Contacts of ligand HEM 501c in PDB entry 2YBB
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.
(In PDB entry 2YBB some ATOMs are from nucleic
acids or have "unusual" 3-letter residue code. The
analysis does not take into account these atoms.)
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 HEM 501c
in PDB entry 2YBB (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
----------------------------------------------------------
41c LEU* 4.1 9.6 - - + -
44c GLN* 3.4 39.3 - - + +
45c ILE* 3.9 22.7 - - + +
48c GLY* 3.3 24.9 - - - +
49c LEU* 3.4 35.2 - - + +
51c LEU* 3.5 34.3 - - + +
52c ALA* 3.7 31.6 - - + +
55c TYR* 3.9 28.3 - - + -
66c VAL* 4.2 19.7 - - + -
69c ILE* 5.0 3.6 - - + -
80c ARG* 2.9 52.5 + - - +
83c HIS* 2.0 39.3 + + + -
84c ALA* 3.9 30.1 - - + +
87c ALA* 3.8 27.4 - - + -
90c PHE* 3.5 34.8 - - + -
91c PHE* 5.4 0.9 - - + -
123c VAL* 4.6 9.4 - - + -
126c THR* 3.8 22.0 - - + -
127c ALA* 3.7 37.7 - - + +
130c GLY* 3.4 30.7 - - - +
131c TYR* 3.7 32.7 - - + +
133c LEU* 3.7 26.5 - - + -
134c PRO* 3.8 22.4 - - + +
179c PHE* 4.2 9.9 - - + -
182c HIS* 2.0 50.3 + + + -
183c PHE* 3.7 42.6 - - + +
186c PRO* 3.6 39.3 - - + -
187c PHE* 4.0 6.3 - - + -
189c ILE* 4.1 19.3 - - + -
255c ASN* 5.2 1.2 + - - -
273c TYR* 3.8 14.8 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand HEM 501c
and protein in PDB entry 2YBB
(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
------------------------------------------------------------------------
13 O1A II ARG 80c NH2 III 3.9 3.8
13 O1A II ARG 80c NE III 4.4 0.2
13 O1A II ASN 255c ND2 III 5.2 1.2
14 O2A II ARG 80c NH2 III 2.9 18.9
14 O2A II ARG 80c NE III 3.3 1.6
37 O1D II ARG 80c NE III 3.8 0.3
38 O2D II ARG 80c NH2 III 4.2 0.2
39 NA I HIS 83c NE2 I 2.8 1.8
39 NA I HIS 182c NE2 I 2.9 2.4
40 NB I HIS 83c NE2 I 2.8 2.0
40 NB I HIS 182c NE2 I 2.8 2.2
41 NC I HIS 182c NE2 I 2.7 2.4
41 NC I HIS 83c NE2 I 2.9 2.4
42 ND I HIS 182c NE2 I 2.8 2.4
42 ND I HIS 83c NE2 I 2.9 2.0
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand HEM 501c
in PDB entry 2YBB (back
to top of page)
Total number of contacts is 184
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 CHA IV GLY 130c O II 3.4 6.7*
1 CHA IV HIS 83c CD2 V 3.6 1.6
2 CHB IV HIS 182c CE1 V 3.5 3.6
2 CHB IV GLN 44c NE2 III 3.9 4.5*
2 CHB IV ALA 127c CA VII 4.0 4.3
2 CHB IV ALA 87c CB IV 4.1 0.7
3 CHC IV PRO 186c CG IV 3.6 4.7
3 CHC IV HIS 83c CE1 V 3.6 3.4
3 CHC IV GLN 44c O II 3.8 4.3*
3 CHC IV GLN 44c CB IV 4.0 0.4
3 CHC IV GLN 44c C VI 4.1 0.2
4 CHD IV HIS 182c CD2 V 3.6 3.8
4 CHD IV GLY 48c O II 3.6 4.9*
4 CHD IV GLY 48c CA VI 3.8 0.4
4 CHD IV LEU 133c CD1 IV 5.0 0.2
