Contacts of ligand 469 400A in PDB entry 3ZSH
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 469 400A
in PDB entry 3ZSH (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
----------------------------------------------------------
30A VAL* 3.9 34.0 - - + +
31A GLY* 4.2 8.2 + - - -
35A TYR* 2.5 88.2 + + + -
38A VAL* 4.1 15.7 - - + +
49A ARG* 5.6 7.6 - - - -
51A ALA* 3.4 46.5 - - + +
53A LYS* 3.7 31.6 - - + -
71A GLU* 5.4 0.9 - - - -
75A LEU* 4.0 15.8 - - + -
84A ILE* 3.7 42.4 - - + -
86A LEU* 3.7 15.2 - - - -
104A LEU* 3.1 42.6 - - + -
105A VAL 3.7 7.1 - - - -
106A THR* 3.5 23.1 - - + -
107A HIS 3.7 9.0 - - - +
108A LEU* 3.6 22.6 - - + +
109A MET* 2.7 35.5 + - + +
110A GLY* 3.0 45.1 + - - +
111A ALA* 3.5 19.7 - - - +
112A ASP* 3.5 23.2 - - + -
115A ASN* 3.3 26.6 + - - -
154A SER 4.8 1.4 - - - +
157A ALA* 3.6 14.1 - - + -
167A LEU* 3.6 49.5 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand 469 400A
and protein in PDB entry 3ZSH
(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
------------------------------------------------------------------------
5 OAG II GLY 31A N III 4.2 5.5
12 NBJ I TYR 35A OH I 3.3 0.4
12 NBJ I ASN 115A OD1 II 3.9 0.4
20 OAH II MET 109A N III 2.7 32.4
20 OAH II GLY 110A N III 3.0 4.3
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand 469 400A
in PDB entry 3ZSH (back
to top of page)
Total number of contacts is 143
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 CAC VI GLY 110A O II 3.7 12.8
1 CAC VI GLY 110A C VI 4.6 0.4
1 CAC VI GLY 110A CA VI 4.8 1.8
1 CAC VI ARG 49A NH1 III 5.6 7.6
1 CAC VI LEU 108A CD2 IV 6.1 0.2
2 NBG I VAL 30A CG1 IV 5.0 0.2*
3 CAD VI VAL 30A CG1 IV 5.5 1.6
4 CAV VI VAL 30A CG1 IV 4.2 5.8
5 OAG II VAL 30A CG1 IV 3.9 9.5*
5 OAG II VAL 30A CB IV 4.1 3.1*
5 OAG II GLY 31A N III 4.2 5.5
5 OAG II VAL 30A CA VII 4.5 0.5
5 OAG II GLY 31A CA VI 5.1 0.2
6 CAU VIII VAL 30A CG1 IV 4.3 4.5
6 CAU VIII VAL 30A CB IV 4.6 0.2
7 OAF II GLY 110A O II 3.7 1.4*
7 OAF II GLY 110A CA VI 3.9 4.0
7 OAF II LEU 108A CD1 IV 4.1 9.9*
7 OAF II VAL 30A CG1 IV 4.1 4.0*
7 OAF II LEU 108A CD2 IV 4.6 2.8*
8 CBB V GLY 110A O II 3.5 2.7
8 CBB V TYR 35A OH I 4.4 0.7
8 CBB V VAL 30A CB IV 5.2 1.1
8 CBB V TYR 35A CE2 V 5.3 0.2
8 CBB V GLY 31A N III 5.4 0.2
9 CBC V GLY 110A C VI 3.6 3.4
9 CBC V TYR 35A OH I 3.9 1.6
9 CBC V TYR 35A CZ V 4.7 0.4
9 CBC V TYR 35A CE2 V 4.8 0.7
10 CAP V GLY 110A C VI 3.7 6.3
10 CAP V GLY 110A CA VI 3.8 0.9
