Contacts of ligand 1PW 302C in PDB entry 4NTO
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 1PW 302C
in PDB entry 4NTO (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
----------------------------------------------------------
52B ILE* 3.9 37.5 - - + -
150B ALA* 3.8 29.8 - - + +
153B LEU* 3.9 25.8 - - + +
154B GLY* 3.8 14.1 - - - +
156B TYR* 3.4 52.6 - - + +
157B ALA* 4.3 6.1 - - + -
301B 1PW 3.6 31.6 - - + -
302B 1PW 5.0 8.7 - - + -
52C ILE* 4.5 19.5 - - + +
55C LYS* 4.1 24.0 - - + -
56C PHE* 3.6 42.4 - - + +
59C MET* 4.3 21.3 - - + +
60C ALA* 3.6 46.2 - - + +
64C LYS* 3.5 20.4 + - - -
94C ALA* 5.3 4.2 - - - +
99C ARG* 3.0 32.9 + - - -
103C ARG* 2.5 61.1 + - + +
106C ARG* 5.6 1.6 - - - +
139C PHE* 5.4 6.1 - - + -
142C HIS* 5.4 1.6 + - - +
143C HIS* 3.7 24.0 + - - +
147C ILE* 3.5 43.3 - - + -
150C ALA* 5.3 6.3 - - + -
301C 1PW 3.9 70.7 + - + +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand 1PW 302C
and protein in PDB entry 4NTO
(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
------------------------------------------------------------------------
17 OAE I 1PW 301C OAE I 4.8 4.5
19 NAW I LYS 64C NZ III 3.9 2.2
22 OAC I HIS 143C NE2 I 3.7 18.5
22 OAC I HIS 142C O II 5.4 0.5
24 OAX II LYS 64C NZ III 3.5 9.5
26 OAF I ARG 99C NH2 III 3.0 23.2
27 OAG I ARG 103C NH1 III 4.4 1.9
27 OAG I ARG 99C NH2 III 4.5 1.2
28 OAD I ARG 103C NE III 2.5 32.9
28 OAD I ARG 103C NH1 III 2.9 4.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand 1PW 302C
in PDB entry 4NTO (back
to top of page)
Total number of contacts is 133
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 CAA IV 1PW 301B CAP IV 3.6 30.1
1 CAA IV ALA 150B O II 4.2 6.5*
1 CAA IV ILE 52B CG1 IV 4.4 14.6
1 CAA IV ALA 150B CB IV 4.7 5.8
1 CAA IV 1PW 301B CAR IV 4.8 0.2
1 CAA IV ALA 150B CA VII 4.8 0.4
1 CAA IV 1PW 301B CAT IV 4.9 1.3
1 CAA IV 1PW 302B CAJ IV 5.0 6.7
1 CAA IV 1PW 302B CAL IV 5.2 1.1
1 CAA IV 1PW 302B CAR IV 6.4 0.9
2 CAJ IV ALA 150B O II 3.8 17.0*
2 CAJ IV GLY 154B N III 3.8 8.3*
2 CAJ IV LEU 153B CB IV 3.9 5.6
2 CAJ IV GLY 154B CA VI 4.0 2.7
2 CAJ IV ILE 52B CG1 IV 4.6 2.2
2 CAJ IV LEU 153B CD1 IV 4.9 0.4
3 CAL IV 1PW 301C CAP IV 3.9 18.4
3 CAL IV LEU 153B CB IV 4.2 6.3
3 CAL IV 1PW 301C CAR IV 4.7 0.2
3 CAL IV LEU 153B CD1 IV 5.0 0.4
4 CAN IV ILE 52B CG2 IV 3.9 19.7
4 CAN IV GLY 154B CA VI 4.1 3.1
