Contacts of ligand C8E 632B 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 632B
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
----------------------------------------------------------
250A GLU* 3.9 18.7 - - - +
251A ARG* 3.6 51.5 + - - +
348A PRO* 3.6 38.6 - - - +
349A GLY 3.5 19.1 - - - +
350A ASP* 4.2 5.3 - - - +
352A ALA* 3.7 31.0 - - - +
353A VAL* 5.0 8.0 - - - +
371A TYR* 3.4 43.3 - - - +
183B ARG* 3.4 25.8 - - - +
238B ARG* 3.4 63.7 - - + +
241B GLU* 3.4 33.9 - - + +
242B ILE* 3.8 24.5 - - + +
245B LEU* 3.8 25.9 - - + +
275B LEU* 3.9 30.8 + - + +
277B MET* 3.7 37.9 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand C8E 632B
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
------------------------------------------------------------------------
12 O12 II ARG 251A NH2 III 4.4 3.6
21 O21 I LEU 275B O II 4.4 4.0
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand C8E 632B
in PDB entry 2SQC (back
to top of page)
Total number of contacts is 92
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 LEU 245B CD2 IV 3.8 18.4
1 C1 IV ILE 242B CG1 IV 3.8 12.6
1 C1 IV LEU 275B CD1 IV 4.0 9.2
1 C1 IV ILE 242B CA VII 4.2 2.9
1 C1 IV ILE 242B N III 4.2 0.2*
1 C1 IV GLU 241B O II 4.3 0.9*
2 C2 IV GLU 241B CB IV 3.4 28.3
2 C2 IV GLU 241B OE1 II 3.6 0.4*
2 C2 IV GLU 241B C VI 3.9 2.2
2 C2 IV LEU 275B CD2 IV 3.9 5.6
2 C2 IV ILE 242B N III 4.0 1.1*
2 C2 IV GLU 241B O II 4.2 0.2*
3 C3 IV ARG 183B NH2 III 3.4 24.9*
3 C3 IV GLU 241B OE1 II 3.5 1.8*
3 C3 IV LEU 275B CD2 IV 3.9 4.5
4 C4 IV ARG 238B CG IV 3.4 24.2
4 C4 IV ARG 238B NH1 III 3.9 2.0*
4 C4 IV ILE 242B CG1 IV 4.1 2.5
5 C5 IV ARG 238B CG IV 4.4 0.2
5 C5 IV ILE 242B CG1 IV 4.7 3.6
6 C6 IV ARG 238B CZ VI 3.4 14.4
6 C6 IV ARG 238B NH2 III 3.6 1.3*
6 C6 IV ARG 238B NH1 III 3.8 0.9*
6 C6 IV ARG 183B NH2 III 5.4 0.9*
7 C7 IV ARG 238B NE III 3.6 13.0*
7 C7 IV ARG 238B NH2 III 3.8 0.2*
7 C7 IV ARG 238B CD VII 4.3 1.6
7 C7 IV ILE 242B CD1 IV 5.6 1.6
8 C8 VIII PRO 348A CG IV 3.7 19.1
8 C8 VIII ARG 238B NH2 III 4.3 4.9
9 O9 II PRO 348A CG IV 3.6 2.3*
10 C10 VIII PRO 348A CB IV 4.3 3.1
10 C10 VIII ALA 352A CB IV 4.5 3.1
10 C10 VIII ARG 238B NH2 III 5.5 0.9
10 C10 VIII ALA 352A O II 5.8 0.2*
11 C11 VIII ALA 352A CB IV 3.7 24.0
11 C11 VIII GLY 349A O II 3.7 1.6*
11 C11 VIII PRO 348A CB IV 4.2 1.6
11 C11 VIII ALA 352A CA VII 4.8 0.2
11 C11 VIII ALA 352A C VI 4.8 3.4
11 C11 VIII VAL 353A N III 5.0 1.3
11 C11 VIII VAL 353A CG2 IV 5.3 4.0
12 O12 II ARG 251A NH2 III 4.4 3.6
12 O12 II ASP 350A OD1 II 4.9 0.3*
12 O12 II ASP 350A CA VII 4.9 0.9
12 O12 II VAL 353A CG2 IV 5.2 2.6*
13 C13 VIII GLY 349A O II 3.5 15.5*
13 C13 VIII PRO 348A O II 3.7 12.1*
13 C13 VIII GLY 349A C VI 3.7 1.8
13 C13 VIII ASP 350A N III 4.3 0.4
13 C13 VIII ASP 350A OD1 II 4.5 0.9*
14 C14 VIII ARG 251A NH2 III 3.6 18.8
14 C14 VIII ARG 251A CZ VI 3.9 0.9
14 C14 VIII ARG 251A NE III 4.2 1.1
14 C14 VIII ASP 350A OD1 II 4.2 2.7*
14 C14 VIII TYR 371A CD1 V 4.5 0.2
14 C14 VIII GLY 349A C VI 4.5 0.2
15 O15 II TYR 371A CD1 V 3.4 13.0
15 O15 II TYR 371A CG V 3.7 2.1