10 CAP V GLY 110A N III 3.8 0.2
10 CAP V LEU 108A CD1 IV 4.0 5.2
10 CAP V TYR 35A OH I 4.5 0.2
10 CAP V TYR 35A CZ V 5.0 0.2
10 CAP V TYR 35A CE2 V 5.0 1.1
10 CAP V VAL 30A CB IV 5.6 2.0
10 CAP V VAL 30A CG2 IV 5.7 0.2
11 CAQ V GLY 110A O II 3.9 4.7
11 CAQ V TYR 35A OH I 4.0 2.2
11 CAQ V ASN 115A OD1 II 4.5 1.1
11 CAQ V TYR 35A CE2 V 5.5 0.2
11 CAQ V GLY 31A N III 5.6 0.9
11 CAQ V GLY 31A CA VI 5.8 1.3
12 NBJ I TYR 35A OH I 3.3 0.4
12 NBJ I ASN 115A OD1 II 3.9 0.4
13 CAE VI ASN 115A OD1 II 3.3 21.8
13 CAE VI TYR 35A OH I 3.4 9.4
13 CAE VI ASP 112A OD2 II 3.5 13.5
13 CAE VI ASP 112A CG VI 4.0 0.2
13 CAE VI ASN 115A CG VI 4.2 1.3
13 CAE VI ASN 115A ND2 III 4.3 2.0
14 CBD V TYR 35A OH I 3.1 3.6
14 CBD V ALA 111A CA VII 3.8 3.1
15 CAO V TYR 35A OH I 3.2 8.5
15 CAO V ALA 111A C VI 3.5 9.6
15 CAO V ASP 112A N III 3.8 1.1
15 CAO V TYR 35A CZ V 4.0 0.2
15 CAO V ASP 112A OD2 II 4.1 4.3
15 CAO V TYR 35A CE1 V 4.5 0.2
16 CAY V ALA 111A O II 3.6 3.8
17 CLA IV LEU 167A CD2 IV 3.6 26.6
17 CLA IV ALA 157A CB IV 3.6 11.2
17 CLA IV ALA 111A O II 3.6 3.1*
17 CLA IV ALA 157A CA VII 4.1 0.8
17 CLA IV ASP 112A CB IV 4.2 4.1
17 CLA IV SER 154A O II 4.8 1.4*
17 CLA IV TYR 35A CE1 V 4.8 1.8
18 CBA V GLY 110A N III 3.9 2.2
19 CAW VI LEU 108A CD1 IV 4.0 2.9
19 CAW VI MET 109A CB IV 4.3 0.7
20 OAH II MET 109A N III 2.7 32.4
20 OAH II GLY 110A N III 3.0 4.3
20 OAH II MET 109A CA VII 3.3 1.6
20 OAH II MET 109A CB IV 3.3 0.7*
20 OAH II LEU 108A C VI 3.6 1.2
22 CBF VI HIS 107A O II 3.7 8.3
22 CBF VI ALA 51A CB IV 4.3 0.7
23 CAS VI ALA 51A CB IV 3.4 15.3
23 CAS VI THR 106A CG2 IV 3.5 4.0
24 CAB IV ILE 84A CD1 IV 3.7 30.3
24 CAB IV LEU 167A CD1 IV 3.9 16.2
24 CAB IV ILE 84A CG1 IV 3.9 1.6
24 CAB IV THR 106A CG2 IV 4.0 2.5
24 CAB IV LEU 167A CG IV 4.1 1.3
24 CAB IV HIS 107A O II 4.1 0.7*
24 CAB IV ALA 157A CB IV 4.5 2.0
24 CAB IV MET 109A CG IV 5.0 0.2
25 CAT VI TYR 35A CZ V 4.2 2.0
25 CAT VI TYR 35A CE2 V 4.2 0.9
25 CAT VI LEU 108A CD1 IV 5.4 0.4
25 CAT VI VAL 38A CG1 IV 5.8 0.2
25 CAT VI VAL 30A CG2 IV 6.1 1.1
26 CBE VI LEU 167A CG IV 5.2 3.8
26 CBE VI LEU 167A CD2 IV 5.4 0.7
27 CAA IV TYR 35A CG V 2.5 40.6
27 CAA IV TYR 35A CD1 V 2.8 5.8
27 CAA IV TYR 35A CB IV 2.9 2.7
27 CAA IV TYR 35A CD2 V 3.0 2.9
27 CAA IV VAL 38A CG2 IV 4.7 0.2
27 CAA IV VAL 38A CG1 IV 4.9 0.2
27 CAA IV LEU 167A CD2 IV 6.0 0.4
28 NBH I ALA 51A CB IV 4.1 1.6*
28 NBH I VAL 38A CG1 IV 4.3 2.0*
29 CAR VI VAL 38A CG2 IV 4.1 11.0