4 CHD IV PHE 179c CE1 V 5.0 2.0
5 C1A V HIS 83c CD2 V 3.5 2.2
5 C1A V GLY 130c CA VI 3.5 3.8
6 C2A V GLY 130c C VI 3.4 3.8
7 C3A V GLY 130c C VI 3.9 3.6
7 C3A V TYR 131c N III 3.9 0.2
7 C3A V ALA 87c CB IV 4.5 1.1
7 C3A V HIS 83c CD2 V 4.6 0.7
7 C3A V HIS 83c O II 5.3 0.2
8 C4A V HIS 182c CE1 V 3.5 4.0
8 C4A V HIS 83c NE2 I 3.7 1.3
8 C4A V GLY 130c CA VI 3.9 0.9
8 C4A V HIS 83c CD2 V 3.9 1.3
8 C4A V GLN 44c NE2 III 4.5 0.2
9 CMA IV ALA 127c O II 3.7 15.0*
9 CMA IV ALA 87c CB IV 3.8 18.6
9 CMA IV TYR 273c OH I 3.8 14.8*
9 CMA IV TYR 131c N III 4.2 1.3*
9 CMA IV ALA 127c CA VII 4.4 1.1
9 CMA IV TYR 131c CB IV 4.6 4.0
9 CMA IV TYR 131c CD1 V 4.8 2.5
9 CMA IV ALA 84c O II 5.2 1.3*
10 CAA IV GLY 130c O II 3.4 10.3*
10 CAA IV GLY 130c C VI 3.7 1.6
10 CAA IV TYR 131c CA VII 3.7 8.3
10 CAA IV TYR 131c CD1 V 4.2 1.6
10 CAA IV PRO 134c CD IV 4.6 0.4
11 CBA IV ALA 84c CB IV 4.1 13.7
11 CBA IV ALA 84c CA VII 4.2 2.5
11 CBA IV ALA 84c N III 4.7 0.7*
11 CBA IV TYR 131c CD1 V 4.9 0.2
11 CBA IV HIS 83c CD2 V 4.9 0.2
12 CGA VI ARG 80c NH2 III 3.8 3.1
12 CGA VI ARG 80c NE III 4.0 4.5
12 CGA VI ALA 84c CB IV 4.1 3.6
12 CGA VI PRO 134c CG IV 4.6 4.5
12 CGA VI TYR 131c CD1 V 4.7 0.4
13 O1A II ARG 80c NH2 III 3.9 3.8
13 O1A II ALA 84c CB IV 3.9 8.3*
13 O1A II TYR 131c CE1 V 4.2 14.0
13 O1A II ARG 80c NE III 4.4 0.2
13 O1A II PRO 134c CG IV 5.0 0.2*
13 O1A II ASN 255c ND2 III 5.2 1.2
14 O2A II ARG 80c NH2 III 2.9 18.9
14 O2A II ARG 80c NE III 3.3 1.6
14 O2A II PRO 134c CG IV 4.0 3.3*
15 C1B V HIS 182c CE1 V 3.2 3.6
15 C1B V GLN 44c NE2 III 3.5 4.0
16 C2B V GLN 44c NE2 III 3.6 2.7
16 C2B V THR 126c CG2 IV 3.9 2.9
17 C3B V GLN 44c CB IV 3.6 2.2
17 C3B V THR 126c CG2 IV 3.8 2.5
18 C4B V HIS 83c CE1 V 3.5 4.0
18 C4B V HIS 182c CE1 V 3.6 3.1
18 C4B V PRO 186c CG IV 4.2 0.2
19 CMB IV GLN 44c NE2 III 4.1 5.4*
19 CMB IV ALA 127c CB IV 4.2 17.0
19 CMB IV PHE 90c CD2 V 4.2 13.0
19 CMB IV THR 126c CG2 IV 4.2 2.9
19 CMB IV ALA 87c CB IV 4.4 6.5
19 CMB IV ALA 127c N III 4.4 0.2*
19 CMB IV VAL 123c CG1 IV 4.6 6.7
19 CMB IV ALA 87c CA VII 4.7 0.4
19 CMB IV PHE 90c CB IV 5.2 0.2
19 CMB IV PHE 91c CE2 V 5.4 0.9
20 CAB IV GLN 44c CB IV 3.4 15.0
20 CAB IV PRO 186c CG IV 3.9 4.9
20 CAB IV PRO 186c CB IV 4.0 2.2
20 CAB IV PHE 90c CE2 V 4.3 0.2
20 CAB IV LEU 41c CD1 IV 4.5 2.2
20 CAB IV ILE 45c N III 5.2 0.2*
21 CBB IV PHE 90c CE2 V 3.5 21.3
21 CBB IV THR 126c CG2 IV 3.8 13.2
21 CBB IV ILE 189c CD1 IV 4.1 19.3
21 CBB IV LEU 41c CD1 IV 4.1 7.4
21 CBB IV PRO 186c CB IV 4.3 1.1
21 CBB IV THR 126c CB VI 4.5 0.4
21 CBB IV VAL 123c CG1 IV 4.8 2.7
22 C1C V HIS 83c CE1 V 3.5 3.6
22 C1C V HIS 182c NE2 I 3.5 2.5
22 C1C V GLN 44c O II 3.9 0.2
