Contacts of ligand SFG 245A in PDB entry 1QAQ
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 SFG 245A
in PDB entry 1QAQ (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
----------------------------------------------------------
10A GLN* 3.1 48.3 - - - +
11A ASN* 2.9 38.1 + - - +
12A PHE* 3.7 18.4 - - + +
13A ILE 3.0 33.2 + - - +
36A GLU* 3.4 10.9 + - - -
37A ILE* 4.3 6.1 - - + +
38A GLY* 3.0 40.1 + - - +
39A SER 3.1 19.0 + - - -
40A GLY* 3.2 32.9 - - - -
41A LYS 4.6 0.7 - - - -
42A GLY 5.3 0.2 - - - -
43A HIS* 4.4 8.9 + - - +
44A PHE* 3.7 19.0 + - - +
58A ILE 3.8 16.4 + - - -
59A GLU* 2.4 44.8 + - - -
60A ILE* 3.3 54.8 + - + +
61A ASP* 3.9 5.2 - - - +
64A LEU* 3.3 17.3 - - - +
83A LYS 3.8 2.7 - - - -
84A ASP* 3.4 21.6 + - - -
85A ILE* 3.0 43.4 + - + +
86A LEU* 4.8 3.0 - - - +
101A ASN* 2.5 71.2 + - + +
102A ILE 4.6 5.5 - - - -
103A PRO* 3.8 25.2 - - + +
106A ILE* 3.6 30.8 - - + +
110A ILE* 5.5 1.3 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand SFG 245A
and protein in PDB entry 1QAQ
(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 N I GLY 38A O II 3.0 17.0
1 N I SER 39A O II 3.1 7.5
1 N I GLU 36A OE2 II 3.4 10.9
1 N I PHE 44A N III 5.0 0.6
4 O II ILE 13A N III 3.0 19.6
4 O II HIS 43A ND1 I 4.8 1.4
5 OXT II ASN 101A ND2 III 2.5 34.5
5 OXT II ILE 13A N III 3.8 0.3
9 NE I ASN 101A O II 2.9 12.3
9 NE I ASN 11A OD1 II 2.9 26.7
9 NE I ASN 11A O II 3.1 0.8
9 NE I ASN 101A OD1 II 4.3 0.2
9 NE I ASN 11A N III 4.3 1.2
14 O3' I GLU 59A OE1 II 2.7 16.1
16 O2' I GLU 59A OE2 II 2.4 22.2
23 N6 I ASP 84A OD1 II 3.4 14.8
23 N6 I ASP 84A OD2 II 3.9 1.0
24 N1 I ILE 85A N III 3.0 16.8
24 N1 I ASP 84A OD1 II 3.6 0.6
26 N3 I ILE 60A N III 3.3 8.1
26 N3 I ILE 58A O II 3.8 6.5
26 N3 I GLY 38A N III 4.3 0.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand SFG 245A
in PDB entry 1QAQ (back
to top of page)
Total number of contacts is 128
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 N I GLY 38A O II 3.0 17.0
1 N I SER 39A O II 3.1 7.5
1 N I GLU 36A OE2 II 3.4 10.9
1 N I PHE 44A CD2 V 4.1 8.7
1 N I ASN 101A CB IV 4.4 3.2*
1 N I PHE 44A CB IV 4.7 1.6*
1 N I PHE 44A N III 5.0 0.6
2 CA VI SER 39A O II 3.2 11.4
2 CA VI GLY 40A CA VI 3.9 2.5
2 CA VI PHE 12A CD1 V 4.2 1.6
2 CA VI LYS 41A N III 4.6 0.7
2 CA VI GLY 42A N III 5.3 0.2
2 CA VI HIS 43A N III 5.5 0.7
3 C VI ILE 13A N III 3.8 4.5
3 C VI PHE 44A CD2 V 4.1 5.4
3 C VI PHE 12A CA VII 4.1 1.8
3 C VI HIS 43A CB IV 5.3 0.4
4 O II ILE 13A N III 3.0 19.6
4 O II ILE 13A O II 3.5 8.8*
4 O II PHE 12A CA VII 3.7 2.1
4 O II PHE 12A CB IV 3.8 3.3*
4 O II PHE 12A CD1 V 4.1 0.9
4 O II PHE 44A CD2 V 4.3 0.5
4 O II HIS 43A CB IV 4.4 6.4*
4 O II HIS 43A ND1 I 4.8 1.4
5 OXT II ASN 101A ND2 III 2.5 34.5
5 OXT II ASN 101A CG VI 3.3 0.2
5 OXT II ASN 101A CB IV 3.4 0.9*
5 OXT II PHE 44A CD2 V 3.7 2.1
5 OXT II PHE 44A CE2 V 3.7 0.2
