Contacts of ligand C8E 635B in PDB entry 2SQC
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 C8E 635B
in PDB entry 2SQC (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
----------------------------------------------------------
147B MET 3.9 21.4 + - - -
148B VAL* 4.5 9.7 - - - +
149B PRO* 3.8 31.4 - - - +
151B GLU* 3.5 37.9 - - - +
152B ILE* 3.8 37.4 - - - +
154B PHE* 3.4 85.2 - - + +
155B LEU* 4.0 28.9 - - - +
159B MET* 4.5 19.3 - - + +
161B LEU* 4.1 18.0 - - - +
166B PHE* 5.2 1.7 - - - -
221B LEU* 4.0 38.1 - - - -
225B LEU* 4.3 11.2 - - - +
236B PHE* 4.4 30.3 - - + -
239B ALA* 6.1 0.4 - - + -
243B ARG* 4.4 18.6 - - - +
432B ILE* 3.9 29.8 - - - +
433B PRO* 6.3 0.4 - - - -
434B PHE* 5.7 0.5 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand C8E 635B
and protein in PDB entry 2SQC
(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
------------------------------------------------------------------------
21 O21 I MET 147B O II 4.1 2.6
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand C8E 635B
in PDB entry 2SQC (back
to top of page)
Total number of contacts is 88
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 IV ARG 243B NH2 III 4.4 18.4*
1 C1 IV PHE 236B CE1 V 5.5 0.4
2 C2 IV PHE 154B CE1 V 4.1 13.0
2 C2 IV PHE 154B CZ V 4.3 2.7
2 C2 IV PHE 236B CD1 V 4.4 15.0
2 C2 IV PHE 236B CE1 V 4.6 2.7
2 C2 IV ALA 239B CB IV 6.1 0.4
3 C3 IV PHE 154B CD2 V 4.7 0.7
3 C3 IV PHE 154B CE2 V 4.8 1.1
3 C3 IV PHE 236B CG V 4.8 7.2
3 C3 IV PHE 236B CD2 V 5.0 3.1
3 C3 IV PHE 236B CE1 V 5.2 0.2
3 C3 IV PHE 236B CE2 V 5.2 1.3
3 C3 IV PHE 236B CZ V 5.3 0.2
4 C4 IV PHE 154B CG V 3.5 21.8
4 C4 IV PHE 154B CD1 V 3.7 0.4
4 C4 IV PHE 154B CD2 V 3.8 3.8
6 C6 IV PHE 154B O II 4.0 7.6*
6 C6 IV PHE 154B CB IV 4.0 0.4
6 C6 IV MET 159B CE IV 5.7 0.4
6 C6 IV ARG 243B NH2 III 6.3 0.2*
7 C7 IV MET 159B CE IV 5.2 2.5
8 C8 VIII PHE 154B O II 3.4 17.3*
8 C8 VIII PHE 154B CB IV 3.9 0.2
8 C8 VIII PHE 154B C VI 4.0 1.1
8 C8 VIII MET 159B CE IV 4.5 12.1
8 C8 VIII LEU 155B N III 4.6 0.2
8 C8 VIII MET 159B SD VIII 4.7 4.3*
9 O9 II LEU 155B CD2 IV 4.2 4.2*
10 C10 VIII PHE 154B CB IV 3.8 8.7
10 C10 VIII PHE 154B CD2 V 4.4 1.8
11 C11 VIII PHE 154B CB IV 4.5 0.7
11 C11 VIII GLU 151B O II 4.6 0.4*
11 C11 VIII PHE 154B CD2 V 4.8 3.6
11 C11 VIII GLU 151B CB IV 4.9 2.9
11 C11 VIII GLU 151B CG IV 5.7 0.2
12 O12 II GLU 151B O II 3.5 8.7*
12 O12 II LEU 155B CD2 IV 4.0 2.1*
12 O12 II PHE 154B CB IV 4.2 0.2*
13 C13 VIII LEU 155B CD2 IV 4.1 9.9
13 C13 VIII GLU 151B CB IV 4.6 2.0
14 C14 VIII GLU 151B O II 3.7 14.8*
14 C14 VIII GLU 151B C VI 3.9 4.9
14 C14 VIII ILE 152B CA VII 4.2 2.2
14 C14 VIII LEU 155B CD1 IV 4.2 4.7
14 C14 VIII GLU 151B CB IV 4.3 3.4
15 O15 II PRO 149B CG IV 3.9 7.6*
15 O15 II LEU 225B CD2 IV 4.7 4.0*
15 O15 II GLU 151B CB IV 4.7 0.5*
16 C16 VIII PRO 149B CG IV 4.2 2.5
16 C16 VIII LEU 155B CD1 IV 4.5 3.6
16 C16 VIII LEU 221B CD1 IV 4.7 15.3
16 C16 VIII LEU 221B CD2 IV 4.9 1.1
16 C16 VIII LEU 225B CD2 IV 5.0 0.4
16 C16 VIII LEU 161B CD1 IV 5.7 1.1
17 C17 VIII PRO 149B CG IV 3.8 11.7
17 C17 VIII ILE 152B CG1 IV 3.9 16.4
17 C17 VIII ILE 152B CB IV 4.1 0.2
17 C17 VIII LEU 155B CD1 IV 4.2 4.3
17 C17 VIII LEU 161B CB IV 5.2 0.2
18 O18 II ILE 152B CD1 IV 3.8 8.3*
18 O18 II ILE 152B CG1 IV 3.9 0.2*