22 C1C V PRO 186c CG IV 4.0 0.9
23 C2C V GLY 48c CA VI 3.9 2.5
23 C2C V PRO 186c CG IV 4.1 2.0
23 C2C V HIS 182c O II 4.2 1.8
24 C3C V GLY 48c CA VI 3.5 1.8
24 C3C V HIS 182c CD2 V 4.3 1.6
24 C3C V HIS 182c O II 4.5 1.8
25 C4C V HIS 182c NE2 I 3.4 2.5
25 C4C V HIS 182c CD2 V 3.5 1.1
25 C4C V GLY 48c CA VI 3.5 2.9
26 CMC IV PRO 186c CG IV 3.6 17.0
26 CMC IV PRO 186c CB IV 3.6 6.1
26 CMC IV ILE 45c CA VII 3.9 18.8
26 CMC IV PHE 183c O II 4.0 5.6*
26 CMC IV ILE 45c CG1 IV 4.0 3.1
26 CMC IV PHE 187c CE2 V 4.0 5.8
26 CMC IV ILE 45c O II 4.4 0.4*
27 CAC IV GLY 48c O II 3.3 11.4*
27 CAC IV GLY 48c C VI 3.3 0.2
27 CAC IV ALA 52c CB IV 4.1 5.4
27 CAC IV PHE 183c CD2 V 4.2 4.7
27 CAC IV PHE 183c CG V 4.3 1.3
27 CAC IV PHE 183c CA VII 4.4 0.4
28 CBC IV LEU 49c CD2 IV 3.4 31.9
28 CBC IV PHE 183c CZ V 3.7 19.1
28 CBC IV PHE 183c CE1 V 3.7 6.1
28 CBC IV PHE 183c CE2 V 3.7 2.0
28 CBC IV PHE 183c CD1 V 3.7 3.4
28 CBC IV LEU 49c CG IV 3.8 1.6
28 CBC IV LEU 49c N III 3.9 0.9*
28 CBC IV LEU 49c CA VII 3.9 0.9
28 CBC IV PHE 187c CE2 V 4.5 0.4
29 C1D V HIS 182c CD2 V 3.5 4.0
29 C1D V HIS 83c NE2 I 3.7 1.8
29 C1D V HIS 83c CD2 V 4.2 0.7
29 C1D V GLY 48c O II 4.4 0.2
29 C1D V HIS 83c CE1 V 4.4 0.2
29 C1D V GLY 48c CA VI 4.5 0.4
30 C2D V LEU 133c CD1 IV 4.0 3.4
30 C2D V LEU 51c CB IV 4.3 2.2
31 C3D V LEU 133c CD1 IV 3.7 3.4
31 C3D V LEU 51c CD1 IV 4.6 0.2
32 C4D V HIS 182c NE2 I 3.6 2.0
32 C4D V HIS 83c NE2 I 3.6 1.8
32 C4D V HIS 83c CD2 V 3.6 0.7
32 C4D V LEU 133c CD1 IV 3.9 2.0
33 CMD IV ALA 52c N III 3.7 22.9*
33 CMD IV LEU 51c CB IV 3.8 4.5
33 CMD IV TYR 55c CB IV 3.9 15.9
33 CMD IV ALA 52c CA VII 3.9 3.4
33 CMD IV TYR 55c CG V 4.1 2.5
33 CMD IV PHE 179c CE1 V 4.2 7.9
33 CMD IV TYR 55c CD2 V 4.3 0.4
34 CAD IV LEU 133c CB IV 3.9 17.5
34 CAD IV TYR 55c CD1 V 4.1 7.0
34 CAD IV TYR 55c CE1 V 4.4 0.7
34 CAD IV VAL 66c CG2 IV 4.9 0.2
35 CBD IV VAL 66c CG2 IV 4.2 14.8
35 CBD IV LEU 51c CD1 IV 4.2 5.4
35 CBD IV TYR 55c CD1 V 4.5 1.8
35 CBD IV LEU 51c CB IV 4.6 2.2
35 CBD IV LEU 51c CG IV 4.8 0.2
35 CBD IV LEU 51c CD2 IV 4.9 1.8
35 CBD IV VAL 66c CG1 IV 5.0 0.7
35 CBD IV ILE 69c CD1 IV 5.0 3.6
36 CGD VI ARG 80c NE III 4.4 3.4
36 CGD VI ARG 80c CG IV 4.4 1.8
36 CGD VI VAL 66c CG2 IV 4.6 4.0
37 O1D II LEU 51c CD1 IV 3.5 17.7*
37 O1D II ARG 80c CG IV 3.6 13.2*
37 O1D II ARG 80c NE III 3.8 0.3
37 O1D II ARG 80c CD VII 4.2 0.2
37 O1D II HIS 83c CD2 V 4.5 1.0
37 O1D II ARG 80c O II 4.6 1.4*
38 O2D II PRO 134c CD IV 3.8 10.6*
38 O2D II PRO 134c CG IV 4.0 0.9*
38 O2D II PRO 134c CB IV 4.1 2.6*
38 O2D II ARG 80c NH2 III 4.2 0.2
39 NA I HIS 83c NE2 I 2.8 1.8
39 NA I HIS 182c NE2 I 2.9 2.4
