Contacts of ligand SY9 401D in PDB entry 3JAD
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 SY9 401D
in PDB entry 3JAD (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
----------------------------------------------------------
115C PHE* 4.1 22.2 - - - -
174C SER 4.7 4.2 + - - -
175C PHE* 3.3 34.1 - - + -
176C GLY* 3.5 24.5 - - - -
178C THR* 5.7 1.3 - - + -
218C TYR* 3.5 63.9 - - + +
220C THR* 3.6 38.4 + - + +
223C PHE* 3.4 40.7 - + + +
60D PHE* 3.8 33.9 - - + +
79D PHE* 3.6 38.5 - - + +
81D ARG* 2.8 52.2 + - + +
133D LEU* 3.4 33.2 - - + -
135D ARG* 3.3 39.9 - - - -
143D LEU* 3.5 25.0 - - + +
145D SER* 4.4 17.2 + - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand SY9 401D
and protein in PDB entry 3JAD
(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 NAH I SER 145D OG I 4.6 0.6
16 NAY I SER 174C O II 4.7 4.2
25 OAJ II ARG 81D NE III 2.8 21.1
25 OAJ II THR 220C OG1 I 4.0 3.8
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand SY9 401D
in PDB entry 3JAD (back
to top of page)
Total number of contacts is 94
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 CAV VI PHE 223C CE2 V 3.6 7.6
1 CAV VI PHE 223C CZ V 3.8 0.4
1 CAV VI PHE 223C CD2 V 4.0 0.7
1 CAV VI PHE 223C CE1 V 4.3 0.2
2 CAU IV TYR 218C CD2 V 3.5 23.8
2 CAU IV PHE 223C CE2 V 3.6 8.3
2 CAU IV TYR 218C CE2 V 3.7 1.1
2 CAU IV PHE 223C CD2 V 3.8 1.1
3 CAT IV TYR 218C CE1 V 3.9 6.1
3 CAT IV TYR 218C CD1 V 4.0 0.2
4 CAN IV TYR 218C CD1 V 4.6 1.8
4 CAN IV TYR 218C CG V 4.7 0.4
4 CAN IV TYR 218C CB IV 5.1 1.8
4 CAN IV THR 220C OG1 I 5.2 1.6*
5 CAK V SER 145D OG I 4.5 3.6
6 NAH I SER 145D OG I 4.6 0.6
7 CAA V THR 220C OG1 I 4.0 2.9
7 CAA V LEU 133D CD2 IV 4.1 2.2
7 CAA V SER 145D CB VI 5.2 0.9
8 CAF V LEU 143D CD2 IV 3.5 16.2
8 CAF V THR 220C OG1 I 3.8 7.4
8 CAF V LEU 133D CD2 IV 4.1 2.9
8 CAF V LEU 143D CG IV 4.5 0.9
8 CAF V SER 145D CB VI 5.6 0.2
9 CAE V ARG 135D NE III 3.3 17.3
9 CAE V THR 220C CG2 IV 3.6 11.9
9 CAE V LEU 133D CD2 IV 3.8 3.1
9 CAE V ARG 135D CD VII 3.8 4.9
9 CAE V LEU 143D CD2 IV 4.1 1.3
10 CAD V LEU 133D CD2 IV 3.4 8.7
10 CAD V ARG 135D NE III 3.5 9.6
10 CAD V ARG 135D NH1 III 3.9 8.1
10 CAD V THR 220C CG2 IV 4.0 6.7
10 CAD V GLY 176C CA VI 4.0 1.1
10 CAD V PHE 223C CZ V 4.0 2.7
10 CAD V PHE 223C CE1 V 4.4 0.9
10 CAD V THR 178C CG2 IV 5.7 1.3
11 CAC V LEU 133D CD2 IV 3.4 5.6
11 CAC V PHE 223C CZ V 3.4 16.2
11 CAC V GLY 176C CA VI 3.6 7.6
12 CAB V LEU 133D CD2 IV 3.7 0.2
12 CAB V PHE 223C CZ V 3.9 1.8
14 CAW IV LEU 133D CD2 IV 3.8 10.3
14 CAW IV PHE 175C CE1 V 3.9 7.4
14 CAW IV PHE 175C CZ V 4.3 1.1
14 CAW IV SER 145D OG I 4.8 3.6*
14 CAW IV PHE 79D CD1 V 5.7 0.2
15 CAX VI PHE 175C CD1 V 3.3 24.5
15 CAX VI GLY 176C N III 3.5 15.7
15 CAX VI PHE 175C CA VII 4.1 1.1
16 NAY I PHE 115C CZ V 4.6 2.0
16 NAY I SER 174C O II 4.7 4.2
16 NAY I PHE 223C CD2 V 4.8 0.4
16 NAY I PHE 223C CG V 5.0 0.2
16 NAY I PHE 223C CB IV 5.7 0.2*
