Contacts of ligand GH32501T in PDB entry 3AVW
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 GH32501T
in PDB entry 3AVW (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
----------------------------------------------------------
906A VAL* 5.2 0.9 - - - +
908A LYS* 2.8 34.0 + - - -
914A ARG* 3.0 77.8 + - - -
968A ASP* 3.3 13.3 + - - -
969A LEU 3.5 0.2 + - - -
970A SER* 2.4 42.4 + - - +
971A ALA* 4.1 5.0 - - - -
972A ALA* 2.9 38.1 + - + +
973A SER* 2.8 24.7 + - - +
1017A MET* 3.7 32.8 - - + +
1018A GLY 3.5 15.2 + - - -
1022A THR* 4.3 3.1 + - - +
1023A PHE* 4.1 3.1 - - - +
1026A GLU* 2.5 40.0 + - - +
1053A ASP* 3.3 18.3 + - - +
1077A ASN* 3.8 10.2 + - - -
3001A CA 2.4 87.5 - - - -
3002A CA 4.3 2.4 - - - -
2008G C* 3.0 87.0 + + - +
2103T C* 2.5 60.8 + + - -
2104T G* 3.1 50.8 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand GH32501T
and protein in PDB entry 3AVW
(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
------------------------------------------------------------------------
2 O1G I LYS 908A NZ III 2.8 23.0
2 O1G I ASN 1077A OD1 II 5.1 0.3
3 O2G I ASP 968A OD1 II 3.3 10.9
3 O2G I SER 970A O II 3.4 0.5
3 O2G I LEU 969A O II 3.5 0.2
3 O2G I ASN 1077A OD1 II 3.8 3.6
4 O3G I SER 970A O II 2.4 21.1
4 O3G I ASN 1077A OD1 II 4.2 6.2
4 O3G I SER 970A OG I 4.2 2.3
4 O3G I LYS 908A NZ III 4.6 0.3
5 O3B II LYS 908A NZ III 3.7 4.3
7 O1B I ARG 914A NH2 III 3.4 15.9
7 O1B I ALA 972A N III 3.8 7.3
7 O1B I SER 970A O II 4.0 0.3
7 O1B I LYS 908A NZ III 4.6 0.5
7 O1B I SER 973A N III 5.2 0.2
8 O2B I ALA 972A N III 2.9 21.5
8 O2B I SER 970A O II 3.1 1.0
9 O3A II ARG 914A NH2 III 3.5 5.4
9 O3A II ARG 914A NH1 III 3.7 0.5
11 O1A I ASP 1053A OD1 II 3.3 7.1
11 O1A I ASP 968A OD2 II 3.7 2.4
12 O2A I ARG 914A NH1 III 3.0 18.4
12 O2A I C 2008G OP2 I 5.1 6.2
13 O5' II ARG 914A NH2 III 3.8 0.2
19 O2' I GLU 1026A OE2 II 2.5 19.4
19 O2' I SER 973A OG I 2.8 9.7
19 O2' I THR 1022A OG1 I 4.3 2.9
23 N7 I ARG 914A NH1 III 3.6 1.8
23 N7 I C 2008G N4 III 3.7 0.4
26 O6 I C 2103T N4 III 3.0 16.6
26 O6 I G 2104T O6 II 3.4 3.5
26 O6 I C 2008G N4 III 3.5 5.4
26 O6 I ARG 914A NE III 3.7 8.7
27 N1 I C 2103T N3 II 2.8 16.8
29 N2 I C 2103T O2 II 2.5 25.7
29 N2 I G 2104T N3 II 3.3 1.0
29 N2 I GLY 1018A N III 3.5 15.2
30 N3 I G 2104T N2 III 3.5 0.4
