Contacts of ligand KTD 601A in PDB entry 4HSG
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 KTD 601A
in PDB entry 4HSG (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
----------------------------------------------------------
387A VAL* 3.8 7.8 - - + +
389A ASP* 3.5 18.7 + - + +
392A LYS* 3.5 35.9 - - + +
393A HIS* 3.7 33.7 - - - -
396A ARG* 2.9 72.3 + - + +
420A VAL* 3.4 27.4 - - + +
422A GLU* 2.8 43.4 + - - +
424A LEU* 3.7 28.5 - - + -
428A THR* 6.0 0.2 - - - -
466A THR* 2.8 27.9 + - - -
467A ALA* 3.5 15.5 - - - +
501A VAL* 4.1 15.9 - - + -
503A LEU* 3.8 30.4 - - + +
618A UNX 4.0 13.2 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand KTD 601A
and protein in PDB entry 4HSG
(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
------------------------------------------------------------------------
4 N1 I THR 466A OG1 I 2.8 24.5
4 N1 I ASP 389A O II 3.7 3.2
5 N2 I THR 466A OG1 I 3.6 1.4
10 N3 I GLU 422A OE1 II 3.1 9.5
10 N3 I GLU 422A OE2 II 3.5 0.2
12 OAB II ARG 396A NH1 III 2.9 18.9
13 N I GLU 422A OE2 II 2.8 14.3
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand KTD 601A
in PDB entry 4HSG (back
to top of page)
Total number of contacts is 75
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 CAJ V LEU 503A CD1 IV 3.8 8.1
1 CAJ V LYS 392A CB IV 4.0 6.7
1 CAJ V ARG 396A CG IV 4.3 4.5
2 CAV V LYS 392A CB IV 3.9 3.1
2 CAV V LEU 503A CD1 IV 4.0 3.1
3 SAP VI HIS 393A N III 3.7 19.1
3 SAP VI HIS 393A CA VII 3.7 7.9
3 SAP VI LEU 503A CG IV 3.9 18.4
3 SAP VI HIS 393A CB IV 3.9 2.9
3 SAP VI HIS 393A CD2 V 4.1 3.8
3 SAP VI ALA 467A CB IV 4.2 2.2
3 SAP VI LEU 503A CD2 IV 4.5 0.2
4 N1 I THR 466A OG1 I 2.8 24.5
4 N1 I THR 466A CB VI 3.5 2.0
4 N1 I ALA 467A CB IV 3.5 5.7*
4 N1 I ASP 389A O II 3.7 3.2
5 N2 I ASP 389A CB IV 3.5 12.9*
5 N2 I THR 466A OG1 I 3.6 1.4
5 N2 I ALA 467A CB IV 3.7 7.5*
5 N2 I VAL 387A CG1 IV 3.8 5.7*
6 CAU V LYS 392A CB IV 4.1 3.4
6 CAU V VAL 501A CG1 IV 4.2 3.6
7 CAI V LEU 424A CD2 IV 3.7 18.2
7 CAI V LYS 392A CD IV 3.9 6.7
7 CAI V VAL 501A CG1 IV 4.1 3.8
7 CAI V LYS 392A CE VII 4.5 1.8
7 CAI V ASP 389A CB IV 4.6 2.2
7 CAI V ASP 389A OD2 II 4.7 0.4
7 CAI V VAL 387A CG1 IV 4.7 2.0
7 CAI V THR 428A OG1 I 6.0 0.2
8 CAH V GLU 422A OE1 II 3.5 11.4
8 CAH V LYS 392A CD IV 3.5 6.7
8 CAH V LEU 424A CD2 IV 3.9 10.3
8 CAH V VAL 501A CG1 IV 4.3 4.3
8 CAH V GLU 422A CD VI 4.4 0.4
8 CAH V VAL 501A CG2 IV 4.5 0.7
9 CAS V LYS 392A CD IV 3.8 3.6
9 CAS V VAL 501A CG1 IV 4.5 3.6
10 N3 I GLU 422A OE1 II 3.1 9.5
10 N3 I GLU 422A OE2 II 3.5 0.2
10 N3 I GLU 422A CD VI 3.5 0.8
10 N3 I LYS 392A CD IV 4.0 2.0*
10 N3 I VAL 420A CG1 IV 4.1 1.4*
11 CAR VI GLU 422A OE2 II 3.6 0.2
11 CAR VI VAL 420A CG1 IV 3.7 7.4
11 CAR VI ARG 396A CD VII 4.0 2.0
11 CAR VI VAL 420A CG2 IV 4.1 0.2
11 CAR VI LYS 392A CD IV 5.0 1.3
11 CAR VI LYS 392A CG IV 5.3 0.4
12 OAB II ARG 396A NH1 III 2.9 18.9
12 OAB II ARG 396A CD VII 3.3 4.0
12 OAB II ARG 396A CG IV 3.3 0.3*
12 OAB II VAL 420A CG2 IV 3.8 2.4*
12 OAB II LEU 503A CD1 IV 4.0 0.5*
13 N I GLU 422A OE2 II 2.8 14.3
13 N I VAL 420A CG1 IV 3.4 1.2*