17 CAS VI PHE 115C CZ V 4.1 20.2
17 CAS VI PHE 79D CE1 V 4.2 6.3
17 CAS VI PHE 79D CZ V 4.3 0.7
17 CAS VI TYR 218C CE2 V 5.0 1.8
17 CAS VI TYR 218C CZ V 5.0 0.2
18 CAR IV TYR 218C CZ V 4.2 0.7
18 CAR IV PHE 79D CD2 V 4.5 0.2
18 CAR IV PHE 79D CG V 4.5 0.9
19 CAQ IV PHE 79D CD2 V 3.6 19.3
19 CAQ IV PHE 79D CG V 3.8 0.4
19 CAQ IV PHE 79D CE2 V 3.8 2.2
19 CAQ IV TYR 218C OH I 3.9 11.0*
19 CAQ IV PHE 60D CD2 V 4.3 1.1
20 CAP VIII PHE 60D CD2 V 3.8 23.1
20 CAP VIII TYR 218C CE1 V 3.8 10.1
20 CAP VIII PHE 60D CB IV 4.0 7.0
20 CAP VIII PHE 60D CG V 4.0 0.4
20 CAP VIII PHE 79D CD2 V 4.1 1.8
20 CAP VIII TYR 218C CD1 V 4.4 0.2
21 OAO II PHE 79D CB IV 4.0 6.4*
21 OAO II PHE 60D CB IV 4.4 2.3*
22 CAM VIII TYR 218C CD1 V 4.7 4.5
22 CAM VIII TYR 218C CB IV 5.6 0.2
23 CAL IV ARG 81D CD VII 3.4 20.0
23 CAL IV ARG 81D NE III 3.9 0.2*
23 CAL IV ARG 81D CG IV 4.1 1.8
23 CAL IV ARG 81D CB IV 4.3 4.3
23 CAL IV SER 145D OG I 4.4 3.8*
24 CAI VI ARG 81D NE III 3.7 0.2
24 CAI VI ARG 81D CD VII 3.7 1.1
24 CAI VI ARG 81D CG IV 4.3 1.6
24 CAI VI THR 220C OG1 I 4.3 4.0
24 CAI VI SER 145D OG I 4.6 3.4
24 CAI VI SER 145D CB VI 4.7 1.1
25 OAJ II ARG 81D NE III 2.8 21.1
25 OAJ II ARG 81D CD VII 3.2 0.5
25 OAJ II ARG 81D CG IV 3.8 1.4*
25 OAJ II LEU 143D CD2 IV 3.8 6.6*
25 OAJ II THR 220C OG1 I 4.0 3.8
------------------------------------------------------------------------
Table V
Complementarity values for the ligand SY9 401D
in PDB entry 3JAD (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 482
Actual value (Å2) 395
Normalised complementarity 0.82
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand SY9 401D
in PDB entry 3JAD (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 | CAV
| VI |
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 2 | CAU
| IV |
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 3 | CAT
| IV |
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 4 | CAN
| IV |
0.82 |
0.82
|
0.82 |
0.82
|
0.83 |
0.83
|
0.83 |
0.83
|
| 5 | CAK
| V |
0.82 |
0.82
|
0.82 |
0.80
|
0.82 |
0.82
|
0.82 |
0.82
|
| 6 | NAH
| I |
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 7 | CAA
| V |
0.81 |
0.81
|
0.81 |
0.81
|
0.82 |
0.82
|
0.82 |
0.82
|
| 8 | CAF
| V |
0.74 |
0.74
|
0.74 |
0.79
|
0.82 |
0.82
|
0.82 |
0.82
|
| 9 | CAE
| V |
0.75 |
0.75
|
0.66 |
0.75
|
0.82 |
0.82
|
0.73 |
0.82
|
| 10 | CAD
| V |
0.75 |
0.75
|
0.68 |
0.75
|
0.82 |
0.82
|
0.75 |
0.82
|
| 11 | CAC
| V |
0.80 |
0.80
|
0.80 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 12 | CAB
| V |
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 14 | CAW
| IV |
0.79 |
0.79
|
0.79 |
0.82
|
0.83 |
0.83
|
0.83 |
0.83
|
| 15 | CAX
| VI |
0.82 |
0.82
|
0.75 |
0.75
|
0.82 |
0.82
|
0.75 |
0.82
|
| 16 | NAY
| I |
0.82 |
0.80
|
0.82 |
0.80
|
0.82 |
0.82
|
0.82 |
0.80
|
| 17 | CAS
| VI |
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 18 | CAR