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand GH32501T
in PDB entry 3AVW (back
to top of page)
Total number of contacts is 120
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
------------------------------------------------------------------------
2 O1G I LYS 908A NZ III 2.8 23.0
2 O1G I LYS 908A CE VII 3.4 4.5
2 O1G I ASN 1077A OD1 II 5.1 0.3
3 O2G I CA 3001A CA VI 2.4 30.5
3 O2G I ASP 968A OD1 II 3.3 10.9
3 O2G I SER 970A O II 3.4 0.5
3 O2G I LEU 969A O II 3.5 0.2
3 O2G I ASN 1077A OD1 II 3.8 3.6
4 O3G I SER 970A O II 2.4 21.1
4 O3G I SER 970A C VI 3.4 2.8
4 O3G I SER 970A CA VII 3.7 2.8
4 O3G I ASN 1077A OD1 II 4.2 6.2
4 O3G I SER 970A OG I 4.2 2.3
4 O3G I LYS 908A NZ III 4.6 0.3
5 O3B II SER 970A O II 2.5 11.6*
5 O3B II LYS 908A NZ III 3.7 4.3
5 O3B II ALA 971A CA VII 4.2 0.5
7 O1B I ARG 914A NH2 III 3.4 15.9
7 O1B I ALA 972A N III 3.8 7.3
7 O1B I SER 970A O II 4.0 0.3
7 O1B I ALA 971A CA VII 4.1 4.0
7 O1B I ALA 971A C VI 4.2 0.5
7 O1B I MET 1017A SD VIII 4.2 6.4
7 O1B I MET 1017A CE IV 4.5 2.9*
7 O1B I LYS 908A NZ III 4.6 0.5
7 O1B I SER 973A N III 5.2 0.2
8 O2B I CA 3001A CA VI 2.5 28.2
8 O2B I ALA 972A N III 2.9 21.5
8 O2B I SER 970A O II 3.1 1.0
8 O2B I ALA 972A CB IV 3.4 4.7*
9 O3A II ARG 914A NH2 III 3.5 5.4
9 O3A II ARG 914A NH1 III 3.7 0.5
11 O1A I CA 3001A CA VI 2.6 28.8
11 O1A I ASP 1053A OD1 II 3.3 7.1
11 O1A I ASP 968A OD2 II 3.7 2.4
11 O1A I CA 3002A CA VI 4.3 2.4
11 O1A I C 2008G C3' VIII 4.5 1.2
12 O2A I ARG 914A NH1 III 3.0 18.4
12 O2A I C 2008G C3' VIII 4.7 3.5
12 O2A I LYS 908A CE VII 5.0 1.2
12 O2A I C 2008G OP2 I 5.1 6.2
12 O2A I C 2008G C6 V 5.6 0.3
12 O2A I C 2008G C5 V 5.9 0.2
13 O5' II ARG 914A NH2 III 3.8 0.2
14 C5' VIII C 2008G C3' VIII 3.4 20.2*
14 C5' VIII ASP 1053A OD1 II 3.6 6.3*
14 C5' VIII ASP 1053A CG VI 3.8 1.8
15 C4' VIII GLU 1026A OE1 II 3.6 13.5*
15 C4' VIII C 2008G C2' II 3.7 3.4*
15 C4' VIII ASP 1053A CB IV 4.0 3.1
15 C4' VIII C 2008G O2' IV 4.1 0.4
16 O4' II C 2008G C2' II 3.0 11.8*
16 O4' II C 2008G O2' IV 3.5 0.7*
16 O4' II C 2008G O2 II 3.6 0.2*
16 O4' II GLU 1026A OE2 II 3.8 1.7*
16 O4' II PHE 1023A CE1 V 4.1 0.7
17 C3' IV SER 973A OG I 3.5 10.1*
17 C3' IV GLU 1026A OE1 II 3.8 3.8*
17 C3' IV ALA 972A CB IV 4.0 4.7
17 C3' IV MET 1017A SD VIII 4.3 0.2
18 C2' VI SER 973A OG I 3.4 4.0
