Contacts of ligand AHE 304A in PDB entry 3BHM
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 AHE 304A
in PDB entry 3BHM (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
----------------------------------------------------------
93A ALA* 3.6 20.7 - - + +
94A PHE* 2.9 28.2 + - - +
95A LYS* 3.3 36.5 + - - +
96A VAL* 2.8 53.6 + - + +
97A ALA 5.1 5.9 + - - -
98A ASP 5.8 0.2 + - - -
102A PHE* 3.5 15.5 - - - -
105A GLN* 3.0 31.0 + - - -
109A THR* 4.9 4.0 + - - -
141A MET* 3.8 17.2 - - - +
190A SER 3.6 1.9 - - - +
191A SER* 3.5 16.2 + - - +
192A ALA* 2.9 29.0 + - - +
193A TYR* 2.7 67.5 + - + +
234A MET* 3.6 25.3 + - + +
235A ALA* 4.0 18.2 + - - -
307A AB3 3.4 60.3 + - + +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand AHE 304A
and protein in PDB entry 3BHM
(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
------------------------------------------------------------------------
1 N1 I GLN 105A OE1 II 3.0 14.8
1 N1 I GLN 105A NE2 III 4.4 1.8
1 N1 I LYS 95A O II 4.7 4.9
1 N1 I ALA 97A N III 5.1 5.9
1 N1 I ASP 98A N III 5.8 0.2
6 OE1 II SER 191A OG I 4.9 3.3
7 N2 I PHE 94A O II 2.9 6.1
7 N2 I VAL 96A N III 4.3 0.6
12 OE2 I AB3 307A N15 I 4.8 1.2
12 OE2 I SER 191A OG I 5.4 0.9
15 N3 I MET 234A O II 3.9 0.2
15 N3 I ALA 235A O II 4.8 0.2
19 O32 II VAL 96A N III 2.8 23.6
21 O11 II ALA 192A N III 2.9 17.0
22 O12 II TYR 193A N III 2.7 25.8
22 O12 II ALA 192A N III 3.3 0.2
22 O12 II THR 109A OG1 I 4.9 4.0
22 O12 II PHE 94A N III 5.2 1.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand AHE 304A
in PDB entry 3BHM (back
to top of page)
Total number of contacts is 106
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 N1 I GLN 105A OE1 II 3.0 14.8
1 N1 I GLN 105A CD VI 4.0 1.8
1 N1 I GLN 105A NE2 III 4.4 1.8
1 N1 I LYS 95A O II 4.7 4.9
1 N1 I PHE 102A CE1 V 4.9 2.8
1 N1 I PHE 102A CD1 V 5.0 1.0
1 N1 I ALA 97A N III 5.1 5.9
1 N1 I ASP 98A N III 5.8 0.2
2 CA1 VI GLN 105A OE1 II 3.4 8.3
2 CA1 VI PHE 94A O II 4.0 4.7
2 CA1 VI PHE 94A CB IV 4.4 1.3
2 CA1 VI PHE 94A C VI 4.7 0.2
3 CB1 IV PHE 94A O II 3.7 2.2*
3 CB1 IV VAL 96A CA VII 4.8 8.1
3 CB1 IV SER 191A OG I 4.9 2.5*
3 CB1 IV SER 191A CB VI 5.6 0.4
3 CB1 IV VAL 96A CB IV 5.6 0.2
4 CG1 IV PHE 94A O II 3.1 7.0*
4 CG1 IV TYR 193A CB IV 4.0 7.2
4 CG1 IV PHE 94A N III 4.5 2.7*
4 CG1 IV SER 191A OG I 4.9 0.7*
5 CD1 VI VAL 96A N III 4.8 1.6
5 CD1 VI VAL 96A CA VII 5.1 0.9
5 CD1 VI VAL 96A CB IV 5.5 0.7
6 OE1 II SER 191A OG I 4.9 3.3
6 OE1 II VAL 96A CB IV 5.6 0.7*
7 N2 I PHE 94A O II 2.9 6.1
7 N2 I ALA 93A CB IV 4.1 0.4*
7 N2 I VAL 96A N III 4.3 0.6
8 CA2 VI VAL 96A N III 4.6 0.4
8 CA2 VI VAL 96A CA VII 5.3 0.2
