Contacts of ligand SMG1200C in PDB entry 1SJC
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 SMG1200C
in PDB entry 1SJC (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
----------------------------------------------------------
19C PHE* 3.9 14.3 - - + -
21C THR* 4.5 1.6 - - + -
23C PHE* 4.0 28.3 - - + -
26C GLN* 3.9 3.4 - - - +
50C MET* 3.0 36.6 - - + -
55C TYR* 3.7 3.9 - - + -
135C SER* 2.7 34.7 + - - -
161C LYS* 2.9 14.6 + - - -
163C LYS* 3.1 20.3 + - - +
191C ASN* 3.2 18.9 + - - -
214C GLU* 3.7 0.9 - - - +
239C ASP* 3.3 0.7 - - - +
261C ASN* 4.5 0.2 + - - -
263C LYS* 2.9 26.3 + - - +
291C GLY* 2.7 24.4 + - - +
292C MET* 3.0 27.3 + - - -
293C ILE* 2.5 81.0 + - + +
294C GLU* 3.9 3.1 + - - +
299C ARG* 4.2 8.6 + - - -
316C ASP* 3.4 43.6 - - + +
318C SER* 4.1 9.0 + - - -
322C ARG* 5.2 0.2 - - - -
323C PHE* 3.4 40.0 - - + -
1201C MG 2.6 29.5 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand SMG1200C
and protein in PDB entry 1SJC
(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
------------------------------------------------------------------------
1 O61 II SER 318C OG I 4.1 9.0
1 O61 II ARG 299C NH1 III 4.2 6.1
2 O62 II ILE 293C N III 2.5 24.9
2 O62 II MET 292C N III 3.0 10.0
2 O62 II GLU 294C N III 4.3 0.5
2 O62 II ARG 299C NH2 III 4.3 1.7
2 O62 II ARG 299C NH1 III 4.8 0.2
6 O31 II SER 135C OG I 2.7 26.2
6 O31 II LYS 163C NZ III 3.5 2.8
6 O31 II LYS 161C NZ III 3.8 0.9
8 N1 I GLY 291C O II 2.7 6.5
9 O11 II LYS 161C NZ III 2.9 13.7
9 O11 II LYS 263C NZ III 3.0 6.8
9 O11 II ASN 261C ND2 III 4.5 0.2
10 O12 II LYS 263C NZ III 2.9 6.8
10 O12 II ASN 191C ND2 III 3.2 18.9
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand SMG1200C
in PDB entry 1SJC (back
to top of page)
Total number of contacts is 79
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 O61 II PHE 323C CE1 V 3.4 9.0
1 O61 II ASP 316C O II 3.4 12.8*
1 O61 II ASP 316C C VI 3.9 4.3
1 O61 II ASP 316C CB IV 4.0 0.5*
1 O61 II SER 318C OG I 4.1 9.0
1 O61 II ARG 299C NH1 III 4.2 6.1
1 O61 II ARG 322C CD VII 5.2 0.2
1 O61 II SER 135C CB VI 5.4 0.5
2 O62 II ILE 293C N III 2.5 24.9
2 O62 II MET 292C N III 3.0 10.0
2 O62 II GLY 291C C VI 3.1 0.2
2 O62 II GLY 291C CA VI 3.2 1.7
2 O62 II ILE 293C CA VII 3.3 0.9
2 O62 II GLU 294C OE1 II 3.9 2.6*
2 O62 II ASP 316C O II 4.2 0.5*
2 O62 II GLU 294C N III 4.3 0.5
2 O62 II ARG 299C NH2 III 4.3 1.7
2 O62 II ARG 299C NH1 III 4.8 0.2
3 C6 VI PHE 323C CE1 V 3.4 11.0
3 C6 VI GLY 291C CA VI 3.8 4.0
3 C6 VI ASP 316C O II 4.0 0.7
3 C6 VI ARG 299C NH2 III 4.8 0.7
4 C5 IV PHE 323C CZ V 3.5 20.0
4 C5 IV GLY 291C O II 3.9 0.4*
4 C5 IV ILE 293C N III 4.0 4.0*
4 C5 IV ILE 293C CG1 IV 4.1 3.4
4 C5 IV SER 135C CB VI 4.5 5.2
4 C5 IV PHE 19C CZ V 5.1 1.1
5 C4 IV GLY 291C O II 3.2 5.4*
5 C4 IV ASP 316C CB IV 3.6 19.7
5 C4 IV ASP 316C CG VI 3.9 0.7
5 C4 IV SER 135C CB VI 4.1 1.1
6 O31 II SER 135C OG I 2.7 26.2
6 O31 II SER 135C CB VI 3.1 1.7
6 O31 II LYS 163C NZ III 3.5 2.8
6 O31 II LYS 161C NZ III 3.8 0.9
6 O31 II PHE 19C CZ V 3.9 3.3
7 C3 VI ASP 316C OD2 II 3.7 2.9
7 C3 VI PHE 19C CZ V 4.7 1.6
8 N1 I GLY 291C O II 2.7 6.5
9 O11 II MG 1201C MG VI 2.6 13.7
9 O11 II LYS 161C NZ III 2.9 13.7
9 O11 II LYS 263C NZ III 3.0 6.8
9 O11 II ASP 239C OD2 II 3.3 0.7*