40 NB I HIS 83c NE2 I 2.8 2.0
40 NB I HIS 182c NE2 I 2.8 2.2
41 NC I HIS 182c NE2 I 2.7 2.4
41 NC I HIS 83c NE2 I 2.9 2.4
42 ND I HIS 182c NE2 I 2.8 2.4
42 ND I HIS 83c NE2 I 2.9 2.0
43 FE VI HIS 182c NE2 I 2.0 5.5
43 FE VI HIS 83c NE2 I 2.0 6.4
------------------------------------------------------------------------
Table V
Complementarity values for the ligand HEM 501c
in PDB entry 2YBB (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 797
Actual value (Å2) 460
Normalised complementarity 0.58
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand HEM 501c
in PDB entry 2YBB (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 | CHA
| IV |
0.59 |
0.58
|
0.59 |
0.58
|
0.59 |
0.59
|
0.59 |
0.58
|
| 2 | CHB
| IV |
0.59 |
0.59
|
0.57 |
0.58
|
0.59 |
0.59
|
0.57 |
0.59
|
| 3 | CHC
| IV |
0.58 |
0.56
|
0.58 |
0.58
|
0.59 |
0.59
|
0.59 |
0.58
|
| 4 | CHD
| IV |
0.59 |
0.58
|
0.59 |
0.58
|
0.59 |
0.59
|
0.59 |
0.58
|
| 5 | C1A
| V |
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 6 | C2A
| V |
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 7 | C3A
| V |
0.58 |
0.57
|
0.57 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 8 | C4A
| V |
0.58 |
0.58
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 9 | CMA
| IV |
0.60 |
0.56
|
0.60 |
0.58
|
0.66 |
0.66
|
0.65 |
0.62
|
| 10 | CAA
| IV |
0.60 |
0.58
|
0.58 |
0.58
|
0.60 |
0.60
|
0.58 |
0.58
|
| 11 | CBA
| IV |
0.55 |
0.55
|
0.54 |
0.58
|
0.58 |
0.58
|
0.57 |
0.58
|
| 12 | CGA
| VI |
0.56 |
0.56
|
0.54 |
0.56
|
0.58 |
0.58
|
0.56 |
0.58
|
| 13 | O1A
| II |
0.58 |
0.58
|
0.56 |
0.59
|
0.60 |
0.60
|
0.59 |
0.60
|
| 14 | O2A
| II |
0.58 |
0.58
|
0.53 |
0.53
|
0.59 |
0.59
|
0.53 |
0.59
|
| 15 | C1B
| V |
0.58 |
0.58
|
0.57 |
0.57
|
0.58 |
0.58
|
0.57 |
0.58
|
| 16 | C2B
| V |
0.57 |
0.57
|
0.56 |
0.57
|
0.58 |
0.58
|
0.57 |
0.58
|
| 17 | C3B
| V |
0.57 |
0.57
|
0.57 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 18 | C4B
| V |
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 19 | CMB
| IV |
0.51 |
0.51
|
0.49 |
0.58
|
0.59 |
0.59
|
0.58 |
0.59
|
| 20 | CAB
| IV |
0.52 |
0.52
|
0.52 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 21 | CBB
| IV |
0.47 |
0.47
|
0.47 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 22 | C1C
| V |
0.58 |
0.58
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 23 | C2C
| V |
0.57 |
0.57
|
0.57 |
0.57
|
0.58 |
0.58
|
0.58 |
0.57
|
| 24 | C3C
| V |
0.58 |
0.57
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.57
|
| 25 | C4C
| V |
0.58 |
0.58
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 26 | CMC
| IV |
0.53 |
0.51
|
0.48 |
0.58
|
0.59 |
0.59
|
0.55 |
0.58
|