8 CA2 VI VAL 96A CB IV 5.4 0.9
9 CB2 IV AB3 307A C30 V 3.7 15.3
9 CB2 IV ALA 93A CB IV 4.0 5.2
9 CB2 IV AB3 307A C27 V 4.2 0.9
9 CB2 IV MET 234A CG IV 4.3 3.6
9 CB2 IV MET 234A O II 4.4 0.2*
10 SG2 VI TYR 193A CD2 V 3.5 17.0
10 SG2 VI TYR 193A CE2 V 3.6 3.1
10 SG2 VI ALA 93A CB IV 3.6 11.9
10 SG2 VI AB3 307A C26 V 3.8 3.6
11 CD2 VI AB3 307A C29 V 3.4 25.8
11 CD2 VI AB3 307A C26 V 3.5 0.2
11 CD2 VI AB3 307A C28 V 3.6 6.1
11 CD2 VI TYR 193A CE2 V 3.6 9.2
11 CD2 VI TYR 193A CD2 V 3.7 1.6
11 CD2 VI AB3 307A C30 V 3.7 0.9
11 CD2 VI AB3 307A C18 V 3.8 2.2
11 CD2 VI MET 141A CG IV 3.8 4.0
11 CD2 VI AB3 307A C27 V 3.8 0.4
11 CD2 VI AB3 307A C13 V 4.6 0.2
12 OE2 I MET 141A CG IV 3.9 7.1*
12 OE2 I MET 141A CE IV 4.2 5.5*
12 OE2 I TYR 193A CD2 V 4.3 0.9
12 OE2 I MET 141A SD VIII 4.4 0.5
12 OE2 I AB3 307A N15 I 4.8 1.2
12 OE2 I SER 191A OG I 5.4 0.9
12 OE2 I AB3 307A C20 IV 5.9 0.5*
13 C2 VI MET 234A O II 3.9 1.8
13 C2 VI PHE 94A O II 4.0 0.2
13 C2 VI VAL 96A N III 4.1 0.7
14 O2 II LYS 95A CA VII 3.3 13.7
14 O2 II PHE 94A O II 3.4 1.4*
14 O2 II MET 234A O II 3.6 6.1*
14 O2 II PHE 94A C VI 3.9 0.7
14 O2 II LYS 95A CG IV 4.2 2.6*
14 O2 II ALA 93A CB IV 4.6 2.6*
14 O2 II ALA 93A O II 4.9 0.7*
14 O2 II MET 234A CG IV 5.0 0.2*
15 N3 I MET 234A O II 3.9 0.2
15 N3 I ALA 235A O II 4.8 0.2
15 N3 I VAL 96A CB IV 4.9 1.2*
15 N3 I ALA 235A CA VII 4.9 1.2
15 N3 I AB3 307A C27 V 5.5 0.8
15 N3 I AB3 307A C20 IV 6.2 2.2*
16 CA3 VI MET 234A O II 3.7 13.2
16 CA3 VI ALA 235A O II 4.0 15.9
16 CA3 VI ALA 235A C VI 4.5 0.9
16 CA3 VI LYS 95A CG IV 5.2 0.2
17 C3 VI VAL 96A N III 3.8 1.8
17 C3 VI LYS 95A CB IV 4.2 3.6
17 C3 VI LYS 95A CG IV 4.4 0.7
18 O31 II LYS 95A CG IV 4.1 9.9*
18 O31 II LYS 95A CB IV 4.2 0.7*
19 O32 II VAL 96A N III 2.8 23.6
19 O32 II VAL 96A CB IV 3.2 11.6*
19 O32 II LYS 95A CB IV 4.0 0.2*
19 O32 II VAL 96A O II 4.4 0.5*
20 C1 VI ALA 192A N III 3.5 4.7
20 C1 VI TYR 193A N III 3.8 0.4
20 C1 VI GLN 105A OE1 II 3.9 4.0
20 C1 VI ALA 192A CB IV 3.9 3.8
20 C1 VI SER 191A OG I 4.3 2.2
20 C1 VI GLN 105A CB IV 5.3 0.2
21 O11 II ALA 192A N III 2.9 17.0
21 O11 II PHE 102A CE1 V 3.5 11.8
21 O11 II SER 191A CA VII 3.5 6.2
21 O11 II SER 190A O II 3.6 1.9*
22 O12 II TYR 193A N III 2.7 25.8
22 O12 II ALA 192A N III 3.3 0.2
22 O12 II TYR 193A CB IV 3.4 2.1*
22 O12 II ALA 192A CB IV 3.5 3.3*
22 O12 II TYR 193A CA VII 3.6 0.2
22 O12 II THR 109A OG1 I 4.9 4.0
22 O12 II PHE 94A N III 5.2 1.2
22 O12 II PHE 94A CB IV 5.2 0.3*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand AHE 304A
in PDB entry 3BHM (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 544