29 CAR VI TYR 35A CB IV 4.3 1.3
29 CAR VI LYS 53A CD IV 5.0 1.1
29 CAR VI LYS 53A NZ III 5.8 0.4
30 CAZ V LYS 53A CB IV 4.4 2.0
30 CAZ V LYS 53A CD IV 4.5 0.4
31 CAM V THR 106A CG2 IV 4.0 1.3
31 CAM V ILE 84A CG2 IV 4.6 3.4
31 CAM V LYS 53A CD IV 4.7 4.5
31 CAM V LYS 53A NZ III 5.4 1.6
31 CAM V LEU 167A CG IV 6.4 0.4
32 CAK V THR 106A CG2 IV 3.8 5.4
32 CAK V LEU 75A CD1 IV 4.2 14.4
32 CAK V THR 106A CB VI 4.2 1.1
32 CAK V ILE 84A CG2 IV 4.3 7.2
32 CAK V LYS 53A CD IV 4.9 3.4
32 CAK V LEU 75A CD2 IV 5.0 0.7
32 CAK V GLU 71A OE2 II 5.4 0.9
33 CAX V THR 106A CG2 IV 3.7 4.0
33 CAX V LEU 104A CB IV 4.0 2.7
33 CAX V LYS 53A CB IV 4.3 1.3
33 CAX V LYS 53A CD IV 4.9 0.2
34 FAI VI LEU 104A CB IV 3.1 26.5
34 FAI VI LEU 104A C VI 3.6 4.2
34 FAI VI VAL 105A N III 3.7 3.2
34 FAI VI LEU 86A CD1 IV 3.7 15.2
34 FAI VI VAL 105A C VI 3.8 4.0
34 FAI VI THR 106A CB VI 3.9 1.6
34 FAI VI LEU 75A CD1 IV 4.0 0.8
35 CAL V ALA 51A O II 3.5 18.2
35 CAL V LEU 104A O II 3.6 9.2
35 CAL V THR 106A CG2 IV 3.6 2.5
35 CAL V LYS 53A CB IV 3.7 5.4
36 CAN V LYS 53A CB IV 3.7 11.2
36 CAN V THR 106A CG2 IV 3.8 0.7
36 CAN V ALA 51A O II 3.8 6.1
36 CAN V ALA 51A CB IV 3.9 4.0
36 CAN V ALA 51A C VI 4.2 0.7
36 CAN V VAL 38A CG1 IV 4.2 2.0
------------------------------------------------------------------------
Table V
Complementarity values for the ligand 469 400A
in PDB entry 3ZSH (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 774
Actual value (Å2) 544
Normalised complementarity 0.70
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand 469 400A
in PDB entry 3ZSH (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 | CAC
| VI |
0.70 |
0.67
|
0.68 |
0.65
|
0.70 |
0.70
|
0.68 |
0.67
|
| 2 | NBG
| I |
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 3 | CAD
| VI |
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 4 | CAV
| VI |
0.69 |
0.69
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 5 | OAG
| II |
0.70 |
0.70
|
0.69 |
0.72
|
0.74 |
0.74
|
0.72 |
0.74
|
| 6 | CAU
| VIII |
0.69 |
0.69
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 7 | OAF
| II |
0.71 |
0.70
|
0.71 |
0.75
|
0.75 |
0.75
|
0.75 |
0.75
|
| 8 | CBB
| V |
0.70 |
0.69
|
0.70 |
0.69
|
0.70 |
0.70
|
0.70 |
0.70
|
| 9 | CBC
| V |
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 10 | CAP
| V |
0.68 |
0.68
|
0.68 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 11 | CAQ
| V |
0.70 |
0.69
|
0.70 |
0.68
|