18 O18 II LEU 161B CD1 IV 4.2 5.0*
18 O18 II LEU 161B CB IV 4.3 1.2*
19 C19 VIII LEU 221B CD2 IV 4.0 18.2
19 C19 VIII LEU 161B CD1 IV 4.1 9.9
19 C19 VIII PRO 149B CD IV 4.2 1.6
19 C19 VIII LEU 225B CD1 IV 4.4 1.8
20 C20 VI MET 147B O II 3.9 18.8
20 C20 VI PRO 149B CD IV 4.0 5.2
20 C20 VI LEU 225B CD1 IV 4.3 4.9
20 C20 VI LEU 221B CD2 IV 4.6 3.6
20 C20 VI ILE 432B CG2 IV 4.8 10.5
20 C20 VI ILE 432B CD1 IV 4.8 0.2
20 C20 VI ILE 432B CB IV 5.0 1.3
20 C20 VI PRO 433B CD IV 6.3 0.4
21 O21 I ILE 432B CD1 IV 3.9 17.5*
21 O21 I MET 147B O II 4.1 2.6
21 O21 I PRO 149B CD IV 4.3 2.9*
21 O21 I ILE 152B CD1 IV 4.3 10.0*
21 O21 I VAL 148B CA VII 4.5 4.3
21 O21 I VAL 148B CG1 IV 4.6 2.8*
21 O21 I VAL 148B CG2 IV 4.7 2.6*
21 O21 I ILE 432B CG2 IV 4.7 0.2*
21 O21 I LEU 161B CD1 IV 5.2 0.3*
21 O21 I PHE 166B CZ V 5.2 1.7
21 O21 I PHE 434B CB IV 5.7 0.5*
21 O21 I LEU 161B CB IV 5.7 0.2*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand C8E 635B
in PDB entry 2SQC (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 643
Actual value (Å2) 136
Normalised complementarity 0.21
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand C8E 635B
in PDB entry 2SQC (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
| IV |
0.27 |
0.27
|
0.21 |
0.21
|
0.27 |
0.27
|
0.21 |
0.27
|
| 2 | C2
| IV |
0.21 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 3 | C3
| IV |
0.21 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 4 | C4
| IV |
0.21 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 6 | C6
| IV |
0.23 |
0.21
|
0.23 |
0.21
|
0.24 |
0.24
|
0.24 |
0.21
|
| 7 | C7
| IV |
0.20 |
0.20
|
0.20 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 8 | C8
| VIII |
0.24 |
0.17
|
0.24 |
0.22
|
0.28 |
0.28
|
0.28 |
0.21
|
| 9 | O9
| II |
0.21 |
0.21
|
0.21 |
0.22
|
0.22 |
0.22
|
0.22 |
0.22
|
| 10 | C10
| VIII |
0.18 |
0.18
|
0.18 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 11 | C11
| VIII |
0.20 |
0.20
|
0.20 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 12 | O12
| II |
0.24 |
0.21
|
0.24 |
0.22
|
0.25 |
0.25
|
0.25 |
0.22
|
| 13 | C13
| VIII |
0.17 |
0.17
|
0.17 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 14 | C14
| VIII |
0.23 |
0.19
|
0.23 |
0.21
|
0.26 |
0.26
|
0.25 |
0.21
|
| 15 | O15
| II |
0.21 |
0.21
|
0.21 |
0.25
|
0.25 |
0.25
|
0.25 |
0.25
|
| 16 | C16
| VIII |
0.14 |
0.14
|
0.14 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 17 | C17
| VIII |
0.11 |
0.11
|
0.11 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 18 | O18
| II |
0.21 |
0.21
|
0.21 |
0.26
|
0.26 |
0.26
|
0.26 |
0.26
|
| 19 | C19
| VIII |
0.11 |
0.11
|
0.11 |
0.21
|
0.21 |
0.21
|
0.21 |
0.21
|
| 20 | C20
| VI |
0.13 |
0.07
|
0.13 |
0.15
|
0.21 |
0.21
|
0.21 |
0.15
|
| 21 | O21
| I |
0.21 |
0.20
|
0.20 |
0.32
|
0.33 |
0.33
|
0.31 |
0.32
|
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 C8E 632
2. Oxygen ("hydroxy" or "carbonyl")
21 O21
Ligand C8E 633
2. Oxygen ("hydroxy" or "carbonyl")
21 O21
Ligand C8E 632
2. Oxygen ("hydroxy" or "carbonyl")
21 O21
Ligand C8E 633
2. Oxygen ("hydroxy" or "carbonyl")
21 O21
Ligand C8E 634
2. Oxygen ("hydroxy" or "carbonyl")
21 O21
Ligand C8E 635
2. Oxygen ("hydroxy" or "carbonyl")
21 O21
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il