Contacts of ligand MTP1002A in PDB entry 2AA0
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 MTP1002A
in PDB entry 2AA0 (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
----------------------------------------------------------
278A THR* 3.8 35.2 - - - +
279A ARG 4.7 0.3 + - - -
280A GLY* 3.6 41.5 + - - -
281A HIS* 3.7 32.2 - - + +
284A VAL* 3.6 16.3 - - - +
302A VAL* 3.3 21.0 - - + +
303A PRO 3.7 4.3 - - - -
304A VAL* 5.3 0.6 - - - -
305A VAL* 3.0 50.0 + - + +
307A ALA* 5.4 6.5 - - + -
310A ILE* 4.7 11.9 - - + -
313A THR* 4.7 18.8 - - + +
316A ALA* 2.9 45.0 + - + +
317A GLY* 2.9 9.6 + - - -
320A PHE* 4.0 5.7 - - - +
342A ASN* 2.6 50.2 + - - +
345A ALA* 3.3 26.5 - - - +
346A GLN* 3.1 32.9 + - - -
349A ILE* 3.9 18.6 - - + +
3001A ACT 3.9 2.6 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand MTP1002A
and protein in PDB entry 2AA0
(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 O5' I GLY 317A N III 2.9 5.2
1 O5' I ALA 316A O II 3.0 0.9
1 O5' I ACT 3001A O I 3.9 0.2
13 N1 I VAL 305A N III 4.6 0.8
15 N3 I GLN 346A NE2 III 3.1 14.3
18 O2' I ASN 342A ND2 III 2.6 24.6
18 O2' I ASN 342A O II 4.0 1.0
20 O3' I ASN 342A ND2 III 3.3 11.3
20 O3' I GLY 280A O II 4.1 0.5
20 O3' I ARG 279A N III 4.7 0.3
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand MTP1002A
in PDB entry 2AA0 (back
to top of page)
Total number of contacts is 101
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 O5' I ALA 316A C VI 2.9 29.6
1 O5' I GLY 317A N III 2.9 5.2
1 O5' I ALA 316A O II 3.0 0.9
1 O5' I GLY 317A CA VI 3.1 4.2
1 O5' I ALA 316A CB IV 3.3 1.9*
1 O5' I ACT 3001A O I 3.9 0.2
1 O5' I PHE 320A CB IV 4.0 0.3*
2 C5' VI THR 278A CB VI 3.8 18.8
2 C5' VI THR 278A CG2 IV 4.0 3.8
2 C5' VI THR 278A OG1 I 4.1 2.2
2 C5' VI ACT 3001A O I 4.1 2.5
2 C5' VI ALA 316A CB IV 4.3 0.9
2 C5' VI GLY 317A CA VI 4.4 0.2
2 C5' VI PHE 320A CB IV 4.4 1.3
2 C5' VI GLY 280A N III 5.3 2.2
2 C5' VI GLY 280A CA VI 5.5 0.2
3 C4' VIII ALA 345A CB IV 3.7 7.9
3 C4' VIII PHE 320A CD1 V 4.5 4.0
4 O4' II ALA 345A CB IV 3.3 4.9*
4 O4' II ALA 316A CB IV 3.7 2.8*
5 C1' VI ALA 345A CB IV 3.7 9.4
5 C1' VI ALA 345A C VI 4.8 4.0
5 C1' VI ALA 316A CB IV 4.8 0.7
5 C1' VI ILE 349A CD1 IV 4.8 0.4
5 C1' VI GLN 346A N III 4.9 0.4
5 C1' VI GLN 346A NE2 III 5.0 0.2
6 N9 I ILE 349A CD1 IV 4.3 0.4*
7 C8 V GLY 280A O II 3.8 3.6
7 C8 V GLY 280A C VI 4.0 1.8
7 C8 V GLY 280A CA VI 4.1 2.9