| IV |
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 19 | CAQ
| IV |
0.87 |
0.87
|
0.87 |
0.82
|
0.87 |
0.87
|
0.87 |
0.87
|
| 20 | CAP
| VIII |
0.79 |
0.79
|
0.79 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 21 | OAO
| II |
0.82 |
0.82
|
0.82 |
0.86
|
0.86 |
0.86
|
0.86 |
0.86
|
| 22 | CAM
| VIII |
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
0.82 |
0.82
|
| 23 | CAL
| IV |
0.81 |
0.81
|
0.73 |
0.82
|
0.84 |
0.84
|
0.75 |
0.84
|
| 24 | CAI
| VI |
0.81 |
0.81
|
0.81 |
0.79
|
0.82 |
0.82
|
0.81 |
0.82
|
| 25 | OAJ
| II |
0.82 |
0.82
|
0.73 |
0.75
|
0.85 |
0.85
|
0.76 |
0.85
|
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 NAG 1
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 2
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 1
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 2
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 1
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 2
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 1
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 2
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 1
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 2
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand SY9 503
1. Carbon (in rings)
1 CAV 2 CAU 3 CAT 4 CAN 5 CAK 13 CAG
1 CAV 2 CAU 3 CAT 18 CAR 17 CAS 1 CAV
13 CAG 14 CAW 15 CAX 4 CAN 5 CAK 24 CAI
23 CAL 22 CAM 5 CAK 7 CAA 12 CAB 13 CAG
7 CAA 8 CAF 9 CAE 10 CAD 11 CAC 12 CAB
2. Oxygen ("hydroxy" or "carbonyl")
25 OAJ
3. Nitrogen ("hydrophilic")
6 NAH 16 NAY
Ligand SY9 401
1. Carbon (in rings)
1 CAV 2 CAU 3 CAT 4 CAN 5 CAK 13 CAG
1 CAV 2 CAU 3 CAT 18 CAR 17 CAS 1 CAV
13 CAG 14 CAW 15 CAX 4 CAN 5 CAK 24 CAI
23 CAL 22 CAM 5 CAK 7 CAA 12 CAB 13 CAG
7 CAA 8 CAF 9 CAE 10 CAD 11 CAC 12 CAB
2. Oxygen ("hydroxy" or "carbonyl")
25 OAJ
3. Nitrogen ("hydrophilic")
6 NAH 16 NAY
Ligand SY9 401
1. Carbon (in rings)
1 CAV 2 CAU 3 CAT 4 CAN 5 CAK 13 CAG
1 CAV 2 CAU 3 CAT 18 CAR 17 CAS 1 CAV
13 CAG 14 CAW 15 CAX 4 CAN 5 CAK 24 CAI
23 CAL 22 CAM 5 CAK 7 CAA 12 CAB 13 CAG
7 CAA 8 CAF 9 CAE 10 CAD 11 CAC 12 CAB
2. Oxygen ("hydroxy" or "carbonyl")
25 OAJ
3. Nitrogen ("hydrophilic")
6 NAH 16 NAY
Ligand SY9 401
1. Carbon (in rings)
1 CAV 2 CAU 3 CAT 4 CAN 5 CAK 13 CAG
1 CAV 2 CAU 3 CAT 18 CAR 17 CAS 1 CAV
13 CAG 14 CAW 15 CAX 4 CAN 5 CAK 24 CAI
23 CAL 22 CAM 5 CAK 7 CAA 12 CAB 13 CAG
7 CAA 8 CAF 9 CAE 10 CAD 11 CAC 12 CAB
2. Oxygen ("hydroxy" or "carbonyl")
25 OAJ
3. Nitrogen ("hydrophilic")
6 NAH 16 NAY
Ligand SY9 401
1. Carbon (in rings)
1 CAV 2 CAU 3 CAT 4 CAN 5 CAK 13 CAG
1 CAV 2 CAU 3 CAT 18 CAR 17 CAS 1 CAV
13 CAG 14 CAW 15 CAX 4 CAN 5 CAK 24 CAI
23 CAL 22 CAM 5 CAK 7 CAA 12 CAB 13 CAG
7 CAA 8 CAF 9 CAE 10 CAD 11 CAC 12 CAB
2. Oxygen ("hydroxy" or "carbonyl")
25 OAJ
3. Nitrogen ("hydrophilic")
6 NAH 16 NAY
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il