5 OXT II ILE 13A N III 3.8 0.3
6 CB IV GLY 38A O II 3.6 2.2*
6 CB IV GLY 40A CA VI 3.7 12.1
6 CB IV PHE 12A CD1 V 3.8 7.6
7 CG IV ASN 101A O II 3.2 9.6*
7 CG IV GLY 38A O II 3.8 1.8*
7 CG IV ASN 11A O II 3.8 0.2*
7 CG IV ASN 101A CB IV 4.1 0.2
8 CD VI ASN 11A O II 3.2 9.2
8 CD VI GLN 10A OE1 II 4.4 0.7
9 NE I ASN 101A O II 2.9 12.3
9 NE I ASN 11A OD1 II 2.9 26.7
9 NE I ASN 11A O II 3.1 0.8
9 NE I ASN 101A CG VI 4.2 4.2
9 NE I ASN 101A OD1 II 4.3 0.2
9 NE I ASN 11A N III 4.3 1.2
9 NE I ILE 102A C VI 4.6 5.5
9 NE I PRO 103A N VI 4.6 0.6
9 NE I PRO 103A CG IV 4.6 1.2*
9 NE I PRO 103A CA IV 5.0 0.6*
10 C5' IV GLN 10A OE1 II 3.4 9.0*
10 C5' IV ASN 101A O II 3.6 5.8*
10 C5' IV PRO 103A CG IV 3.8 8.5
10 C5' IV PRO 103A CD IV 4.1 0.9
10 C5' IV ASN 101A C VI 4.7 0.2
10 C5' IV ILE 37A O II 5.2 0.2*
11 C4' VIII GLY 38A CA VI 3.8 6.7
12 O4' II GLY 38A CA VI 3.2 8.0
12 O4' II ILE 37A O II 4.3 1.4*
12 O4' II PRO 103A CG IV 4.4 0.3*
12 O4' II PRO 103A CD IV 4.6 1.2*
12 O4' II ILE 37A C VI 4.6 0.2
12 O4' II ILE 37A CG2 IV 5.6 0.3*
13 C3' VI GLN 10A OE1 II 3.5 2.5
13 C3' VI LEU 64A CD1 IV 4.3 3.1
13 C3' VI GLN 10A CD VI 4.3 1.6
13 C3' VI GLN 10A CG IV 4.3 2.2
13 C3' VI GLN 10A CB IV 4.3 2.0
13 C3' VI PHE 12A CE1 V 4.8 1.1
14 O3' I GLU 59A OE1 II 2.7 16.1
14 O3' I GLY 40A CA VI 3.2 18.4
14 O3' I LEU 64A CD1 IV 3.3 4.2*
15 C2' VI GLN 10A OE1 II 3.1 7.9
15 C2' VI GLN 10A CD VI 3.7 2.7
16 O2' I GLU 59A OE2 II 2.4 22.2
16 O2' I LEU 64A CD1 IV 3.4 10.0*
16 O2' I ASP 61A CB IV 3.9 5.2*
16 O2' I ILE 60A CG2 IV 4.1 2.4*
16 O2' I GLN 10A CG IV 4.1 3.6*
17 C1' VI GLU 59A OE2 II 3.3 4.0
17 C1' VI GLU 59A OE1 II 3.6 2.5
17 C1' VI GLY 38A CA VI 3.8 0.4
19 C8 V GLN 10A OE1 II 3.4 11.7
19 C8 V PRO 103A CG IV 3.8 11.0
19 C8 V GLN 10A CD VI 4.1 3.8
19 C8 V ILE 60A CG2 IV 4.2 3.4
19 C8 V PRO 103A CD IV 4.4 0.2
19 C8 V GLN 10A NE2 III 4.5 0.7
20 N7 I ILE 106A CD1 IV 3.6 12.5*
20 N7 I ILE 60A CG2 IV 4.1 1.6*
20 N7 I PRO 103A CG IV 4.3 0.2*
20 N7 I ILE 60A CD1 IV 4.8 1.0*
21 C5 V ILE 60A CG2 IV 3.7 3.8
21 C5 V ILE 106A CD1 IV 4.1 2.5
21 C5 V ILE 85A CG2 IV 4.8 0.2
21 C5 V ILE 110A CD1 IV 5.5 1.3
22 C6 V ILE 60A CB IV 3.8 4.7
22 C6 V ILE 85A CG2 IV 3.9 4.9
22 C6 V ILE 106A CD1 IV 4.2 0.2
23 N6 I ASP 84A OD1 II 3.4 14.8
23 N6 I ILE 106A CD1 IV 3.6 15.6*
23 N6 I ASP 84A CG VI 3.7 5.1
23 N6 I ILE 60A CD1 IV 3.8 5.3*
23 N6 I ILE 85A CG2 IV 3.8 3.4*
23 N6 I ASP 84A OD2 II 3.9 1.0
23 N6 I LEU 86A CG IV 4.8 2.2*
23 N6 I LEU 86A CD1 IV 5.0 0.8*
24 N1 I ILE 85A N III 3.0 16.8
24 N1 I ILE 85A CG2 IV 3.5 1.2*
24 N1 I ILE 60A CB IV 3.6 3.4*
24 N1 I ASP 84A OD1 II 3.6 0.6
25 C2 V ILE 60A N III 3.5 15.9
25 C2 V ILE 60A CB IV 3.5 0.9
25 C2 V ILE 85A N III 3.5 10.5
25 C2 V LYS 83A O II 3.8 2.7
25 C2 V ILE 58A O II 3.9 9.9
25 C2 V ILE 85A CB IV 4.0 6.3
25 C2 V GLY 38A N III 4.9 0.9
25 C2 V ILE 37A CG2 IV 4.9 0.7
26 N3 I ILE 60A N III 3.3 8.1
