Contacts of ligand PIR 400C in PDB entry 2MAS
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 PIR 400C
in PDB entry 2MAS (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
----------------------------------------------------------
14C ASP* 2.7 28.5 + - - -
15C ASP* 3.4 0.3 + - - -
39C ASN* 3.2 36.5 + - - -
78C ALA* 4.1 8.3 - - + -
81C ILE* 3.1 51.8 - - + +
82C HIS* 3.7 7.6 - + - -
126C THR 2.9 6.1 + - - -
152C MET* 3.5 20.4 - - - -
160C ASN* 3.0 31.6 + - - -
166C GLU* 2.6 28.2 + - - +
167C PHE* 3.8 27.7 - + + +
168C ASN* 2.9 21.3 + - - -
191C LEU* 4.5 1.1 - - - -
225C TYR* 4.2 8.7 - - - -
229C TYR* 3.9 23.1 + + - -
233C ARG* 3.7 24.5 + - - +
241C HIS* 3.8 24.2 - + - -
242C ASP* 2.7 22.7 + - - -
316C CA 2.5 33.6 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand PIR 400C
and protein in PDB entry 2MAS
(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
------------------------------------------------------------------------
6 N5 I ARG 233C NH1 III 4.2 2.6
6 N5 I TYR 229C OH I 4.5 4.0
6 N5 I ASN 160C ND2 III 4.7 2.2
10 O2' I ASP 14C OD1 II 2.7 15.2
10 O2' I ASN 39C OD1 II 3.2 8.5
10 O2' I ASP 242C OD2 II 3.3 0.3
10 O2' I ASP 15C OD1 II 3.4 0.3
12 O3' I ASP 242C OD1 II 2.7 11.8
12 O3' I THR 126C O II 2.9 6.1
12 O3' I ASN 168C ND2 III 3.3 2.4
14 N4' I ASN 168C OD1 II 2.9 15.2
14 N4' I GLU 166C OE2 II 3.6 0.8
16 O5' I GLU 166C OE2 II 2.6 14.4
16 O5' I ASN 160C ND2 III 3.0 23.6
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand PIR 400C
in PDB entry 2MAS (back
to top of page)
Total number of contacts is 77
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 V HIS 82C NE2 I 3.8 4.7
1 C1 V HIS 241C CE1 V 4.1 5.8
1 C1 V HIS 241C ND1 I 4.2 0.7
1 C1 V TYR 225C OH I 4.2 3.8
1 C1 V HIS 82C CE1 V 4.4 0.2
2 C2 V ASN 39C ND2 III 3.6 2.2
2 C2 V HIS 82C NE2 I 3.7 0.7
3 C3 V ASN 39C ND2 III 3.3 16.8
3 C3 V HIS 82C NE2 I 3.7 1.6
3 C3 V PHE 167C CD1 V 3.9 10.5
3 C3 V PHE 167C CG V 3.9 0.7
3 C3 V ALA 78C CB IV 4.1 1.1
4 C4 V ILE 81C CG1 IV 3.9 9.6
4 C4 V ALA 78C CB IV 4.1 7.2
4 C4 V HIS 82C NE2 I 4.3 0.2
4 C4 V PHE 167C CG V 4.3 7.4
4 C4 V PHE 167C CB IV 4.5 2.9
4 C4 V PHE 167C CD2 V 4.5 1.1
4 C4 V ASN 160C ND2 III 4.8 1.1
4 C4 V ARG 233C NH1 III 5.0 4.5
5 C5 V ILE 81C CG2 IV 3.6 3.8
5 C5 V ASN 160C ND2 III 4.5 3.4
6 N5 I ILE 81C CG1 IV 3.1 19.8*
6 N5 I ILE 81C CD1 IV 3.4 6.5*
6 N5 I ILE 81C CG2 IV 3.5 1.0*
6 N5 I ARG 233C CD VII 3.7 17.2
6 N5 I ARG 233C NH1 III 4.2 2.6
6 N5 I TYR 229C OH I 4.5 4.0
6 N5 I ARG 233C CG IV 4.6 0.2*
6 N5 I ASN 160C ND2 III 4.7 2.2
6 N5 I TYR 229C CE1 V 4.8 1.4
7 C6 V ILE 81C CG2 IV 3.8 11.0
7 C6 V TYR 229C OH I 3.9 17.0
7 C6 V TYR 225C OH I 4.2 4.9
7 C6 V TYR 229C CE1 V 4.3 0.7
7 C6 V HIS 241C CE1 V 4.3 0.7
7 C6 V ASN 160C ND2 III 4.7 0.7
8 C1' VI ASN 39C ND2 III 3.5 8.7
8 C1' VI ASN 39C OD1 II 4.0 0.2
8 C1' VI ASN 168C OD1 II 4.0 1.1
9 C2' VI ASP 14C OD1 II 3.3 7.9
9 C2' VI ASP 14C OD2 II 3.4 0.9
10 O2' I CA 316C CA VI 2.7 12.6
10 O2' I ASP 14C OD1 II 2.7 15.2
10 O2' I ASN 39C OD1 II 3.2 8.5
10 O2' I ASP 242C OD2 II 3.3 0.3
10 O2' I ASP 15C OD1 II 3.4 0.3
10 O2' I HIS 82C CE1 V 4.2 0.2
11 C3' VI ASP 242C OD1 II 3.3 10.5
11 C3' VI ASP 14C OD2 II 3.4 4.5
11 C3' VI MET 152C SD VIII 3.7 2.9
11 C3' VI HIS 241C CB IV 4.2 0.2
