Contacts of ligand FPP 6C in PDB entry 1KZR
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 FPP 6C
in PDB entry 1KZR (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
----------------------------------------------------------
1001 ZN 3.5 9.9 - - - -
1002 MG 2.6 26.2 - - - -
164A LYS* 3.0 34.3 + - - +
166A TYR* 3.6 24.0 - - - +
102B TRP* 3.9 34.1 - - + -
151B ALA* 4.6 7.0 - - + -
154B TYR* 4.7 1.8 - - + -
202B ARG* 3.4 23.1 - - + +
205B TYR* 4.0 25.1 - - + -
206B CYS* 3.9 23.1 - - - -
248B HIS* 3.0 36.3 + - + +
250B GLY* 3.4 37.7 - - - +
251B TYR* 4.3 19.5 - - + -
254B CYS* 3.6 16.6 - - - -
290B GLY* 4.4 3.5 + - - -
291B ARG* 2.6 39.8 + - - +
294B LYS* 2.6 37.4 + - - +
295B LEU 4.8 5.5 + - - -
297B ASP* 3.5 4.1 + - - +
299B CYS* 3.7 2.2 - - - -
300B TYR* 2.6 50.4 + - + +
303B TRP* 4.0 32.1 - - + +
361B TYR* 3.4 15.5 - - - +
1C ALA 4.8 3.2 + - - -
2C CYS* 1.9 56.6 - - + -
3C VAL 3.7 21.5 - - - +
4C ILE* 3.2 51.1 - - + +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand FPP 6C
and protein in PDB entry 1KZR
(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
------------------------------------------------------------------------
2 O1 II TYR 300B OH I 3.0 4.9
18 O1A I LYS 164A NZ III 3.0 20.1
18 O1A I ALA 1C O II 4.8 2.8
19 O2A I LYS 164A NZ III 4.1 3.3
20 O3A II TYR 300B OH I 3.8 0.3
20 O3A II LYS 164A NZ III 4.1 3.1
20 O3A II ARG 291B NH2 III 4.2 3.5
20 O3A II HIS 248B NE2 I 4.4 1.2
22 O1B I ARG 291B NE III 2.6 31.0
22 O1B I HIS 248B NE2 I 3.0 14.0
22 O1B I ARG 291B NH2 III 3.1 1.4
23 O2B I TYR 300B OH I 2.6 21.1
23 O2B I GLY 290B N III 4.5 1.0
23 O2B I LEU 295B O II 4.8 4.3
23 O2B I ASP 297B OD2 II 5.0 0.2
24 O3B I LYS 294B NZ III 2.6 27.4
24 O3B I LYS 164A NZ III 4.7 0.2
24 O3B I LEU 295B N III 5.2 1.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand FPP 6C
in PDB entry 1KZR (back
to top of page)
Total number of contacts is 113
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 C1 VIII CYS 2C SG VI 1.9 30.7
1 C1 VIII CYS 2C CB IV 3.0 1.6
1 C1 VIII ZN 1001 ZN VI 3.5 3.1
1 C1 VIII ASP 297B OD2 II 3.5 3.4*
1 C1 VIII CYS 2C CA VII 3.6 0.7
1 C1 VIII ALA 1C C VI 5.2 0.2
2 O1 II TYR 300B OH I 3.0 4.9
3 C2 IV CYS 2C SG VI 2.4 13.0
3 C2 IV CYS 2C CB IV 3.0 0.4
3 C2 IV TYR 300B OH I 3.4 7.4*
3 C2 IV ZN 1001 ZN VI 3.5 6.7
3 C2 IV CYS 299B SG VI 3.7 2.2
4 C3 IV CYS 2C CB IV 3.4 2.5
4 C3 IV TYR 300B OH I 3.7 0.7*
5 C4 IV VAL 3C O II 3.7 17.3*
5 C4 IV CYS 2C CB IV 3.8 4.3
5 C4 IV VAL 3C N III 3.9 3.1*
5 C4 IV TYR 300B OH I 4.4 0.4*
5 C4 IV HIS 248B CE1 V 5.3 1.1
5 C4 IV HIS 248B NE2 I 5.5 0.2*