Actual value (Å2) 277
Normalised complementarity 0.51
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand AHE 304A
in PDB entry 3BHM (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 | N1
| I |
0.51 |
0.44
|
0.48 |
0.41
|
0.51 |
0.51
|
0.48 |
0.44
|
| 2 | CA1
| VI |
0.50 |
0.46
|
0.50 |
0.46
|
0.51 |
0.51
|
0.51 |
0.46
|
| 3 | CB1
| IV |
0.53 |
0.52
|
0.50 |
0.51
|
0.53 |
0.53
|
0.50 |
0.52
|
| 4 | CG1
| IV |
0.52 |
0.50
|
0.51 |
0.51
|
0.55 |
0.55
|
0.54 |
0.52
|
| 5 | CD1
| VI |
0.51 |
0.51
|
0.50 |
0.50
|
0.51 |
0.51
|
0.50 |
0.51
|
| 6 | OE1
| II |
0.51 |
0.51
|
0.51 |
0.50
|
0.51 |
0.51
|
0.51 |
0.51
|
| 7 | N2
| I |
0.51 |
0.49
|
0.51 |
0.49
|
0.51 |
0.51
|
0.51 |
0.49
|
| 8 | CA2
| VI |
0.51 |
0.51
|
0.50 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 9 | CB2
| IV |
0.48 |
0.48
|
0.48 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 10 | SG2
| VI |
0.47 |
0.47
|
0.47 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 11 | CD2
| VI |
0.49 |
0.49
|
0.49 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 12 | OE2
| I |
0.51 |
0.51
|
0.51 |
0.55
|
0.56 |
0.56
|
0.56 |
0.56
|
| 13 | C2
| VI |
0.51 |
0.50
|
0.51 |
0.50
|
0.51 |
0.51
|
0.51 |
0.50
|
| 14 | O2
| II |
0.54 |
0.51
|
0.49 |
0.53
|
0.56 |
0.56
|
0.51 |
0.53
|
| 15 | N3
| I |
0.51 |
0.51
|
0.50 |
0.52
|
0.52 |
0.52
|
0.52 |
0.52
|
| 16 | CA3
| VI |
0.51 |
0.40
|
0.51 |
0.40
|
0.51 |
0.51
|
0.51 |
0.40
|
| 17 | C3
| VI |
0.49 |
0.49
|
0.49 |
0.50
|
0.51 |
0.51
|
0.50 |
0.51
|
| 18 | O31
| II |
0.51 |
0.51
|
0.51 |
0.55
|
0.55 |
0.55
|
0.55 |
0.55
|
| 19 | O32
| II |
0.51 |
0.51
|
0.42 |
0.47
|
0.55 |
0.55
|
0.47 |
0.55
|
| 20 | C1
| VI |
0.49 |
0.48
|
0.48 |
0.47
|
0.51 |
0.51
|
0.49 |
0.49
|
| 21 | O11
| II |
0.52 |
0.51
|
0.43 |
0.45
|
0.52 |
0.52
|
0.43 |
0.51
|
| 22 | O12
| II |
0.51 |
0.51
|
0.41 |
0.42
|
0.53 |
0.53
|
0.43 |
0.53
|
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 AHE 304
2. Oxygen ("hydroxy" or "carbonyl")
6 OE1 12 OE2 14 O2 18 O31 19 O32 21 O11
22 O12
3. Nitrogen ("hydrophilic")
1 N1 7 N2 15 N3
Ligand AB3 307
1. Carbon (in rings)
14 C13 13 C4 7 C7 7 C7 9 C6 11 C2
13 C4 15 C18 16 C28 20 C29 19 C26 18 C30
17 C27
2. Oxygen ("hydroxy" or "carbonyl")
21 O33
3. Nitrogen ("hydrophilic")
5 N11 6 N15 8 N3 10 N5 12 N1
Ligand AB3 308
1. Carbon (in rings)
14 C13 13 C4 7 C7 7 C7 9 C6 11 C2
13 C4 15 C18 16 C28 20 C29 19 C26 18 C30
17 C27
2. Oxygen ("hydroxy" or "carbonyl")
21 O33
3. Nitrogen ("hydrophilic")
5 N11 6 N15 8 N3 10 N5 12 N1
Ligand NAP 309
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 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il