7 C8 V ILE 349A CD1 IV 4.6 4.0
7 C8 V ALA 316A CB IV 4.7 8.3
7 C8 V ILE 349A CG2 IV 5.1 0.7
7 C8 V THR 313A CG2 IV 5.2 2.9
7 C8 V THR 313A CB VI 5.5 1.1
8 N7 I GLY 280A C VI 3.8 5.1
8 N7 I GLY 280A CA VI 4.0 2.2
8 N7 I ILE 349A CD1 IV 4.5 1.4*
8 N7 I THR 313A CG2 IV 4.7 8.9*
9 C5 V GLY 280A O II 3.9 3.4
9 C5 V ILE 349A CD1 IV 4.1 3.8
10 C6 V HIS 281A CB IV 3.9 4.0
10 C6 V VAL 305A CG1 IV 3.9 2.7
10 C6 V ILE 349A CD1 IV 4.5 1.6
11 S6 VI HIS 281A CB IV 3.8 7.6
11 S6 VI HIS 281A CA VII 4.4 0.2
11 S6 VI HIS 281A N III 4.4 1.1
11 S6 VI VAL 305A CG1 IV 4.6 0.9
11 S6 VI ILE 310A CG1 IV 4.8 6.1
11 S6 VI ILE 310A CD1 IV 4.9 0.2
11 S6 VI THR 313A CG2 IV 5.5 5.8
11 S6 VI ILE 310A CG2 IV 5.6 0.4
12 CS IV HIS 281A CB IV 3.7 13.5
12 CS IV VAL 305A O II 3.9 18.2*
12 CS IV VAL 305A CG1 IV 4.1 1.1
12 CS IV HIS 281A CG V 4.6 0.9
12 CS IV ILE 310A CG1 IV 4.7 5.2
12 CS IV VAL 305A N III 5.4 0.7*
12 CS IV HIS 281A CD2 V 5.4 0.2
12 CS IV ALA 307A CA VII 5.4 4.9
12 CS IV ALA 307A CB IV 5.6 1.6
13 N1 I VAL 305A CG1 IV 3.0 11.3*
13 N1 I HIS 281A CB IV 4.0 2.6*
13 N1 I VAL 305A N III 4.6 0.8
13 N1 I VAL 304A CA VII 5.6 0.2
14 C2 V GLN 346A NE2 III 3.2 17.9
14 C2 V VAL 305A CG1 IV 3.2 14.1
14 C2 V VAL 302A CG1 IV 3.5 9.6
14 C2 V PRO 303A O II 3.7 4.3
14 C2 V ILE 349A CD1 IV 4.5 0.2
14 C2 V HIS 281A CA VII 4.6 1.8
14 C2 V VAL 305A N III 4.7 0.2
14 C2 V HIS 281A CB IV 4.8 0.2
14 C2 V VAL 304A CA VII 5.3 0.4
15 N3 I GLN 346A NE2 III 3.1 14.3
15 N3 I VAL 302A CG1 IV 3.3 3.6*
15 N3 I ILE 349A CD1 IV 4.1 1.8*
16 C4 V GLY 280A O II 3.8 2.2
16 C4 V ILE 349A CD1 IV 3.9 4.3
17 C2' VI GLY 280A O II 3.7 4.5
17 C2' VI ASN 342A ND2 III 3.8 1.1
17 C2' VI VAL 302A CG1 IV 3.8 6.1
18 O2' I ASN 342A ND2 III 2.6 24.6
18 O2' I ASN 342A CG VI 3.4 3.5
18 O2' I ASN 342A CA VII 3.5 8.5
18 O2' I ASN 342A CB IV 3.8 0.2*
18 O2' I ALA 345A CB IV 3.8 0.3*
18 O2' I VAL 302A CG1 IV 4.0 1.6*
18 O2' I ASN 342A O II 4.0 1.0
19 C3' VI GLY 280A O II 3.6 11.4
19 C3' VI THR 278A CB VI 4.4 2.0
19 C3' VI GLY 280A C VI 4.5 0.7
19 C3' VI GLY 280A N III 4.7 0.7
20 O3' I ASN 342A ND2 III 3.3 11.3
20 O3' I VAL 284A CG2 IV 3.6 16.3*
20 O3' I THR 278A CB VI 3.8 6.6
20 O3' I THR 278A CG2 IV 3.9 1.6*
20 O3' I GLY 280A O II 4.1 0.5
20 O3' I VAL 302A CG2 IV 4.3 0.2*
20 O3' I THR 278A CA VII 4.4 0.2
20 O3' I ARG 279A N III 4.7 0.3
------------------------------------------------------------------------
Table V