0.70 |
0.70
|
0.70 |
0.69
|
| 12 | NBJ
| I |
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 13 | CAE
| VI |
0.70 |
0.61
|
0.70 |
0.58
|
0.70 |
0.70
|
0.70 |
0.61
|
| 14 | CBD
| V |
0.70 |
0.70
|
0.70 |
0.69
|
0.70 |
0.70
|
0.70 |
0.70
|
| 15 | CAO
| V |
0.70 |
0.69
|
0.70 |
0.67
|
0.70 |
0.70
|
0.70 |
0.69
|
| 16 | CAY
| V |
0.70 |
0.69
|
0.70 |
0.69
|
0.70 |
0.70
|
0.70 |
0.69
|
| 17 | CLA
| IV |
0.61 |
0.60
|
0.60 |
0.70
|
0.72 |
0.72
|
0.71 |
0.70
|
| 18 | CBA
| V |
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 19 | CAW
| VI |
0.69 |
0.69
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 20 | OAH
| II |
0.70 |
0.70
|
0.60 |
0.61
|
0.71 |
0.71
|
0.61 |
0.71
|
| 22 | CBF
| VI |
0.70 |
0.68
|
0.70 |
0.68
|
0.70 |
0.70
|
0.70 |
0.68
|
| 23 | CAS
| VI |
0.65 |
0.65
|
0.65 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 24 | CAB
| IV |
0.57 |
0.56
|
0.57 |
0.70
|
0.71 |
0.71
|
0.71 |
0.70
|
| 25 | CAT
| VI |
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 26 | CBE
| VI |
0.69 |
0.69
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 27 | CAA
| IV |
0.69 |
0.69
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 28 | NBH
| I |
0.70 |
0.70
|
0.70 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
| 29 | CAR
| VI |
0.67 |
0.67
|
0.67 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 30 | CAZ
| V |
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 31 | CAM
| V |
0.68 |
0.68
|
0.67 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 32 | CAK
| V |
0.62 |
0.62
|
0.62 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 33 | CAX
| V |
0.68 |
0.68
|
0.68 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 34 | FAI
| VI |
0.59 |
0.59
|
0.59 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 35 | CAL
| V |
0.68 |
0.61
|
0.68 |
0.63
|
0.70 |
0.70
|
0.70 |
0.63
|
| 36 | CAN
| V |
0.66 |
0.64
|
0.66 |
0.69
|
0.70 |
0.70
|
0.70 |
0.69
|
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 469 400
1. Carbon (in rings)
8 CBB 9 CBC 14 CBD 11 CAQ 9 CBC 10 CAP
18 CBA 16 CAY 15 CAO 14 CBD 22 CBF 23 CAS
26 CBE 25 CAT 30 CAZ 31 CAM 32 CAK 33 CAX
35 CAL 36 CAN
2. Oxygen ("hydroxy" or "carbonyl")
5 OAG 7 OAF 20 OAH
3. Nitrogen ("hydrophilic")
2 NBG 12 NBJ 21 NBI 28 NBH
Ligand BOG 1353
1. Carbon (in rings)
1 C1 3 C2 5 C3 7 C4 9 C5
2. Oxygen ("hydroxy" or "carbonyl")
4 O2 6 O3 8 O4 12 O6
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il