18 C2' VI MET 1017A CG IV 3.7 7.0
18 C2' VI MET 1017A SD VIII 3.8 0.4
19 O2' I GLU 1026A OE2 II 2.5 19.4
19 O2' I SER 973A OG I 2.8 9.7
19 O2' I SER 973A CB VI 3.6 0.7
19 O2' I MET 1017A CG IV 3.7 4.0*
19 O2' I THR 1022A OG1 I 4.3 2.9
19 O2' I PHE 1023A CD1 V 4.6 0.9
19 O2' I PHE 1023A CA VII 5.0 0.5
19 O2' I PHE 1023A CB IV 5.3 0.2*
20 C1' VI C 2008G O2 II 3.7 6.5
20 C1' VI GLU 1026A OE2 II 4.0 1.6
20 C1' VI G 2104T N2 III 4.1 2.7
20 C1' VI PHE 1023A CD1 V 4.3 0.4
22 C8 V C 2008G N3 II 3.6 8.7
22 C8 V C 2008G C2 V 3.6 2.2
22 C8 V ARG 914A NH2 III 3.8 4.7
22 C8 V C 2008G C4 V 3.8 0.9
22 C8 V ARG 914A CZ VI 3.9 0.9
22 C8 V C 2008G N1 V 4.0 1.1
22 C8 V C 2008G C5 V 4.2 1.1
23 N7 I C 2008G C4 V 3.5 7.7
23 N7 I ARG 914A CZ VI 3.5 9.5
23 N7 I ARG 914A NH1 III 3.6 1.8
23 N7 I C 2008G N4 III 3.7 0.4
23 N7 I C 2008G C5 V 4.0 0.8
24 C5 V C 2008G N3 II 3.6 3.8
24 C5 V ARG 914A NE III 4.0 3.8
25 C6 V G 2104T O6 II 3.3 6.7
25 C6 V C 2103T N4 III 3.6 0.9
25 C6 V C 2008G N4 III 3.8 0.2
25 C6 V ARG 914A CD VII 4.0 6.3
26 O6 I C 2103T N4 III 3.0 16.6
26 O6 I G 2104T O6 II 3.4 3.5
26 O6 I C 2008G N4 III 3.5 5.4
26 O6 I ARG 914A NE III 3.7 8.7
26 O6 I VAL 906A CG1 IV 5.2 0.9*
27 N1 I C 2103T N3 II 2.8 16.8
27 N1 I G 2104T C6 V 3.1 2.8
27 N1 I ARG 914A CD VII 4.6 1.8
28 C2 V G 2104T N1 III 3.3 6.3
28 C2 V C 2103T N3 II 3.5 0.4
28 C2 V C 2103T C2 V 4.0 0.2
28 C2 V MET 1017A CB IV 4.3 6.1
29 N2 I C 2103T O2 II 2.5 25.7
29 N2 I G 2104T C4 V 3.1 15.4
29 N2 I G 2104T N3 II 3.3 1.0
29 N2 I G 2104T N9 V 3.5 0.8
29 N2 I GLY 1018A N III 3.5 15.2
29 N2 I MET 1017A C VI 4.0 1.0
29 N2 I G 2104T C1' VI 4.1 0.8
29 N2 I MET 1017A CA VII 4.3 0.2
29 N2 I THR 1022A CG2 IV 6.0 0.2*
30 N3 I G 2104T C2 V 3.3 5.7
30 N3 I G 2104T N2 III 3.5 0.4
30 N3 I MET 1017A CG IV 3.9 3.0*
30 N3 I PHE 1023A CB IV 6.1 0.4*
31 C4 V G 2104T N1 III 3.6 4.7
31 C4 V MET 1017A CG IV 4.4 1.6
------------------------------------------------------------------------
Table V
Complementarity values for the ligand GH32501T
in PDB entry 3AVW (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 618
Actual value (Å2) 448
Normalised complementarity 0.73
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand GH32501T
in PDB entry 3AVW (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 |
|---|
