Contacts of ligand COG 307A in PDB entry 1LY3
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 COG 307A
in PDB entry 1LY3 (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 ILE* 2.9 36.6 + - - +
11A VAL* 3.5 30.9 + - - -
12A ALA* 3.8 9.6 - - + +
24A SER* 4.5 9.6 - - - -
25A LEU* 3.4 55.2 - - + +
27A TRP* 6.1 0.4 - - - -
32A GLU* 2.7 41.8 + - - -
33A ILE* 3.2 68.5 - - + +
35A TYR* 5.0 1.2 - - - -
36A PHE* 3.5 50.2 - + - +
61A THR* 3.9 25.1 - - - -
64A SER* 3.3 37.2 - - - +
65A ILE* 4.2 25.4 - - + +
66A PRO* 3.6 26.5 - - + -
69A PHE* 3.2 46.0 - + - -
72A LEU* 4.4 10.9 - - + +
123A ILE* 2.7 49.2 + - - +
144A THR* 3.7 3.0 + - - -
207A NAP 3.4 29.1 - + - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand COG 307A
and protein in PDB entry 1LY3
(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
------------------------------------------------------------------------
18 N1' I GLU 32A OE1 II 2.8 13.3
19 N2' I GLU 32A OE2 II 2.7 22.2
19 N2' I VAL 11A O II 3.5 2.6
19 N2' I THR 144A OG1 I 3.7 3.0
21 N4' I ILE 123A O II 2.7 28.3
21 N4' I ILE 10A O II 2.9 15.0
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand COG 307A
in PDB entry 1LY3 (back
to top of page)
Total number of contacts is 111
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 C2B V ALA 12A N III 3.8 6.7
1 C2B V PHE 36A CD1 V 3.9 6.1
2 C4B V NAP 207A O7N II 3.4 5.4
2 C4B V PHE 36A CE1 V 3.5 5.2
3 C4A V NAP 207A O7N II 3.6 2.7
3 C4A V PHE 36A CE1 V 3.7 2.7
4 C5B V NAP 207A C4N V 3.6 8.1
4 C5B V PHE 36A CZ V 3.9 3.4
5 C6B V LEU 25A CD1 IV 4.1 1.6
5 C6B V PHE 36A CZ V 4.5 0.9
5 C6B V NAP 207A C4N V 4.5 0.4
6 C7B V ILE 33A CD1 IV 3.2 16.6
6 C7B V LEU 25A CD1 IV 3.5 7.6
6 C7B V PHE 36A CD2 V 4.7 0.9
7 C8A V PHE 36A CD1 V 3.9 4.3
7 C8A V NAP 207A O7N II 4.1 2.7
7 C8A V NAP 207A C7N VI 4.7 0.7
8 C21 VIII SER 64A O II 3.3 22.0*
8 C21 VIII LEU 25A CG IV 4.2 14.1
8 C21 VIII LEU 25A N III 4.2 11.2
8 C21 VIII SER 64A C VI 4.2 1.3
8 C21 VIII SER 64A CB VI 4.3 6.5
8 C21 VIII SER 24A CA VII 4.5 5.8
8 C21 VIII LEU 25A CB IV 4.5 0.7
8 C21 VIII SER 24A CB VI 4.5 3.8
8 C21 VIII NAP 207A O2D I 5.0 0.7
8 C21 VIII PRO 66A CD IV 5.1 0.2
8 C21 VIII PRO 66A CG IV 5.7 0.2
9 C7' VI LEU 25A CD1 IV 4.0 3.1
9 C7' VI ILE 65A CG1 IV 4.5 4.7
9 C7' VI LEU 25A CG IV 4.7 0.9
9 C7' VI SER 64A CB VI 4.9 5.8
9 C7' VI THR 61A CG2 IV 5.0 1.6
9 C7' VI NAP 207A C5N V 5.3 2.5
9 C7' VI NAP 207A C6N V 5.5 1.6
9 C7' VI NAP 207A O2D I 5.6 0.7
10 C61 VI THR 61A CG2 IV 3.9 23.6
10 C61 VI PHE 36A CZ V 4.2 12.1
10 C61 VI ILE 123A CD1 IV 4.2 10.3
10 C61 VI ILE 65A CG1 IV 4.3 6.7
10 C61 VI PHE 36A CE2 V 4.4 0.2