6 C5 IV TYR 361B OH I 3.4 15.5*
6 C5 IV TYR 300B OH I 4.1 1.1*
6 C5 IV ILE 4C CG2 IV 4.1 7.4
6 C5 IV TYR 300B CE2 V 4.5 2.2
7 C6 IV HIS 248B CE1 V 3.8 18.4
7 C6 IV TYR 300B OH I 4.2 0.2*
7 C6 IV TYR 300B CE2 V 4.4 0.7
8 C7 IV GLY 250B CA VI 3.7 10.1
8 C7 IV ILE 4C CG2 IV 4.2 2.9
8 C7 IV TRP 303B NE1 III 4.3 8.5*
8 C7 IV GLY 250B N III 4.4 0.2*
8 C7 IV TRP 303B CD1 V 4.5 0.2
9 C8 IV GLY 250B CA VI 3.6 2.9
9 C8 IV ILE 4C CG2 IV 4.3 0.7
10 C10 IV TYR 166A OH I 3.6 24.0*
10 C10 IV TYR 251B CE2 V 4.3 14.4
10 C10 IV TYR 251B CZ V 4.3 2.7
10 C10 IV GLY 250B CA VI 4.4 2.7
10 C10 IV ARG 202B CD VII 4.4 0.4
10 C10 IV ILE 4C CA VII 4.8 5.4
10 C10 IV VAL 3C O II 4.8 1.1*
10 C10 IV TYR 251B CE1 V 4.8 2.2
10 C10 IV TYR 251B CD1 V 5.1 0.2
10 C10 IV HIS 248B ND1 I 5.2 0.9*
10 C10 IV HIS 248B CE1 V 5.3 0.4
11 C9 IV GLY 250B CA VI 3.4 17.0
11 C9 IV GLY 250B C VI 3.7 4.0
11 C9 IV GLY 250B O II 3.8 0.7*
11 C9 IV TRP 303B CZ2 V 4.5 6.3
11 C9 IV TRP 303B CE2 V 4.5 0.2
11 C9 IV TRP 303B CH2 V 4.6 0.2
11 C9 IV CYS 254B SG VI 4.6 0.7
12 C11 IV ARG 202B CD VII 3.8 4.9
12 C11 IV ARG 202B CG IV 3.9 0.2
12 C11 IV ILE 4C CB IV 3.9 8.7
12 C11 IV ILE 4C CG2 IV 4.0 1.1
12 C11 IV TRP 303B CH2 V 4.6 0.2
13 C12 IV CYS 254B SG VI 3.6 12.8
13 C12 IV ARG 202B CG IV 3.9 0.2
13 C12 IV TRP 303B CH2 V 4.0 11.9
13 C12 IV TRP 303B CZ2 V 4.4 0.2
14 C13 IV ARG 202B CG IV 3.8 2.5
14 C13 IV TRP 102B CH2 V 4.4 2.5
15 C14 IV ILE 4C O II 3.2 21.8*
15 C14 IV ARG 202B CD VII 3.4 11.0
15 C14 IV ARG 202B CG IV 3.7 0.4
15 C14 IV TRP 102B CZ2 V 3.9 17.5
15 C14 IV ILE 4C CB IV 4.0 3.1
15 C14 IV ARG 202B CB IV 4.2 1.6
15 C14 IV ARG 202B NH1 III 4.5 1.3*
15 C14 IV ALA 151B CB IV 4.6 7.0
15 C14 IV CYS 206B SG VI 4.8 0.4
16 C15 IV CYS 206B SG VI 3.9 22.7
16 C15 IV TYR 205B CD2 V 4.0 21.1
16 C15 IV CYS 254B SG VI 4.0 3.1
16 C15 IV TRP 102B CH2 V 4.0 14.1
16 C15 IV TYR 205B CE2 V 4.2 4.0
16 C15 IV ARG 202B CG IV 4.6 0.4
16 C15 IV TRP 303B CH2 V 4.7 4.3
16 C15 IV TYR 154B CD2 V 4.7 1.6
16 C15 IV TYR 154B CE2 V 4.8 0.2
18 O1A I LYS 164A NZ III 3.0 20.1
18 O1A I LYS 164A CE VII 3.8 2.8
18 O1A I LYS 164A CD IV 3.9 4.5*
18 O1A I CYS 2C CA VII 4.7 3.5
18 O1A I ALA 1C O II 4.8 2.8
18 O1A I ALA 1C C VI 5.5 0.2
19 O2A I MG 1002 MG VI 2.6 26.2
19 O2A I LYS 164A NZ III 4.1 3.3
20 O3A II TYR 300B OH I 3.8 0.3
20 O3A II LYS 164A NZ III 4.1 3.1
20 O3A II ARG 291B NH2 III 4.2 3.5
20 O3A II HIS 248B NE2 I 4.4 1.2
20 O3A II LYS 164A CE VII 4.9 0.3
22 O1B I ARG 291B NE III 2.6 31.0
22 O1B I HIS 248B NE2 I 3.0 14.0
22 O1B I ARG 291B NH2 III 3.1 1.4
22 O1B I ARG 291B CD VII 3.6 1.2
22 O1B I ARG 291B CG IV 3.6 2.8*