4 CAN IV ILE 52B CG1 IV 4.8 0.9
4 CAN IV ILE 52C CD1 IV 5.1 1.8
5 CAP IV 1PW 301C CAT IV 4.4 8.3
5 CAP IV ILE 52C CD1 IV 4.5 13.7
5 CAP IV 1PW 301C CAP IV 4.5 2.2
5 CAP IV ALA 157B CB IV 4.9 0.2
5 CAP IV ILE 52C CG1 IV 5.2 0.7
5 CAP IV ALA 150C CB IV 6.0 0.2
6 CAR IV LEU 153B O II 3.9 12.8*
6 CAR IV ALA 157B CB IV 4.3 5.8
6 CAR IV 1PW 301C CAQ IV 4.7 4.7
6 CAR IV 1PW 301C CAT IV 4.7 0.2
6 CAR IV LEU 153B CB IV 5.5 0.2
7 CAT IV 1PW 301C CAQ IV 4.5 5.4
7 CAT IV 1PW 301C CAS IV 4.5 3.1
7 CAT IV 1PW 301C CAT IV 4.7 1.3
7 CAT IV LYS 55C CB IV 4.7 5.4
7 CAT IV ILE 52C CD1 IV 5.0 2.2
7 CAT IV ALA 150C CB IV 5.3 5.4
7 CAT IV ILE 52C O II 5.6 1.1*
8 CAU IV TYR 156B CB IV 4.0 4.3
8 CAU IV TYR 156B O II 4.0 7.2*
8 CAU IV LYS 55C CG IV 4.1 17.5
8 CAU IV LYS 55C CB IV 4.3 1.1
9 CAS IV TYR 156B CB IV 3.4 17.9
9 CAS IV 1PW 301C CAQ IV 3.9 7.9
9 CAS IV TYR 156B O II 4.1 0.4*
10 CAQ IV PHE 56C CB IV 3.9 13.5
10 CAQ IV PHE 56C CA VII 3.9 1.6
10 CAQ IV PHE 56C N III 4.3 0.4*
10 CAQ IV 1PW 301C CAQ IV 4.6 1.6
10 CAQ IV TYR 156B O II 4.7 0.4*
10 CAQ IV ILE 147C CG1 IV 4.9 2.2
10 CAQ IV ILE 147C CG2 IV 5.0 2.2
10 CAQ IV 1PW 301C CAS IV 5.1 0.7
10 CAQ IV ILE 147C CA VII 5.8 0.2
10 CAQ IV ALA 150C CB IV 6.3 0.7
11 CAO IV ILE 147C CG1 IV 4.1 14.6
11 CAO IV ILE 147C CD1 IV 4.2 0.7
11 CAO IV PHE 56C CB IV 4.3 0.2
11 CAO IV TYR 156B CB IV 4.5 4.7
11 CAO IV TYR 156B CD1 V 4.6 4.5
11 CAO IV 1PW 301C CAQ IV 4.7 2.7
11 CAO IV 1PW 301C CAO IV 4.7 0.9
11 CAO IV 1PW 301C CAM IV 4.9 0.2
11 CAO IV 1PW 301C CAH IV 5.0 0.4
12 CAM IV PHE 56C CB IV 3.6 11.2
12 CAM IV PHE 56C CA VII 3.7 4.3
12 CAM IV PHE 56C O II 4.3 1.1*
12 CAM IV TYR 156B O II 5.1 4.5*
12 CAM IV TYR 156B CD1 V 5.2 1.6
12 CAM IV MET 59C CB IV 5.4 3.6
12 CAM IV MET 59C CG IV 6.0 0.2
13 CAK IV ILE 147C CD1 IV 3.5 17.0
13 CAK IV PHE 56C CB IV 4.0 9.9
13 CAK IV ILE 147C CG2 IV 4.6 0.9
13 CAK IV PHE 56C O II 4.6 0.2*
13 CAK IV HIS 143C NE2 I 4.9 2.0*
14 CAH IV ILE 147C CD1 IV 4.3 4.7
14 CAH IV 1PW 301C OAE I 4.6 7.6*
14 CAH IV MET 59C CB IV 5.1 2.0
14 CAH IV TYR 156B CD1 V 5.5 4.7
14 CAH IV TYR 156B CE1 V 5.9 0.2
15 CAI IV ALA 60C CB IV 4.6 5.4
15 CAI IV ALA 60C N III 4.7 1.6*
15 CAI IV MET 59C CB IV 4.7 0.2
15 CAI IV ILE 147C CD1 IV 5.1 0.7
15 CAI IV 1PW 301C OAE I 5.4 0.2*
16 CAZ VI MET 59C CB IV 4.3 14.1
17 OAE I MET 59C CB IV 4.8 0.7*