10 C61 VI ILE 123A O II 4.5 0.7
10 C61 VI ILE 65A CD1 IV 4.7 0.4
10 C61 VI LEU 72A CD1 IV 5.4 0.4
11 C1' V ILE 65A CG1 IV 4.4 2.0
12 C2' V LEU 25A CD1 IV 4.0 1.8
12 C2' V SER 64A O II 4.3 1.6
13 C3' V PRO 66A CD IV 3.7 9.6
13 C3' V PRO 66A CG IV 4.3 2.5
13 C3' V ILE 33A CD1 IV 4.4 4.3
13 C3' V ILE 33A CG1 IV 5.2 0.9
14 C4' V PRO 66A CD IV 3.6 9.2
14 C4' V ILE 33A CD1 IV 4.1 5.8
14 C4' V PRO 66A CG IV 4.3 2.0
14 C4' V PHE 69A CD2 V 4.7 0.7
14 C4' V ILE 33A CG1 IV 4.9 1.1
14 C4' V ILE 33A CG2 IV 5.2 0.4
14 C4' V PHE 69A CE2 V 5.3 0.4
15 C5' V ILE 33A CD1 IV 4.1 5.2
15 C5' V PRO 66A CD IV 4.2 2.7
15 C5' V ILE 65A CG2 IV 4.4 1.1
16 C51 VIII PHE 69A CB IV 3.2 33.2
16 C51 VIII PHE 69A CG V 3.3 6.3
16 C51 VIII PHE 69A CD2 V 3.8 0.4
16 C51 VIII PHE 69A CD1 V 3.8 4.0
16 C51 VIII ILE 65A CG2 IV 4.5 0.9
16 C51 VIII PHE 69A CE2 V 4.6 0.7
16 C51 VIII LEU 72A CD2 IV 4.7 5.6
16 C51 VIII ILE 33A CG2 IV 4.8 13.5
16 C51 VIII PHE 69A CZ V 5.0 0.2
16 C51 VIII PHE 36A CD2 V 6.2 0.2
17 C6' V ILE 65A CG1 IV 4.2 8.1
17 C6' V ILE 65A CG2 IV 4.6 0.2
17 C6' V PHE 36A CE2 V 5.0 3.4
17 C6' V LEU 72A CD2 IV 5.4 0.9
18 N1' I GLU 32A OE1 II 2.8 13.3
18 N1' I GLU 32A CD VI 3.5 0.4
18 N1' I PHE 36A CD1 V 4.0 2.0
18 N1' I PHE 36A CB IV 4.0 1.0*
18 N1' I ALA 12A CB IV 4.1 2.0*
19 N2' I GLU 32A OE2 II 2.7 22.2
19 N2' I VAL 11A C VI 3.5 16.8
19 N2' I VAL 11A O II 3.5 2.6
19 N2' I GLU 32A CD VI 3.5 0.8
19 N2' I THR 144A OG1 I 3.7 3.0
19 N2' I ILE 10A CG1 IV 3.8 11.3*
19 N2' I ILE 10A CD1 IV 4.3 2.0*
19 N2' I PHE 36A CB IV 4.7 1.0*
19 N2' I TYR 35A CD2 V 5.0 1.2
20 N3' I VAL 11A CA VII 3.5 11.5
20 N3' I ILE 10A CG1 IV 3.5 8.3*
21 N4' I ILE 123A O II 2.7 28.3
21 N4' I ILE 10A O II 2.9 15.0
21 N4' I NAP 207A C4N V 3.4 3.8
21 N4' I ILE 123A C VI 3.5 2.4
21 N4' I ILE 123A CA VII 3.6 4.2
21 N4' I ILE 123A CB IV 3.6 3.4*
21 N4' I PHE 36A CE1 V 3.6 0.8
22 C8' V ILE 33A CD1 IV 3.2 19.3
22 C8' V GLU 32A OE1 II 3.7 5.2
22 C8' V LEU 25A CD1 IV 3.9 8.1
22 C8' V PHE 36A CG V 4.4 2.0
22 C8' V ALA 12A CB IV 5.5 0.9
22 C8' V TRP 27A NE1 III 6.1 0.4
23 O2' II LEU 25A CD1 IV 3.4 6.1*
24 O5' II ILE 65A CG2 IV 4.3 1.2*
24 O5' II LEU 72A CD2 IV 4.4 4.0*
24 O5' II ILE 33A CD1 IV 4.5 1.2*
24 O5' II ILE 33A CG2 IV 4.8 0.2*
24 O5' II PHE 36A CE2 V 5.1 3.6
24 O5' II PHE 36A CD2 V 5.3 0.5
------------------------------------------------------------------------
Table V
Complementarity values for the ligand COG 307A
in PDB entry 1LY3 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 584
Actual value (Å2) 429
Normalised complementarity 0.73