Complementarity values for the ligand MTP1002A
in PDB entry 2AA0 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 471
Actual value (Å2) 272
Normalised complementarity 0.58
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand MTP1002A
in PDB entry 2AA0 (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 | O5'
| I |
0.58 |
0.57
|
0.56 |
0.56
|
0.59 |
0.59
|
0.57 |
0.58
|
| 2 | C5'
| VI |
0.55 |
0.55
|
0.54 |
0.55
|
0.58 |
0.58
|
0.57 |
0.58
|
| 3 | C4'
| VIII |
0.54 |
0.54
|
0.54 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 4 | O4'
| II |
0.58 |
0.58
|
0.58 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 5 | C1'
| VI |
0.53 |
0.53
|
0.53 |
0.57
|
0.58 |
0.58
|
0.57 |
0.58
|
| 6 | N9
| I |
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 7 | C8
| V |
0.51 |
0.49
|
0.51 |
0.56
|
0.58 |
0.58
|
0.58 |
0.56
|
| 8 | N7
| I |
0.58 |
0.58
|
0.58 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 9 | C5
| V |
0.56 |
0.55
|
0.56 |
0.56
|
0.58 |
0.58
|
0.58 |
0.56
|
| 10 | C6
| V |
0.54 |
0.54
|
0.54 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 11 | S6
| VI |
0.49 |
0.49
|
0.48 |
0.57
|
0.58 |
0.58
|
0.57 |
0.58
|
| 12 | CS
| IV |
0.57 |
0.49
|
0.54 |
0.58
|
0.66 |
0.66
|
0.63 |
0.58
|
| 13 | N1
| I |
0.58 |
0.58
|
0.57 |
0.63
|
0.64 |
0.64
|
0.63 |
0.64
|
| 14 | C2
| V |
0.47 |
0.46
|
0.39 |
0.48
|
0.58 |
0.58
|
0.49 |
0.56
|
| 15 | N3
| I |
0.58 |
0.58
|
0.52 |
0.54
|
0.60 |
0.60
|
0.54 |
0.60
|
| 16 | C4
| V |
0.56 |
0.55
|
0.56 |
0.57
|
0.58 |
0.58
|
0.58 |
0.57
|
| 17 | C2'
| VI |
0.55 |
0.53
|
0.55 |
0.55
|
0.58 |
0.58
|
0.57 |
0.56
|
| 18 | O2'
| I |
0.58 |
0.57
|
0.44 |
0.48
|
0.59 |
0.59
|
0.45 |
0.58
|
| 19 | C3'
| VI |
0.58 |
0.53
|
0.57 |
0.53
|
0.58 |
0.58
|
0.57 |
0.53
|
| 20 | O3'
| I |
0.58 |
0.58
|
0.53 |
0.60
|
0.65 |
0.65
|
0.60 |
0.65
|
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 ACT 3001
2. Oxygen ("hydroxy" or "carbonyl")
2 O 3 OXT
Ligand MTP 1001
1. Carbon (in rings)
3 C4' 5 C1' 17 C2' 19 C3' 7 C8 9 C5
16 C4 9 C5 10 C6 14 C2 16 C4
2. Oxygen ("hydroxy" or "carbonyl")
1 O5' 18 O2' 20 O3'
3. Nitrogen ("hydrophilic")
6 N9 8 N7 13 N1 15 N3
Ligand MTP 1002
1. Carbon (in rings)
3 C4' 5 C1' 17 C2' 19 C3' 7 C8 9 C5
16 C4 9 C5 10 C6 14 C2 16 C4
2. Oxygen ("hydroxy" or "carbonyl")
1 O5' 18 O2' 20 O3'
3. Nitrogen ("hydrophilic")
6 N9 8 N7 13 N1 15 N3
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il