9 O11 II LYS 263C CE VII 3.4 3.1
9 O11 II GLU 214C OE2 II 3.7 0.9*
9 O11 II ASP 316C OD2 II 4.1 1.4*
9 O11 II ASN 261C ND2 III 4.5 0.2
10 O12 II MG 1201C MG VI 2.7 12.0
10 O12 II LYS 263C NZ III 2.9 6.8
10 O12 II ASN 191C ND2 III 3.2 18.9
10 O12 II TYR 55C CE1 V 3.7 0.3
11 C2 VI MG 1201C MG VI 3.0 3.8
11 C2 VI LYS 263C NZ III 3.0 4.7
11 C2 VI LYS 163C NZ III 3.3 7.0
12 C1 VI LYS 163C NZ III 3.1 6.1
12 C1 VI PHE 19C CE1 V 4.7 0.4
13 CB IV GLY 291C O II 3.5 6.1*
13 CB IV LYS 263C NZ III 3.7 4.9*
13 CB IV MET 292C SD VIII 3.8 0.2
14 CG IV PHE 23C CZ V 4.1 13.7
14 CG IV PHE 23C CE2 V 4.3 3.6
14 CG IV LYS 163C NZ III 4.4 4.5*
14 CG IV PHE 19C CE1 V 4.4 7.9
14 CG IV THR 21C CG2 IV 4.5 1.6
14 CG IV TYR 55C CD1 V 4.7 0.4
15 SD VI MET 50C CE IV 3.5 11.7
15 SD VI MET 292C SD VIII 3.7 10.8
15 SD VI MET 50C SD VIII 3.9 5.4
15 SD VI PHE 23C CZ V 4.0 11.0
15 SD VI MET 292C CE IV 4.2 2.9
15 SD VI TYR 55C CD1 V 4.6 2.2
15 SD VI TYR 55C CB IV 5.1 0.9
16 CE IV ILE 293C CD1 IV 2.7 39.7
16 CE IV MET 50C CE IV 3.0 17.9
16 CE IV ILE 293C CG1 IV 3.1 8.1
16 CE IV MET 50C SD VIII 3.8 1.6
16 CE IV GLN 26C NE2 III 3.9 3.4*
16 CE IV MET 292C C VI 4.1 3.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand SMG1200C
in PDB entry 1SJC (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 443
Actual value (Å2) 374
Normalised complementarity 0.84
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand SMG1200C
in PDB entry 1SJC (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 | O61
| II |
0.90 |
0.84
|
0.87 |
0.78
|
0.90 |
0.90
|
0.88 |
0.85
|
| 2 | O62
| II |
0.86 |
0.84
|
0.69 |
0.68
|
0.86 |
0.86
|
0.69 |
0.84
|
| 3 | C6
| VI |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 4 | C5
| IV |
0.85 |
0.85
|
0.83 |
0.84
|
0.86 |
0.86
|
0.85 |
0.86
|
| 5 | C4
| IV |
0.78 |
0.76
|
0.78 |
0.84
|
0.87 |
0.87
|
0.87 |
0.84
|
| 6 | O31
| II |
0.84 |
0.84
|
0.83 |
0.71
|
0.84 |
0.84
|
0.83 |
0.84
|
| 7 | C3
| VI |
0.84 |
0.83
|
0.84 |
0.83
|
0.84 |
0.84
|
0.84 |
0.83
|
| 8 | N1
| I |
0.84 |
0.82
|
0.84 |
0.82
|
0.84 |
0.84
|
0.84 |
0.82
|
| 9 | O11
| II |
0.86 |
0.84
|
0.75 |
0.75
|
0.86 |
0.86
|
0.75 |
0.84
|
| 10 | O12
| II |
0.84 |
0.84
|
0.73 |
0.73
|
0.84 |
0.84
|
0.73 |
0.84
|
| 11 | C2
| VI |
0.84 |
0.84
|
0.79 |
0.79
|
0.84 |
0.84
|
0.79 |
0.84
|
| 12 | C1
| VI |
0.84 |
0.84
|
0.82 |
0.82
|
0.84 |
0.84
|
0.82 |
0.84
|
| 13 | CB
| IV |
0.89 |
0.87
|
0.87 |
0.84
|
0.89 |
0.89
|
0.87 |
0.87
|
| 14 | CG
| IV |
0.86 |
0.86
|
0.84 |
0.84
|
0.86 |
0.86
|
0.84 |
0.86
|
| 15 | SD
| VI |
0.77 |
0.70
|
0.77 |
0.84
|
0.84 |
0.84
|
0.84 |
0.77
|
| 16 | CE
| IV |
0.56 |
0.56
|
0.55 |
0.84
|
0.86 |
0.86
|
0.84 |
0.85
|
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 SMG 1000
2. Oxygen ("hydroxy" or "carbonyl")
1 O61 2 O62 6 O31 9 O11 10 O12
3. Nitrogen ("hydrophilic")
8 N1
Ligand SMG 1100
2. Oxygen ("hydroxy" or "carbonyl")
1 O61 2 O62 6 O31 9 O11 10 O12
3. Nitrogen ("hydrophilic")
8 N1
Ligand SMG 1200
2. Oxygen ("hydroxy" or "carbonyl")
1 O61 2 O62 6 O31 9 O11 10 O12
3. Nitrogen ("hydrophilic")
8 N1
Ligand SMG 1300
2. Oxygen ("hydroxy" or "carbonyl")
1 O61 2 O62 6 O31 9 O11 10 O12
3. Nitrogen ("hydrophilic")
8 N1
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il