12 O3' I CA 316C CA VI 2.5 21.0
12 O3' I ASP 242C OD1 II 2.7 11.8
12 O3' I THR 126C O II 2.9 6.1
12 O3' I ASN 168C ND2 III 3.3 2.4
13 C4' VI GLU 166C OE2 II 3.3 8.1
13 C4' VI ASN 168C OD1 II 3.5 2.5
13 C4' VI MET 152C SD VIII 3.5 4.7
14 N4' I ASN 168C OD1 II 2.9 15.2
14 N4' I GLU 166C OE2 II 3.6 0.8
14 N4' I PHE 167C CD1 V 3.8 3.0
15 C5' VI GLU 166C OE2 II 3.2 4.0
15 C5' VI MET 152C SD VIII 3.7 10.8
15 C5' VI HIS 241C ND1 I 3.8 11.0
15 C5' VI HIS 241C CG V 3.9 2.0
15 C5' VI HIS 241C CE1 V 4.0 2.7
15 C5' VI ASN 160C ND2 III 4.1 0.7
15 C5' VI MET 152C CE IV 4.2 2.0
15 C5' VI HIS 241C CD2 V 4.2 1.1
15 C5' VI GLU 166C CD VI 4.2 0.2
15 C5' VI LEU 191C CD2 IV 4.5 1.1
16 O5' I GLU 166C OE2 II 2.6 14.4
16 O5' I ASN 160C ND2 III 3.0 23.6
16 O5' I GLU 166C CD VI 3.6 0.5
16 O5' I GLU 166C CG IV 3.8 0.2*
16 O5' I PHE 167C CB IV 3.9 2.1*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand PIR 400C
in PDB entry 2MAS (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 389
Actual value (Å2) 346
Normalised complementarity 0.89
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand PIR 400C
in PDB entry 2MAS (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
| V |
0.89 |
0.89
|
0.89 |
0.84
|
0.89 |
0.89
|
0.89 |
0.89
|
| 2 | C2
| V |
0.89 |
0.89
|
0.88 |
0.87
|
0.89 |
0.89
|
0.88 |
0.89
|
| 3 | C3
| V |
0.88 |
0.88
|
0.80 |
0.80
|
0.89 |
0.89
|
0.80 |
0.89
|
| 4 | C4
| V |
0.79 |
0.79
|
0.76 |
0.86
|
0.89 |
0.89
|
0.86 |
0.89
|
| 5 | C5
| V |
0.87 |
0.87
|
0.85 |
0.87
|
0.89 |
0.89
|
0.87 |
0.89
|
| 6 | N5
| I |
0.89 |
0.89
|
0.78 |
0.99
|
1.03 |
1.03
|
0.92 |
1.03
|
| 7 | C6
| V |
0.83 |
0.83
|
0.83 |
0.77
|
0.89 |
0.89
|
0.89 |
0.89
|
| 8 | C1'
| VI |
0.89 |
0.88
|
0.84 |
0.84
|
0.89 |
0.89
|
0.84 |
0.88
|
| 9 | C2'
| VI |
0.89 |
0.84
|
0.89 |
0.84
|
0.89 |
0.89
|
0.89 |
0.84
|
| 10 | O2'
| I |
0.89 |
0.76
|
0.89 |
0.76
|
0.89 |
0.89
|
0.89 |
0.76
|
| 11 | C3'
| VI |
0.89 |
0.80
|
0.89 |
0.81
|
0.89 |
0.89
|
0.89 |
0.80
|
| 12 | O3'
| I |
0.89 |
0.80
|
0.88 |
0.79
|
0.89 |
0.89
|
0.88 |
0.80
|
| 13 | C4'
| VI |
0.89 |
0.81
|
0.89 |
0.84
|
0.89 |
0.89
|
0.89 |
0.81
|
| 14 | N4'
| I |
0.89 |
0.81
|
0.89 |
0.81
|
0.89 |
0.89
|
0.89 |
0.81
|
| 15 | C5'
| VI |
0.87 |
0.80
|
0.87 |
0.81
|
0.89 |
0.89
|
0.89 |
0.81
|
| 16 | O5'
| I |
0.89 |
0.82
|
0.77 |
0.71
|
0.90 |
0.90
|
0.78 |
0.83
|
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 PIR 400
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5 7 C6
8 C1' 9 C2' 11 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
10 O2' 12 O3' 16 O5'
3. Nitrogen ("hydrophilic")
6 N5 14 N4'
Ligand PIR 400
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5 7 C6
8 C1' 9 C2' 11 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
10 O2' 12 O3' 16 O5'
3. Nitrogen ("hydrophilic")
6 N5 14 N4'
Ligand PIR 400
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5 7 C6
8 C1' 9 C2' 11 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
10 O2' 12 O3' 16 O5'
3. Nitrogen ("hydrophilic")
6 N5 14 N4'
Ligand PIR 400
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5 7 C6
8 C1' 9 C2' 11 C3' 13 C4'
2. Oxygen ("hydroxy" or "carbonyl")
10 O2' 12 O3' 16 O5'
3. Nitrogen ("hydrophilic")
6 N5 14 N4'
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il