| 27 | CAC
| IV |
0.59 |
0.56
|
0.59 |
0.58
|
0.61 |
0.61
|
0.61 |
0.58
|
| 28 | CBC
| IV |
0.50 |
0.50
|
0.49 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 29 | C1D
| V |
0.58 |
0.58
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 30 | C2D
| V |
0.56 |
0.56
|
0.56 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 31 | C3D
| V |
0.57 |
0.57
|
0.57 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 32 | C4D
| V |
0.57 |
0.57
|
0.57 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 33 | CMD
| IV |
0.58 |
0.58
|
0.52 |
0.58
|
0.64 |
0.64
|
0.57 |
0.64
|
| 34 | CAD
| IV |
0.53 |
0.53
|
0.53 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 35 | CBD
| IV |
0.51 |
0.51
|
0.51 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 36 | CGD
| VI |
0.56 |
0.56
|
0.55 |
0.57
|
0.58 |
0.58
|
0.57 |
0.58
|
| 37 | O1D
| II |
0.58 |
0.58
|
0.58 |
0.65
|
0.66 |
0.66
|
0.66 |
0.66
|
| 38 | O2D
| II |
0.58 |
0.58
|
0.58 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 39 | NA
| I |
0.58 |
0.58
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 40 | NB
| I |
0.58 |
0.58
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 41 | NC
| I |
0.58 |
0.58
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 42 | ND
| I |
0.58 |
0.58
|
0.58 |
0.57
|
0.58 |
0.58
|
0.58 |
0.58
|
| 43 | FE
| VI |
0.58 |
0.58
|
0.58 |
0.55
|
0.58 |
0.58
|
0.58 |
0.58
|
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 FMN 440
1. Carbon (in rings)
2 C2 5 C4 7 C4A 18 C10 7 C4A 9 C5A
16 C9A 18 C10 9 C5A 10 C6 11 C7 13 C8
15 C9 16 C9A
2. Oxygen ("hydroxy" or "carbonyl")
3 O2 6 O4 21 O2' 23 O3' 25 O4'
3. Nitrogen ("hydrophilic")
1 N1 4 N3 8 N5 17 N10
Ligand NAI 441
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 11 O2B 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Ligand HEM 501
1. Carbon (in rings)
5 C1A 6 C2A 7 C3A 8 C4A 15 C1B 16 C2B
17 C3B 18 C4B 22 C1C 23 C2C 24 C3C 25 C4C
29 C1D 30 C2D 31 C3D 32 C4D
2. Oxygen ("hydroxy" or "carbonyl")
13 O1A 14 O2A 37 O1D 38 O2D
3. Nitrogen ("hydrophilic")
39 NA 40 NB 41 NC 42 ND
Ligand HEM 502
1. Carbon (in rings)
5 C1A 6 C2A 7 C3A 8 C4A 15 C1B 16 C2B
17 C3B 18 C4B 22 C1C 23 C2C 24 C3C 25 C4C
29 C1D 30 C2D 31 C3D 32 C4D
2. Oxygen ("hydroxy" or "carbonyl")
13 O1A 14 O2A 37 O1D 38 O2D
3. Nitrogen ("hydrophilic")
39 NA 40 NB 41 NC 42 ND
Ligand SMA 2001
1. Carbon (in rings)
1 C2 2 C3 4 C4 5 C4A 12 C8A 5 C4A
6 C5 8 C6 9 C7 11 C8 12 C8A
2. Oxygen ("hydroxy" or "carbonyl")
32 O4 35 O8
Ligand UQ1 2002
1. Carbon (in rings)
1 C1 3 C2 6 C3 9 C4 11 C5 13 C6
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 10 O4
Ligand HEC 501
1. Carbon (in rings)