15 O15 II ARG 251A CG IV 3.8 2.8*
15 O15 II TYR 371A CB IV 4.4 0.2*
16 C16 VIII TYR 371A CE1 V 3.9 2.9
16 C16 VIII ARG 251A CG IV 3.9 17.7
16 C16 VIII GLU 250A O II 4.0 3.8*
16 C16 VIII ARG 251A CZ VI 4.1 4.3
16 C16 VIII ARG 251A NH1 III 4.2 1.8
16 C16 VIII GLU 250A CB IV 4.3 1.3
16 C16 VIII ARG 251A NH2 III 4.4 0.4
16 C16 VIII GLU 250A OE1 II 5.0 0.7*
17 C17 VIII TYR 371A CE1 V 3.5 17.7
17 C17 VIII TYR 371A CZ V 3.6 3.1
17 C17 VIII GLU 250A O II 3.9 3.1*
17 C17 VIII PRO 348A O II 5.2 0.4*
18 O18 II GLU 250A CB IV 4.1 8.0*
18 O18 II LEU 245B CD2 IV 4.4 1.2*
18 O18 II GLU 250A CG IV 4.5 0.5*
18 O18 II GLU 250A OE1 II 4.9 0.7*
18 O18 II GLU 250A CD VI 4.9 0.5
19 C19 VIII MET 277B SD VIII 3.7 17.5*
19 C19 VIII LEU 245B CD2 IV 4.1 4.3
19 C19 VIII MET 277B CE IV 4.1 3.6
19 C19 VIII TYR 371A OH I 4.1 4.0
19 C19 VIII MET 277B CG IV 4.2 0.9
19 C19 VIII LEU 275B O II 5.1 0.2*
20 C20 VI MET 277B SD VIII 3.8 14.1
20 C20 VI LEU 245B CD2 IV 3.8 2.0
20 C20 VI MET 277B CG IV 4.4 1.8
20 C20 VI LEU 275B O II 4.5 5.6
20 C20 VI LEU 275B CB IV 4.6 1.3
21 O21 I LEU 275B O II 4.4 4.0
21 O21 I LEU 275B CB IV 5.1 0.2*
21 O21 I LEU 275B CD2 IV 5.3 0.2*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand C8E 632B
in PDB entry 2SQC (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 540
Actual value (Å2) 206
Normalised complementarity 0.38
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand C8E 632B
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 |
0.24 |
0.23
|
0.23 |
0.38
|
0.39 |
0.39
|
0.37 |
0.38
|
| 2 | C2
| IV |
0.26 |
0.26
|
0.26 |
0.38
|
0.39 |
0.39
|
0.38 |
0.39
|
| 3 | C3
| IV |
0.46 |
0.46
|
0.37 |
0.38
|
0.48 |
0.48
|
0.39 |
0.47
|
| 4 | C4
| IV |
0.29 |
0.29
|
0.28 |
0.38
|
0.39 |
0.39
|
0.38 |
0.39
|
| 5 | C5
| IV |
0.37 |
0.37
|
0.37 |
0.38
|
0.38 |
0.38
|
0.38 |
0.38
|
| 6 | C6
| IV |
0.39 |
0.39
|
0.38 |
0.38
|
0.39 |
0.39
|
0.38 |
0.39
|
| 7 | C7
| IV |
0.42 |
0.42
|
0.37 |
0.38
|
0.43 |
0.43
|
0.38 |
0.43
|
| 8 | C8
| VIII |
0.31 |
0.31
|
0.29 |
0.36
|
0.38 |
0.38
|
0.36 |
0.38
|
| 9 | O9
| II |
0.38 |
0.38
|
0.38 |
0.39
|
0.39 |
0.39
|
0.39 |
0.39
|
| 10 | C10
| VIII |
0.36 |
0.36
|
0.36 |
0.38
|
0.38 |
0.38
|
0.38 |
0.38
|
| 11 | C11
| VIII |
0.28 |
0.27
|
0.27 |
0.38
|
0.39 |
0.39
|
0.38 |
0.38
|
| 12 | O12
| II |
0.38 |
0.38
|
0.37 |
0.38
|
0.39 |
0.39
|
0.38 |
0.39
|
| 13 | C13
| VIII |
0.49 |
0.38
|
0.49 |
0.38
|
0.49 |
0.49
|
0.49 |
0.38
|
| 14 | C14
| VIII |
0.39 |
0.38
|
0.32 |
0.31
|
0.39 |
0.39
|
0.32 |
0.38
|
| 15 | O15
| II |
0.38 |
0.38
|
0.38 |
0.39
|
0.39 |
0.39
|
0.39 |
0.39
|
| 16 | C16
| VIII |
0.33 |
0.31
|
0.32 |
0.37
|
0.40 |
0.40
|
0.39 |
0.38
|
| 17 | C17
| VIII |
0.40 |
0.38
|
0.40 |
0.38
|
0.40 |
0.40
|
0.40 |
0.38
|
| 18 | O18
| II |
0.38 |
0.38
|
0.38 |
0.42
|
0.42 |
0.42
|
0.42 |
0.42
|
| 19 | C19
| VIII |
0.42 |
0.35
|
0.42 |
0.43
|
0.45 |
0.45
|
0.45 |
0.38
|
| 20 | C20
| VI |
0.36 |
0.29
|
0.36 |
0.36
|
0.38 |
0.38
|
0.38 |
0.31
|
| 21 | O21
| I |
0.38 |
0.37
|
0.38 |
0.37
|
0.38 |
0.38
|
0.38 |
0.37
|
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