Contacts of ligand F3S 401B in PDB entry 5CH7
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 F3S 401B
in PDB entry 5CH7 (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
----------------------------------------------------------
149B CYS* 2.5 38.1 - - - -
150B PRO* 4.0 3.8 - - - -
151B ASN* 3.3 24.7 - - - -
153B ALA* 4.2 3.8 - - - -
154B ILE* 3.8 31.0 - - - -
165B ILE* 3.8 12.3 - - - -
170B CYS* 2.3 25.1 - - - -
171B LYS 3.3 26.2 - - - -
172B GLY* 3.6 10.3 - - - -
173B ALA* 3.5 27.8 - - - -
174B GLN* 3.2 35.9 - - - -
175B ALA* 3.4 16.2 - - - -
176B CYS* 2.5 40.1 - - - -
177B VAL* 5.8 0.4 - - - -
187B PHE* 4.8 0.9 - - - -
194B ALA* 3.6 21.8 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand F3S 401B
and protein in PDB entry 5CH7
(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
------------------------------------------------------------------------
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand F3S 401B
in PDB entry 5CH7 (back
to top of page)
Total number of contacts is 40
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 FE1 VI CYS 170B SG VI 2.3 12.3
2 FE3 VI CYS 149B SG VI 2.5 11.4
3 FE4 VI CYS 176B SG VI 2.5 13.0
4 S1 VI LYS 171B N III 3.3 26.2
4 S1 VI ASN 151B ND2 III 3.3 24.2
4 S1 VI ALA 173B N III 3.5 17.5
4 S1 VI CYS 170B SG VI 3.8 0.4
4 S1 VI CYS 149B SG VI 3.9 3.6
4 S1 VI ALA 173B CB IV 3.9 0.4
4 S1 VI CYS 170B CA VII 4.0 3.8
4 S1 VI ASN 151B CG VI 4.3 0.2
4 S1 VI ASN 151B CB IV 4.3 0.2
5 S2 VI GLN 174B N III 3.2 26.9
5 S2 VI ALA 173B N III 3.5 9.6
5 S2 VI GLY 172B CA VI 3.6 10.1
5 S2 VI ALA 194B CB IV 3.6 19.3
5 S2 VI GLY 172B C VI 3.7 0.2
5 S2 VI CYS 170B SG VI 3.7 1.6
5 S2 VI GLN 174B CA VII 3.7 4.5
5 S2 VI ALA 194B N III 3.9 2.0
5 S2 VI GLN 174B CG IV 4.4 3.1
5 S2 VI PHE 187B CD1 V 4.8 0.9
5 S2 VI VAL 177B CG2 IV 5.8 0.4
6 S3 VI ILE 154B CD1 IV 3.8 24.7
6 S3 VI CYS 170B SG VI 3.8 7.0
6 S3 VI ILE 154B CG1 IV 3.8 6.3
6 S3 VI ILE 165B CG2 IV 3.8 12.3
6 S3 VI CYS 149B SG VI 4.0 2.0
6 S3 VI CYS 176B SG VI 4.0 1.8
6 S3 VI ALA 153B CB IV 4.2 3.8
6 S3 VI ALA 194B CB IV 4.2 0.4
7 S4 VI CYS 176B N III 3.3 24.7
7 S4 VI ALA 175B N III 3.4 14.1
7 S4 VI GLN 174B N III 3.8 1.3
7 S4 VI CYS 149B CB IV 3.8 15.5
7 S4 VI CYS 149B CA VII 3.8 5.6
7 S4 VI CYS 176B CB IV 3.8 0.7
7 S4 VI ALA 175B CB IV 4.0 2.0
7 S4 VI PRO 150B CD IV 4.0 3.8
7 S4 VI ALA 173B CB IV 4.1 0.2
------------------------------------------------------------------------
Table V
Complementarity values for the ligand F3S 401B
in PDB entry 5CH7 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 295
Actual value (Å2) 318
Normalised complementarity 1.08
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand F3S 401B
in PDB entry 5CH7 (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 | FE1
| VI |
1.08 |
1.08
|
1.08 |
1.08
|
1.08 |
1.08
|
1.08 |
1.08
|
| 2 | FE3
| VI |
1.08 |
1.08
|
1.08 |
1.08
|
1.08 |
1.08
|
1.08 |
1.08
|
| 3 | FE4
| VI |
1.08 |
1.08
|
1.08 |
1.08
|
1.08 |
1.08
|
1.08 |
1.08
|
| 4 | S1
| VI |
1.07 |
1.07
|
0.59 |
0.62
|
1.08 |
1.08
|
0.59 |
1.08
|
| 5 | S2
| VI |
0.92 |
0.92
|
0.63 |
0.82
|
1.08 |
1.08
|
0.79 |
1.08
|
| 6 | S3
| VI |
0.76 |
0.76
|
0.76 |
1.08
|
1.08 |
1.08
|
1.08 |
1.08
|
| 7 | S4
| VI |
0.93 |
0.93
|
0.62 |
0.81