7 C1A 8 C2A 9 C3A 10 C4A 18 C1B 19 C2B
20 C3B 21 C4B 26 C1C 27 C2C 28 C3C 29 C4C
34 C1D 35 C2D 36 C3D 37 C4D
2. Oxygen ("hydroxy" or "carbonyl")
15 O1A 16 O2A 42 O1D 43 O2D
3. Nitrogen ("hydrophilic")
6 NA 17 NB 25 NC 33 ND
Ligand CDL 2003
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 13 OA7 18 OA9 30 OB7 38 OB9
Ligand CDL 2004
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 13 OA7 19 OA9 38 OB7 43 OB9
Ligand HEA 515
1. Carbon (in rings)
7 C1A 8 C2A 9 C3A 10 C4A 19 C1B 20 C2B
21 C3B 22 C4B 25 C1C 26 C2C 27 C3C 28 C4C
33 C1D 34 C2D 35 C3D 36 C4D
2. Oxygen ("hydroxy" or "carbonyl")
12 OMA 16 O1A 17 O2A 41 O1D 42 O2D 44 O11
3. Nitrogen ("hydrophilic")
6 NA 18 NB 24 NC 32 ND
Ligand HEA 516
1. Carbon (in rings)
7 C1A 8 C2A 9 C3A 10 C4A 19 C1B 20 C2B
21 C3B 22 C4B 25 C1C 26 C2C 27 C3C 28 C4C
33 C1D 34 C2D 35 C3D 36 C4D
2. Oxygen ("hydroxy" or "carbonyl")
12 OMA 16 O1A 17 O2A 41 O1D 42 O2D 44 O11
3. Nitrogen ("hydrophilic")
6 NA 18 NB 24 NC 32 ND
Ligand HEM 500
1. Carbon (in rings)
5 C1A 6 C2A 7 C3A 8 C4A 15 C1B 16 C2B
17 C3B 18 C4B 22 C1C 23 C2C 24 C3C 25 C4C
29 C1D 30 C2D 31 C3D 32 C4D
2. Oxygen ("hydroxy" or "carbonyl")
13 O1A 14 O2A 37 O1D 38 O2D
3. Nitrogen ("hydrophilic")
39 NA 40 NB 41 NC 42 ND
Ligand HEM 501
1. Carbon (in rings)
5 C1A 6 C2A 7 C3A 8 C4A 15 C1B 16 C2B
17 C3B 18 C4B 22 C1C 23 C2C 24 C3C 25 C4C
29 C1D 30 C2D 31 C3D 32 C4D
2. Oxygen ("hydroxy" or "carbonyl")
13 O1A 14 O2A 37 O1D 38 O2D
3. Nitrogen ("hydrophilic")
39 NA 40 NB 41 NC 42 ND
Ligand HEM 502
1. Carbon (in rings)
5 C1A 6 C2A 7 C3A 8 C4A 15 C1B 16 C2B
17 C3B 18 C4B 22 C1C 23 C2C 24 C3C 25 C4C
29 C1D 30 C2D 31 C3D 32 C4D
2. Oxygen ("hydroxy" or "carbonyl")
13 O1A 14 O2A 37 O1D 38 O2D
3. Nitrogen ("hydrophilic")
39 NA 40 NB 41 NC 42 ND
Ligand SMA 3001
1. Carbon (in rings)
1 C2 2 C3 4 C4 5 C4A 12 C8A 5 C4A
6 C5 8 C6 9 C7 11 C8 12 C8A
2. Oxygen ("hydroxy" or "carbonyl")
32 O4 35 O8
Ligand UQ1 3002
1. Carbon (in rings)
1 C1 3 C2 6 C3 9 C4 11 C5 13 C6
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 10 O4
Ligand HEC 501
1. Carbon (in rings)
7 C1A 8 C2A 9 C3A 10 C4A 18 C1B 19 C2B
20 C3B 21 C4B 26 C1C 27 C2C 28 C3C 29 C4C
34 C1D 35 C2D 36 C3D 37 C4D
2. Oxygen ("hydroxy" or "carbonyl")
15 O1A 16 O2A 42 O1D 43 O2D
3. Nitrogen ("hydrophilic")
6 NA 17 NB 25 NC 33 ND
Ligand CDL 3003
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 13 OA7 21 OA9 44 OB7 49 OB9
Ligand CDL 3004
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 13 OA7 18 OA9 30 OB7 41 OB9
Please E-mail any questions and/or suggestions
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Vladimir.Sobolev@weizmann.ac.il