23 O2B I TYR 300B OH I 2.6 21.1
23 O2B I TYR 300B CE1 V 3.4 11.3
23 O2B I GLY 290B CA VI 4.4 2.4
23 O2B I GLY 290B N III 4.5 1.0
23 O2B I LEU 295B O II 4.8 4.3
23 O2B I ASP 297B OD2 II 5.0 0.2
23 O2B I LYS 294B CB IV 5.2 0.9*
23 O2B I ASP 297B CB IV 5.3 0.5*
24 O3B I LYS 294B NZ III 2.6 27.4
24 O3B I LYS 294B CE VII 3.0 6.1
24 O3B I LYS 294B CD IV 3.4 0.5*
24 O3B I LYS 294B CB IV 4.2 2.6*
24 O3B I LYS 164A NZ III 4.7 0.2
24 O3B I LEU 295B N III 5.2 1.2
------------------------------------------------------------------------
Table V
Complementarity values for the ligand FPP 6C
in PDB entry 1KZR (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 655
Actual value (Å2) 402
Normalised complementarity 0.61
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand FPP 6C
in PDB entry 1KZR (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 | C1
| VIII |
0.62 |
0.61
|
0.62 |
0.61
|
0.62 |
0.62
|
0.62 |
0.61
|
| 2 | O1
| II |
0.61 |
0.61
|
0.61 |
0.60
|
0.61 |
0.61
|
0.61 |
0.61
|
| 3 | C2
| IV |
0.64 |
0.64
|
0.64 |
0.61
|
0.64 |
0.64
|
0.64 |
0.64
|
| 4 | C3
| IV |
0.61 |
0.61
|
0.61 |
0.61
|
0.62 |
0.62
|
0.62 |
0.62
|
| 5 | C4
| IV |
0.67 |
0.61
|
0.66 |
0.61
|
0.68 |
0.68
|
0.67 |
0.63
|
| 6 | C5
| IV |
0.64 |
0.64
|
0.64 |
0.61
|
0.66 |
0.66
|
0.66 |
0.66
|
| 7 | C6
| IV |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 8 | C7
| IV |
0.63 |
0.63
|
0.60 |
0.61
|
0.64 |
0.64
|
0.61 |
0.64
|
| 9 | C8
| IV |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 10 | C10
| IV |
0.69 |
0.69
|
0.68 |
0.61
|
0.69 |
0.69
|
0.68 |
0.69
|
| 11 | C9
| IV |
0.62 |
0.61
|
0.62 |
0.61
|
0.62 |
0.62
|
0.62 |
0.61
|
| 12 | C11
| IV |
0.58 |
0.58
|
0.57 |
0.61
|
0.61 |
0.61
|
0.60 |
0.61
|
| 13 | C12
| IV |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 14 | C13
| IV |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 15 | C14
| IV |
0.65 |
0.58
|
0.61 |
0.61
|
0.68 |
0.68
|
0.65 |
0.62
|
| 16 | C15
| IV |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 18 | O1A
| I |
0.61 |
0.61
|
0.53 |
0.56
|
0.63 |
0.63
|
0.55 |
0.62
|
| 19 | O2A
| I |
0.61 |
0.61
|
0.60 |
0.60
|
0.61 |
0.61
|
0.60 |
0.61
|
| 20 | O3A
| II |
0.61 |
0.61
|
0.59 |
0.59
|
0.61 |
0.61
|
0.59 |
0.61
|
| 22 | O1B
| I |
0.61 |
0.61
|
0.51 |
0.48
|
0.62 |
0.62
|
0.52 |
0.62
|
| 23 | O2B
| I |
0.61 |
0.60
|
0.61 |
0.54
|
0.62 |
0.62
|
0.61 |
0.60
|
| 24 | O3B
| I |
0.61 |
0.61
|
0.51 |
0.54
|
0.62 |
0.62
|
0.52 |
0.62
|
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:
NONE.
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il