106A CB IV 4.1 1.4*
35 NAL I ALA 96A CA VII 4.2 2.0
35 NAL I VAL 49A CG2 IV 4.4 2.6*
35 NAL I TYR 57A CE1 V 4.6 4.0
35 NAL I TYR 57A OH I 4.8 0.8
36 CAK V VAL 49A CG2 IV 3.8 4.7
36 CAK V TYR 106A CD1 V 4.3 4.5
36 CAK V TYR 106A CB IV 4.4 0.7
37 CAN IV PHE 44A O II 3.4 17.3*
37 CAN IV PHE 45A CE1 V 3.5 28.7
37 CAN IV PHE 45A CD1 V 3.6 4.0
37 CAN IV VAL 49A CG2 IV 3.8 10.5
37 CAN IV PHE 44A C VI 3.9 2.5
37 CAN IV PHE 45A CZ V 3.9 2.0
37 CAN IV PHE 45A CE2 V 4.2 0.7
37 CAN IV PHE 45A CA VII 4.3 1.1
37 CAN IV PHE 44A CB IV 4.3 0.4
37 CAN IV ALA 96A CB IV 4.8 0.2
37 CAN IV TYR 57A OH I 5.6 0.7*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand Y1Z 201A
in PDB entry 4NQN (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 693
Actual value (Å2) 349
Normalised complementarity 0.50
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand Y1Z 201A
in PDB entry 4NQN (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 | OBD
| I |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 2 | SBB
| VI |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 3 | OBC
| I |
0.50 |
0.50
|
0.50 |
0.46
|
0.50 |
0.50
|
0.50 |
0.50
|
| 5 | CBF
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 6 | CBG
| V |
0.50 |
0.47
|
0.50 |
0.47
|
0.50 |
0.50
|
0.50 |
0.47
|
| 7 | CBH
| V |
0.50 |
0.45
|
0.49 |
0.46
|
0.50 |
0.50
|
0.49 |
0.46
|
| 8 | CBI
| V |
0.46 |
0.46
|
0.46 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 10 | CL
| IV |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 11 | NAU
| I |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 12 | CAS
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 15 | CBA
| VI |
0.47 |
0.47
|
0.47 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 18 | CAX
| VIII |
0.54 |
0.50
|
0.54 |
0.50
|
0.54 |
0.54
|
0.54 |
0.50
|
| 19 | CAW
| VI |
0.50 |
0.43
|
0.50 |
0.43
|
0.50 |
0.50
|
0.50 |
0.43
|
| 20 | CAQ
| V |
0.48 |
0.46
|
0.48 |
0.48
|
0.50 |
0.50
|
0.50 |
0.48
|
| 21 | CAP
| V |
0.46 |
0.43
|
0.46 |
0.48
|
0.50 |
0.50
|
0.50 |
0.48
|
| 22 | CAO
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 23 | CAT
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 24 | CAG
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 25 | CAD
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 26 | CAC
| V |
0.47 |
0.47
|
0.47 |
0.49
|
0.50 |
0.50
|
0.50 |
0.50
|
| 27 | CAB
| V |
0.50 |
0.46
|
0.50 |
0.46
|
0.50 |
0.50
|
0.50 |
0.46
|
| 28 | CAA
| V |
0.48 |
0.47
|
0.47 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 29 | CAF
| V |
0.48 |
0.44
|
0.48 |
0.46
|
0.50 |
0.50
|
0.50 |
0.46
|
| 30 | CAE
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 31 | CAJ
| V |
0.49 |
0.49
|
0.49 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 32 | NAI
| I |
0.50 |
0.50
|
0.50 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 33 | NAH
| I |
0.50 |
0.50
|
0.50 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 34 | NAM
| I |
0.50 |
0.50
|
0.44 |
0.44
|
0.50 |
0.50
|
0.44 |
0.50
|
| 35 | NAL
| I |
0.50 |
0.50
|
0.48 |
0.53
|
0.55 |
0.55
|
0.52 |
0.55
|
| 36 | CAK
| V |
0.49 |
0.49
|
0.49 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 37 | CAN
| IV |
0.52 |
0.47
|
0.52 |
0.50
|
0.56 |
0.56
|
0.55 |
0.51
|
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 Y1Z 201
1. Carbon (in rings)
4 CBE 5 CBF 6 CBG 7 CBH 8 CBI 9 CBJ
12 CAS 13 CAR 20 CAQ 21 CAP 22 CAO 23 CAT
15 CBA 16 CAZ 18 CAX 19 CAW 24 CAG 25 CAD
30 CAE 31 CAJ 25 CAD 26 CAC 27 CAB 28 CAA
29 CAF 30 CAE 31 CAJ 36 CAK
3. Nitrogen ("hydrophilic")
11 NAU 14 NAV 32 NAI 33 NAH 34 NAM 35 NAL
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il