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand COG 307A
in PDB entry 1LY3 (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 | C2B
| V |
0.73 |
0.73
|
0.71 |
0.71
|
0.73 |
0.73
|
0.71 |
0.73
|
| 2 | C4B
| V |
0.73 |
0.72
|
0.73 |
0.72
|
0.73 |
0.73
|
0.73 |
0.72
|
| 3 | C4A
| V |
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 4 | C5B
| V |
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 5 | C6B
| V |
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 6 | C7B
| V |
0.65 |
0.65
|
0.65 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 7 | C8A
| V |
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 8 | C21
| VIII |
0.76 |
0.68
|
0.70 |
0.69
|
0.81 |
0.81
|
0.75 |
0.73
|
| 9 | C7'
| VI |
0.70 |
0.70
|
0.70 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 10 | C61
| VI |
0.59 |
0.59
|
0.59 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 11 | C1'
| V |
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 12 | C2'
| V |
0.73 |
0.72
|
0.73 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 13 | C3'
| V |
0.68 |
0.68
|
0.68 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 14 | C4'
| V |
0.67 |
0.67
|
0.67 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 15 | C5'
| V |
0.70 |
0.70
|
0.70 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 16 | C51
| VIII |
0.55 |
0.55
|
0.55 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 17 | C6'
| V |
0.70 |
0.70
|
0.70 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 18 | N1'
| I |
0.73 |
0.69
|
0.73 |
0.70
|
0.74 |
0.74
|
0.74 |
0.70
|
| 19 | N2'
| I |
0.73 |
0.65
|
0.73 |
0.69
|
0.78 |
0.78
|
0.78 |
0.70
|
| 20 | N3'
| I |
0.73 |
0.73
|
0.70 |
0.76
|
0.76 |
0.76
|
0.72 |
0.76
|
| 21 | N4'
| I |
0.73 |
0.59
|
0.72 |
0.60
|
0.75 |
0.75
|
0.73 |
0.60
|
| 22 | C8'
| V |
0.64 |
0.62
|
0.64 |
0.72
|
0.73 |
0.73
|
0.73 |
0.72
|
| 23 | O2'
| II |
0.73 |
0.73
|
0.73 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
| 24 | O5'
| II |
0.73 |
0.73
|
0.73 |
0.76
|
0.76 |
0.76
|
0.76 |
0.76
|
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 NAP 207
1. Carbon (in rings)
6 C4B 12 C1B 10 C2B 8 C3B 14 C8A 16 C5A
22 C4A 16 C5A 17 C6A 20 C2A 22 C4A 29 C4D
35 C1D 33 C2D 31 C3D 37 C2N 38 C3N 42 C4N
43 C5N 44 C6N
2. Oxygen ("hydroxy" or "carbonyl")
9 O3B 11 O2B 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Ligand COG 307
1. Carbon (in rings)
1 C2B 7 C8A 3 C4A 2 C4B 3 C4A 4 C5B
5 C6B 6 C7B 22 C8' 7 C8A 11 C1' 12 C2'
13 C3' 14 C4' 15 C5' 17 C6'
3. Nitrogen ("hydrophilic")
18 N1' 19 N2' 20 N3' 21 N4' 25 N6'
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il