17 OAE I 1PW 301C OAE I 4.8 4.5
17 OAE I TYR 156B CD1 V 6.0 1.2
17 OAE I TYR 156B CE1 V 6.0 0.9
19 NAW I ALA 60C CA VII 3.7 6.3
19 NAW I LYS 64C NZ III 3.9 2.2
20 CAY VI ALA 60C CB IV 3.6 5.2
21 CAB IV ALA 60C CB IV 3.6 16.4
21 CAB IV ALA 60C CA VII 3.6 3.6
21 CAB IV ALA 60C O II 3.7 7.6*
21 CAB IV ARG 103C CD VII 3.8 17.3
21 CAB IV ARG 103C CG IV 3.9 2.0
21 CAB IV ARG 103C NE III 3.9 0.2*
21 CAB IV ARG 103C CB IV 4.1 1.3
21 CAB IV LYS 64C CE VII 4.5 0.7
21 CAB IV ARG 103C CZ VI 4.9 0.2
21 CAB IV PHE 139C CE1 V 5.4 5.8
21 CAB IV ARG 106C NH1 III 5.6 1.3*
21 CAB IV PHE 139C CD1 V 5.9 0.2
21 CAB IV ARG 106C CD VII 6.4 0.2
22 OAC I HIS 143C NE2 I 3.7 18.5
22 OAC I ALA 60C CB IV 3.9 0.2*
22 OAC I HIS 143C CD2 V 4.1 3.5
22 OAC I HIS 142C O II 5.4 0.5
22 OAC I HIS 142C CB IV 5.9 1.0*
23 CAV VIII LYS 64C NZ III 4.0 7.6
23 CAV VIII MET 59C CB IV 5.6 0.4
24 OAX II LYS 64C NZ III 3.5 9.5
24 OAX II LYS 64C CE VII 4.2 0.2
26 OAF I ARG 99C NH2 III 3.0 23.2
26 OAF I ARG 99C CZ VI 3.5 4.3
26 OAF I ARG 99C CD VII 3.9 3.8
26 OAF I ALA 94C CB IV 5.3 4.0*
26 OAF I ALA 94C CA VII 5.5 0.2
27 OAG I ARG 103C NH1 III 4.4 1.9
27 OAG I ARG 99C NH2 III 4.5 1.2
28 OAD I ARG 103C NE III 2.5 32.9
28 OAD I ARG 103C NH1 III 2.9 4.2
28 OAD I ARG 103C CZ VI 3.0 0.3
28 OAD I ARG 103C CG IV 4.0 0.7*
28 OAD I ARG 99C CD VII 4.4 0.3
28 OAD I LYS 64C CE VII 4.8 0.2
------------------------------------------------------------------------
Table V
Complementarity values for the ligand 1PW 302C
in PDB entry 4NTO (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 761
Actual value (Å2) 457
Normalised complementarity 0.60
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand 1PW 302C
in PDB entry 4NTO (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 | CAA
| IV |
0.46 |
0.44
|
0.46 |
0.60
|
0.62 |
0.62
|
0.62 |
0.60
|
| 2 | CAJ
| IV |
0.64 |
0.60
|
0.62 |
0.60
|
0.67 |
0.67
|
0.64 |
0.62
|
| 3 | CAL
| IV |
0.53 |
0.53
|
0.53 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 4 | CAN
| IV |
0.54 |
0.54
|
0.54 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 5 | CAP
| IV |
0.53 |
0.53
|
0.53 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 6 | CAR
| IV |
0.60 |
0.57
|
0.60 |
0.60
|
0.63 |
0.63
|
0.63 |
0.60
|
| 7 | CAT
| IV |
0.54 |
0.54
|
0.54 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 8 | CAU
