Contacts of ligand P341001A in PDB entry 1XK9
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 P341001A
in PDB entry 1XK9 (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
----------------------------------------------------------
440A HIS* 3.0 30.8 - + - -
441A GLY 2.4 48.9 + - - -
442A THR* 4.8 5.8 - - - -
443A PHE* 6.0 4.9 - - - -
470A TYR* 3.3 51.1 - + + -
471A ILE 3.6 26.2 - - - -
472A ALA* 4.2 0.2 - - + -
477A LEU* 3.9 24.9 - - + -
478A ALA* 3.2 18.2 - - - +
481A TYR* 3.2 84.9 - + + +
483A GLN 5.5 0.7 - - - -
485A GLN* 2.8 55.3 - - - -
553A GLU* 3.9 22.4 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand P341001A
and protein in PDB entry 1XK9
(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
------------------------------------------------------------------------
18 OAD II GLY 441A N III 2.4 23.6
19 NAN I GLY 441A O II 2.5 13.5
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand P341001A
in PDB entry 1XK9 (back
to top of page)
Total number of contacts is 81
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 CAA VI TYR 481A CD1 V 3.2 23.6
1 CAA VI GLN 485A NE2 III 3.3 10.5
1 CAA VI GLN 485A CD VI 3.4 1.1
1 CAA VI TYR 481A CE1 V 3.5 4.3
1 CAA VI GLN 485A OE1 II 3.6 1.8
2 N I GLN 485A CD VI 2.8 7.7
3 CAB VI GLN 485A CG IV 2.8 25.1
3 CAB VI GLN 485A CD VI 3.0 0.9
3 CAB VI GLN 485A NE2 III 3.2 2.2
3 CAB VI TYR 481A O II 5.2 2.7
3 CAB VI GLN 483A O II 5.5 0.7
3 CAB VI PHE 443A CD1 V 6.0 4.7
3 CAB VI PHE 443A CE1 V 6.3 0.2
3 CAB VI THR 442A CA VII 6.5 0.4
4 CA VI GLN 485A OE1 II 4.0 3.6
4 CA VI GLN 485A CD VI 4.0 0.4
4 CA VI GLN 485A CG IV 4.1 1.8
7 NAM I TYR 481A CE1 V 4.5 0.4
9 CAK V TYR 481A CD1 V 3.4 7.6
9 CAK V TYR 481A CE1 V 3.5 2.0
9 CAK V TYR 470A CB IV 4.4 5.2
9 CAK V TYR 470A CG V 4.9 2.2
9 CAK V TYR 470A CD2 V 5.1 0.7
9 CAK V TYR 470A CD1 V 5.6 0.2
10 CAU V TYR 481A CG V 3.4 3.1
10 CAU V TYR 470A CB IV 4.0 3.1
11 CAT V TYR 481A CD2 V 3.4 2.2
11 CAT V TYR 470A CB IV 3.5 3.4
12 CAI V TYR 481A CE2 V 3.4 8.7
12 CAI V TYR 470A CB IV 3.5 8.5
12 CAI V TYR 481A CZ V 3.5 2.7
12 CAI V TYR 470A CD2 V 3.9 4.5
12 CAI V TYR 481A OH I 3.9 0.9
13 CAF V TYR 481A CE2 V 3.7 6.1
13 CAF V GLU 553A OE1 II 3.9 20.4
13 CAF V TYR 470A CB IV 3.9 4.9
13 CAF V TYR 470A CD2 V 4.1 2.0
13 CAF V TYR 481A CZ V 4.2 0.4
13 CAF V GLU 553A CB IV 4.3 1.1
13 CAF V TYR 481A OH I 4.3 1.1
13 CAF V LEU 477A CG IV 4.5 2.2
13 CAF V LEU 477A CD1 IV 5.0 0.2
14 CAE V ILE 471A O II 3.6 15.3
14 CAE V LEU 477A CG IV 3.9 20.0
14 CAE V ILE 471A C VI 4.0 0.2
14 CAE V LEU 477A CD2 IV 4.1 2.5
14 CAE V TYR 481A CE2 V 4.1 0.4
14 CAE V GLU 553A CB IV 4.3 0.9
14 CAE V ILE 471A N III 4.3 0.4
15 CAH V TYR 470A O II 3.7 6.3
15 CAH V ILE 471A C VI 3.8 10.3
15 CAH V ALA 478A CA VII 3.8 13.7
15 CAH V TYR 481A CD2 V 4.1 0.2
15 CAH V ALA 472A CB IV 4.2 0.2
16 CAS V TYR 470A O II 3.4 2.5
16 CAS V TYR 481A CD2 V 3.5 3.1
17 CAQ V TYR 470A O II 3.3 7.4
17 CAQ V GLY 441A N III 3.3 1.3
17 CAQ V HIS 440A ND1 I 3.6 0.2
17 CAQ V TYR 481A CB IV 4.0 4.5
17 CAQ V TYR 481A CD2 V 4.0 0.7