|
1.08 |
1.08
|
0.77 |
1.08
|
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 MGD 1003
1. Carbon (in rings)
11 C4' 17 C1' 15 C2' 13 C3' 19 C8 21 C5
28 C4 21 C5 22 C6 25 C2 28 C4 30 C11
47 C23 36 C14 34 C13 32 C12 36 C14 38 C16
45 C21 47 C23 38 C16 39 C17 42 C19 45 C21
2. Oxygen ("hydroxy" or "carbonyl")
14 O3' 16 O2' 23 O6 40 O17
3. Nitrogen ("hydrophilic")
18 N9 20 N7 24 N1 26 N2 27 N3 37 N15
41 N18 43 N19 44 N20 46 N22
Ligand MD1 1004
1. Carbon (in rings)
13 C14 15 C16 22 C20 24 C7 15 C16 16 C15
19 C17 22 C20 30 C4' 32 C1' 44 C2' 46 C3'
34 C4 41 C5 43 C8 34 C4 36 C2 39 C6
41 C5
2. Oxygen ("hydroxy" or "carbonyl")
8 O11 17 O14 40 O6 45 O2' 47 O3'
3. Nitrogen ("hydrophilic")
14 N15 18 N17 20 N16 21 N18 23 N8 33 N9
35 N3 37 N2 38 N1 42 N7
Ligand EDO 1005
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1006
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1007
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand GOL 1010
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand EDO 1012
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 405
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 406
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 407
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand MGD 1003
1. Carbon (in rings)
11 C4' 17 C1' 15 C2' 13 C3' 19 C8 21 C5
28 C4 21 C5 22 C6 25 C2 28 C4 30 C11
47 C23 36 C14 34 C13 32 C12 36 C14 38 C16
45 C21 47 C23 38 C16 39 C17 42 C19 45 C21
2. Oxygen ("hydroxy" or "carbonyl")
14 O3' 16 O2' 23 O6 40 O17
3. Nitrogen ("hydrophilic")
18 N9 20 N7 24 N1 26 N2 27 N3 37 N15
41 N18 43 N19 44 N20 46 N22
Ligand MD1 1004
1. Carbon (in rings)
13 C14 15 C16 22 C20 24 C7 15 C16 16 C15
19 C17 22 C20 30 C4' 32 C1' 44 C2' 46 C3'
34 C4 41 C5 43 C8 34 C4 36 C2 39 C6
41 C5
2. Oxygen ("hydroxy" or "carbonyl")
8 O11 17 O14 40 O6 45 O2' 47 O3'
3. Nitrogen ("hydrophilic")
14 N15 18 N17 20 N16 21 N18 23 N8 33 N9
35 N3 37 N2 38 N1 42 N7
Ligand EDO 1005
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1006
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand ACT 1008
2. Oxygen ("hydroxy" or "carbonyl")
2 O 3 OXT
Ligand EDO 401
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 406
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand MGD 1003
1. Carbon (in rings)
11 C4' 17 C1' 15 C2' 13 C3' 19 C8 21 C5
28 C4 21 C5 22 C6 25 C2 28 C4 30 C11
47 C23 36 C14 34 C13 32 C12 36 C14 38 C16
45 C21 47 C23 38 C16 39 C17 42 C19 45 C21
2. Oxygen ("hydroxy" or "carbonyl")
14 O3' 16 O2' 23 O6 40 O17
3. Nitrogen ("hydrophilic")
18 N9 20 N7 24 N1 26 N2 27 N3 37 N15
41 N18 43 N19 44 N20 46 N22
Ligand MD1 1004
1. Carbon (in rings)
13 C14 15 C16 22 C20 24 C7 15 C16 16 C15
19 C17 22 C20 30 C4' 32 C1' 44 C2' 46 C3'
34 C4 41 C5 43 C8 34 C4 36 C2 39 C6
41 C5
2. Oxygen ("hydroxy" or "carbonyl")
8 O11 17 O14 40 O6 45 O2' 47 O3'
3. Nitrogen ("hydrophilic")
14 N15 18 N17 20 N16 21 N18 23 N8 33 N9
35 N3 37 N2 38 N1 42 N7
Ligand EDO 1005
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1006
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 1007
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 405
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 406
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il