| IV |
0.56 |
0.54
|
0.56 |
0.60
|
0.62 |
0.62
|
0.62 |
0.60
|
| 9 | CAS
| IV |
0.53 |
0.53
|
0.53 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 10 | CAQ
| IV |
0.55 |
0.55
|
0.54 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 11 | CAO
| IV |
0.54 |
0.54
|
0.54 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 12 | CAM
| IV |
0.58 |
0.56
|
0.56 |
0.60
|
0.61 |
0.61
|
0.60 |
0.60
|
| 13 | CAK
| IV |
0.53 |
0.53
|
0.53 |
0.60
|
0.61 |
0.61
|
0.61 |
0.61
|
| 14 | CAH
| IV |
0.60 |
0.60
|
0.60 |
0.60
|
0.62 |
0.62
|
0.62 |
0.62
|
| 15 | CAI
| IV |
0.59 |
0.59
|
0.58 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 16 | CAZ
| VI |
0.56 |
0.56
|
0.56 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 17 | OAE
| I |
0.60 |
0.60
|
0.60 |
0.59
|
0.60 |
0.60
|
0.60 |
0.60
|
| 19 | NAW
| I |
0.60 |
0.60
|
0.58 |
0.59
|
0.60 |
0.60
|
0.58 |
0.60
|
| 20 | CAY
| VI |
0.59 |
0.59
|
0.59 |
0.60
|
0.60 |
0.60
|
0.60 |
0.60
|
| 21 | CAB
| IV |
0.57 |
0.55
|
0.51 |
0.60
|
0.62 |
0.62
|
0.56 |
0.60
|
| 22 | OAC
| I |
0.60 |
0.60
|
0.60 |
0.55
|
0.60 |
0.60
|
0.60 |
0.60
|
| 23 | CAV
| VIII |
0.60 |
0.60
|
0.58 |
0.58
|
0.60 |
0.60
|
0.58 |
0.60
|
| 24 | OAX
| II |
0.60 |
0.60
|
0.57 |
0.57
|
0.60 |
0.60
|
0.57 |
0.60
|
| 26 | OAF
| I |
0.60 |
0.60
|
0.53 |
0.55
|
0.61 |
0.61
|
0.54 |
0.61
|
| 27 | OAG
| I |
0.60 |
0.60
|
0.59 |
0.59
|
0.60 |
0.60
|
0.59 |
0.60
|
| 28 | OAD
| I |
0.60 |
0.60
|
0.50 |
0.50
|
0.60 |
0.60
|
0.50 |
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 1PW 301
2. Oxygen ("hydroxy" or "carbonyl")
17 OAE 22 OAC
3. Nitrogen ("hydrophilic")
19 NAW
Ligand 1PW 302
2. Oxygen ("hydroxy" or "carbonyl")
11 OAE 16 OAC
3. Nitrogen ("hydrophilic")
13 NAW
Ligand PEG 303
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 7 O4
Ligand 1PW 301
2. Oxygen ("hydroxy" or "carbonyl")
13 OAE 18 OAC
3. Nitrogen ("hydrophilic")
15 NAW
Ligand 1PW 302
2. Oxygen ("hydroxy" or "carbonyl")
17 OAE 22 OAC
3. Nitrogen ("hydrophilic")
19 NAW
Ligand PEG 303
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 7 O4
Ligand 1PW 301
2. Oxygen ("hydroxy" or "carbonyl")
13 OAE 18 OAC
3. Nitrogen ("hydrophilic")
15 NAW
Ligand 1PW 302
2. Oxygen ("hydroxy" or "carbonyl")
17 OAE 22 OAC
3. Nitrogen ("hydrophilic")
19 NAW
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il