17 CAQ V ALA 478A CA VII 4.1 0.7
18 OAD II GLY 441A N III 2.4 23.6
18 OAD II HIS 440A CA VII 3.0 10.2
18 OAD II ALA 478A CB IV 3.2 3.8*
19 NAN I GLY 441A O II 2.5 13.5
19 NAN I HIS 440A CE1 V 3.3 5.5
19 NAN I TYR 481A CB IV 3.5 0.6*
20 CAR V GLY 441A O II 3.3 0.2
20 CAR V TYR 481A CB IV 3.4 3.4
20 CAR V HIS 440A CE1 V 3.8 3.6
20 CAR V TYR 470A CB IV 4.8 0.2
21 CAJ V GLY 441A O II 3.2 10.3
21 CAJ V TYR 481A CB IV 3.8 4.9
21 CAJ V HIS 440A CE1 V 3.9 10.3
21 CAJ V HIS 440A NE2 I 4.4 0.9
21 CAJ V TYR 481A O II 4.7 1.1
21 CAJ V THR 442A CA VII 4.8 2.9
21 CAJ V THR 442A CB VI 4.8 1.3
21 CAJ V THR 442A OG1 I 5.0 0.7
22 CAG V THR 442A OG1 I 5.6 0.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand P341001A
in PDB entry 1XK9 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 506
Actual value (Å2) 365
Normalised complementarity 0.72
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand P341001A
in PDB entry 1XK9 (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 | CAA
| VI |
0.72 |
0.71
|
0.68 |
0.67
|
0.72 |
0.72
|
0.68 |
0.71
|
| 2 | N
| I |
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 3 | CAB
| VI |
0.62 |
0.61
|
0.61 |
0.70
|
0.72 |
0.72
|
0.71 |
0.71
|
| 4 | CA
| VI |
0.71 |
0.70
|
0.71 |
0.71
|
0.72 |
0.72
|
0.72 |
0.71
|
| 7 | NAM
| I |
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 9 | CAK
| V |
0.70 |
0.70
|
0.70 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 10 | CAU
| V |
0.71 |
0.71
|
0.71 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 11 | CAT
| V |
0.71 |
0.71
|
0.71 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 12 | CAI
| V |
0.69 |
0.69
|
0.69 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 13 | CAF
| V |
0.69 |
0.61
|
0.69 |
0.64
|
0.72 |
0.72
|
0.72 |
0.64
|
| 14 | CAE
| V |
0.63 |
0.57
|
0.63 |
0.66
|
0.72 |
0.72
|
0.72 |
0.66
|
| 15 | CAH
| V |
0.72 |
0.70
|
0.67 |
0.70
|
0.72 |
0.72
|
0.67 |
0.70
|
| 16 | CAS
| V |
0.72 |
0.71
|
0.72 |
0.71
|
0.72 |
0.72
|
0.72 |
0.71
|
| 17 | CAQ
| V |
0.70 |
0.68
|
0.70 |
0.69
|
0.72 |
0.72
|
0.71 |
0.69
|
| 18 | OAD
| II |
0.72 |
0.72
|
0.59 |
0.64
|
0.74 |
0.74
|
0.60 |
0.74
|
| 19 | NAN
| I |
0.72 |
0.67
|
0.72 |
0.67
|
0.72 |
0.72
|
0.72 |
0.67
|
| 20 | CAR
| V |
0.71 |
0.71
|
0.71 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 21 | CAJ
| V |
0.70 |
0.66
|
0.69 |
0.67
|
0.72 |
0.72
|
0.71 |
0.68
|
| 22 | CAG
| V |
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
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 P34 1001
1. Carbon (in rings)
8 CAP 9 CAK 10 CAU 20 CAR 21 CAJ 22 CAG
10 CAU 11 CAT 16 CAS 17 CAQ 20 CAR 11 CAT
12 CAI 13 CAF 14 CAE 15 CAH 16 CAS
2. Oxygen ("hydroxy" or "carbonyl")
6 O 18 OAD
3. Nitrogen ("hydrophilic")
2 N 7 NAM 19 NAN
Ligand P34 2001
1. Carbon (in rings)
8 CAP 9 CAK 10 CAU 20 CAR 21 CAJ 22 CAG
10 CAU 11 CAT 16 CAS 17 CAQ 20 CAR 11 CAT
12 CAI 13 CAF 14 CAE 15 CAH 16 CAS
2. Oxygen ("hydroxy" or "carbonyl")
6 O 18 OAD
3. Nitrogen ("hydrophilic")
2 N 7 NAM 19 NAN
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il