26 N3 I ILE 58A O II 3.8 6.5
26 N3 I GLY 38A CA VI 4.1 2.6
26 N3 I GLY 38A N III 4.3 0.2
26 N3 I ILE 37A CG2 IV 4.9 0.4*
27 C4 V ILE 60A CG2 IV 3.5 4.3
27 C4 V GLY 38A CA VI 4.7 0.2
27 C4 V ILE 37A CG2 IV 5.3 2.9
27 C4 V PRO 103A CD IV 5.6 0.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand SFG 245A
in PDB entry 1QAQ (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 595
Actual value (Å2) 356
Normalised complementarity 0.60
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand SFG 245A
in PDB entry 1QAQ (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 | N
| I |
0.60 |
0.48
|
0.60 |
0.49
|
0.62 |
0.62
|
0.61 |
0.50
|
| 2 | CA
| VI |
0.60 |
0.56
|
0.59 |
0.56
|
0.60 |
0.60
|
0.59 |
0.56
|
| 3 | C
| VI |
0.60 |
0.60
|
0.58 |
0.58
|
0.60 |
0.60
|
0.58 |
0.60
|
| 4 | O
| II |
0.63 |
0.60
|
0.56 |
0.56
|
0.66 |
0.66
|
0.59 |
0.63
|
| 5 | OXT
| II |
0.60 |
0.60
|
0.48 |
0.49
|
0.60 |
0.60
|
0.49 |
0.60
|
| 6 | CB
| IV |
0.61 |
0.60
|
0.61 |
0.60
|
0.61 |
0.61
|
0.61 |
0.60
|
| 7 | CG
| IV |
0.64 |
0.60
|
0.64 |
0.60
|
0.64 |
0.64
|
0.64 |
0.60
|
| 8 | CD
| VI |
0.60 |
0.57
|
0.60 |
0.57
|
0.60 |
0.60
|
0.60 |
0.57
|
| 9 | NE
| I |
0.60 |
0.46
|
0.60 |
0.47
|
0.61 |
0.61
|
0.60 |
0.47
|
| 10 | C5'
| IV |
0.62 |
0.57
|
0.62 |
0.60
|
0.65 |
0.65
|
0.65 |
0.60
|
| 11 | C4'
| VIII |
0.60 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 12 | O4'
| II |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 13 | C3'
| VI |
0.57 |
0.57
|
0.57 |
0.59
|
0.60 |
0.60
|
0.60 |
0.59
|
| 14 | O3'
| I |
0.60 |
0.55
|
0.60 |
0.56
|
0.61 |
0.61
|
0.61 |
0.56
|
| 15 | C2'
| VI |
0.60 |
0.57
|
0.60 |
0.57
|
0.60 |
0.60
|
0.60 |
0.57
|
| 16 | O2'
| I |
0.60 |
0.52
|
0.60 |
0.60
|
0.67 |
0.67
|
0.67 |
0.60
|
| 17 | C1'
| VI |
0.60 |
0.58
|
0.60 |
0.58
|
0.60 |
0.60
|
0.60 |
0.58
|
| 19 | C8
| V |
0.55 |
0.51
|
0.55 |
0.56
|
0.60 |
0.60
|
0.60 |
0.56
|
| 20 | N7
| I |
0.60 |
0.60
|
0.60 |
0.65
|
0.65 |
0.65
|
0.65 |
0.65
|
| 21 | C5
| V |
0.57 |
0.57
|
0.57 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 22 | C6
| V |
0.57 |
0.57
|
0.57 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 23 | N6
| I |
0.60 |
0.55
|
0.60 |
0.64
|
0.69 |
0.69
|
0.69 |
0.64
|
| 24 | N1
| I |
0.60 |
0.60
|
0.54 |
0.56
|
0.61 |
0.61
|
0.56 |
0.61
|
| 25 | C2
| V |
0.57 |
0.53
|
0.48 |
0.47
|
0.60 |
0.60
|
0.51 |
0.56
|
| 26 | N3
| I |
0.60 |
0.58
|
0.57 |
0.55
|
0.60 |
0.60
|
0.57 |
0.58
|
| 27 | C4
| V |
0.57 |
0.57
|
0.57 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
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 SFG 245
1. Carbon (in rings)
11 C4' 17 C1' 15 C2' 13 C3' 19 C8 21 C5
27 C4 21 C5 22 C6 25 C2 27 C4
2. Oxygen ("hydroxy" or "carbonyl")
4 O 5 OXT 14 O3' 16 O2'
3. Nitrogen ("hydrophilic")
1 N 9 NE 18 N9 20 N7 23 N6 24 N1
26 N3
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il