| 2 | O1G
| I |
0.73 |
0.73
|
0.64 |
0.65
|
0.73 |
0.73
|
0.64 |
0.73
|
| 3 | O2G
| I |
0.73 |
0.68
|
0.73 |
0.68
|
0.73 |
0.73
|
0.73 |
0.68
|
| 4 | O3G
| I |
0.73 |
0.64
|
0.72 |
0.63
|
0.73 |
0.73
|
0.72 |
0.64
|
| 5 | O3B
| II |
0.76 |
0.73
|
0.75 |
0.71
|
0.76 |
0.76
|
0.75 |
0.73
|
| 7 | O1B
| I |
0.73 |
0.70
|
0.64 |
0.66
|
0.74 |
0.74
|
0.65 |
0.71
|
| 8 | O2B
| I |
0.73 |
0.72
|
0.66 |
0.67
|
0.74 |
0.74
|
0.67 |
0.74
|
| 9 | O3A
| II |
0.73 |
0.73
|
0.71 |
0.71
|
0.73 |
0.73
|
0.71 |
0.73
|
| 11 | O1A
| I |
0.73 |
0.69
|
0.73 |
0.70
|
0.73 |
0.73
|
0.73 |
0.69
|
| 12 | O2A
| I |
0.73 |
0.72
|
0.66 |
0.65
|
0.73 |
0.73
|
0.66 |
0.72
|
| 13 | O5'
| II |
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 14 | C5'
| VIII |
0.81 |
0.73
|
0.81 |
0.79
|
0.81 |
0.81
|
0.81 |
0.73
|
| 15 | C4'
| VIII |
0.77 |
0.71
|
0.77 |
0.73
|
0.78 |
0.78
|
0.78 |
0.73
|
| 16 | O4'
| II |
0.77 |
0.73
|
0.77 |
0.73
|
0.77 |
0.77
|
0.77 |
0.73
|
| 17 | C3'
| IV |
0.76 |
0.74
|
0.76 |
0.73
|
0.77 |
0.77
|
0.77 |
0.76
|
| 18 | C2'
| VI |
0.70 |
0.70
|
0.70 |
0.71
|
0.73 |
0.73
|
0.73 |
0.72
|
| 19 | O2'
| I |
0.73 |
0.66
|
0.72 |
0.64
|
0.74 |
0.74
|
0.74 |
0.68
|
| 20 | C1'
| VI |
0.73 |
0.70
|
0.72 |
0.69
|
0.73 |
0.73
|
0.72 |
0.70
|
| 22 | C8
| V |
0.73 |
0.70
|
0.71 |
0.68
|
0.73 |
0.73
|
0.71 |
0.70
|
| 23 | N7
| I |
0.73 |
0.73
|
0.72 |
0.72
|
0.73 |
0.73
|
0.72 |
0.73
|
| 24 | C5
| V |
0.73 |
0.71
|
0.71 |
0.70
|
0.73 |
0.73
|
0.71 |
0.71
|
| 25 | C6
| V |
0.73 |
0.70
|
0.70 |
0.70
|
0.73 |
0.73
|
0.70 |
0.70
|
| 26 | O6
| I |
0.73 |
0.72
|
0.63 |
0.62
|
0.73 |
0.73
|
0.63 |
0.72
|
| 27 | N1
| I |
0.73 |
0.67
|
0.72 |
0.67
|
0.73 |
0.73
|
0.72 |
0.67
|
| 28 | C2
| V |
0.71 |
0.71
|
0.69 |
0.70
|
0.73 |
0.73
|
0.71 |
0.72
|
| 29 | N2
| I |
0.73 |
0.64
|
0.68 |
0.59
|
0.73 |
0.73
|
0.68 |
0.64
|
| 30 | N3
| I |
0.73 |
0.73
|
0.72 |
0.74
|
0.74 |
0.74
|
0.74 |
0.74
|
| 31 | C4
| V |
0.72 |
0.72
|
0.71 |
0.71
|
0.73 |
0.73
|
0.71 |
0.73
|
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 GH3 2501
1. Carbon (in rings)
15 C4' 20 C1' 18 C2' 17 C3' 22 C8 24 C5
31 C4 24 C5 25 C6 28 C2 31 C4
2. Oxygen ("hydroxy" or "carbonyl")
19 O2' 26 O6
3. Nitrogen ("hydrophilic")
21 N9 23 N7 27 N1 29 N2 30 N3
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il