14 CA VI ARG 396A NH1 III 3.6 3.6
14 CA VI GLU 422A OE2 II 3.7 4.5
14 CA VI VAL 420A CG1 IV 3.7 11.9
14 CA VI VAL 420A CG2 IV 4.0 0.7
15 C VIII ARG 396A CD VII 3.6 4.3
15 C VIII GLU 422A OE2 II 4.4 0.7*
16 O II ARG 396A CD VII 3.6 5.5
16 O II UNX 618A UNK VI 4.0 13.2
16 O II GLU 422A OE2 II 4.3 1.4*
17 CAT V ARG 396A NE III 3.8 2.0
18 CAF V ARG 396A NE III 4.2 3.6
18 CAF V ARG 396A CD VII 4.5 0.9
19 CAD V ARG 396A NE III 4.8 1.1
20 CAC V ARG 396A NH2 III 4.5 1.8
21 CAE V ARG 396A NH2 III 3.8 9.2
22 CAG V ARG 396A CZ VI 3.6 9.9
22 CAG V ARG 396A NH2 III 3.7 0.4
22 CAG V ARG 396A NH1 III 3.9 0.2
22 CAG V VAL 420A CG2 IV 5.3 2.2
------------------------------------------------------------------------
Table V
Complementarity values for the ligand KTD 601A
in PDB entry 4HSG (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 528
Actual value (Å2) 287
Normalised complementarity 0.54
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand KTD 601A
in PDB entry 4HSG (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 | CAJ
| V |
0.47 |
0.47
|
0.47 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 2 | CAV
| V |
0.52 |
0.52
|
0.52 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 3 | SAP
| VI |
0.45 |
0.45
|
0.35 |
0.47
|
0.54 |
0.54
|
0.44 |
0.54
|
| 4 | N1
| I |
0.54 |
0.53
|
0.54 |
0.46
|
0.57 |
0.57
|
0.57 |
0.55
|
| 5 | N2
| I |
0.54 |
0.54
|
0.54 |
0.64
|
0.64 |
0.64
|
0.64 |
0.64
|
| 6 | CAU
| V |
0.52 |
0.52
|
0.52 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 7 | CAI
| V |
0.42 |
0.42
|
0.41 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 8 | CAH
| V |
0.46 |
0.42
|
0.46 |
0.50
|
0.54 |
0.54
|
0.54 |
0.50
|
| 9 | CAS
| V |
0.52 |
0.52
|
0.52 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 10 | N3
| I |
0.54 |
0.51
|
0.54 |
0.52
|
0.56 |
0.56
|
0.56 |
0.52
|
| 11 | CAR
| VI |
0.51 |
0.51
|
0.50 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 12 | OAB
| II |
0.54 |
0.54
|
0.46 |
0.48
|
0.56 |
0.56
|
0.47 |
0.56
|
| 13 | N
| I |
0.54 |
0.49
|
0.54 |
0.49
|
0.55 |
0.55
|
0.55 |
0.49
|
| 14 | CA
| VI |
0.50 |
0.48
|
0.48 |
0.51
|
0.54 |
0.54
|
0.53 |
0.53
|
| 15 | C
| VIII |
0.55 |
0.54
|
0.53 |
0.54
|
0.55 |
0.55
|
0.53 |
0.54
|
| 16 | O
| II |
0.55 |
0.54
|
0.53 |
0.54
|
0.55 |
0.55
|
0.53 |
0.54
|
| 17 | CAT
| V |
0.54 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 18 | CAF
| V |
0.54 |
0.54
|
0.53 |
0.53
|
0.54 |
0.54
|
0.53 |
0.54
|
| 19 | CAD
| V |
0.54 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 20 | CAC
| V |
0.54 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 21 | CAE
| V |
0.54 |
0.54
|
0.51 |
0.51
|
0.54 |
0.54
|
0.51 |
0.54
|
| 22 | CAG
| V |
0.53 |
0.53
|
0.53 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
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 KTD 601
1. Carbon (in rings)
1 CAJ 2 CAV 6 CAU 7 CAI 8 CAH 9 CAS
17 CAT 18 CAF 19 CAD 20 CAC 21 CAE 22 CAG
2. Oxygen ("hydroxy" or "carbonyl")
12 OAB 16 O
3. Nitrogen ("hydrophilic")
4 N1 5 N2 10 N3 13 N
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il