Contacts of ligand HEM 719A in PDB entry 1Y28
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 HEM 719A
in PDB entry 1Y28 (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
----------------------------------------------------------
157A ILE* 3.3 45.8 - - + +
159A ILE* 3.5 27.1 - - + -
176A PHE* 4.3 6.7 - - + -
188A VAL* 3.5 20.9 - - + -
191A LEU* 3.4 42.0 - - + +
192A MET* 3.5 25.4 - - + -
196A ASP* 3.4 47.6 - - - +
200A HIS* 2.4 33.3 + + + -
203A TYR* 3.2 74.1 - + + +
204A ILE* 4.0 15.9 - - + -
206A ARG* 4.3 12.3 + - - +
207A TYR* 3.6 26.1 - - + +
213A PRO* 3.7 6.9 - - - +
214A HIS* 2.8 79.5 + - + +
215A ILE* 3.0 37.5 + - + +
216A ILE* 3.0 42.0 + - + +
222A VAL* 3.4 33.9 - - + -
223A THR 3.5 17.0 - - - +
234A MET* 3.7 33.4 - - + -
236A LEU* 3.5 32.6 - - + +
238A ILE* 3.4 26.7 - - + +
249A PHE* 3.5 60.1 - - + +
250A THR 4.5 0.7 - - - +
251A GLY* 3.1 34.5 - - - +
253A VAL* 5.0 2.5 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand HEM 719A
and protein in PDB entry 1Y28
(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 I HIS 214A ND1 I 2.8 16.1
13 O1A I ARG 206A NE III 5.0 2.6
13 O1A I ARG 206A NH1 III 5.3 0.3
14 O2A II HIS 214A ND1 I 3.1 1.6
37 O1D II ILE 216A N III 3.0 29.1
37 O1D II ILE 215A N III 3.0 6.4
37 O1D II HIS 214A N III 3.2 3.1
38 O2D II HIS 214A N III 3.3 13.2
38 O2D II ARG 206A NH1 III 4.3 5.4
39 NA I HIS 200A NE2 I 3.4 2.0
40 NB I HIS 200A NE2 I 3.2 2.4
41 NC I HIS 200A NE2 I 3.0 2.2
42 ND I HIS 200A NE2 I 3.1 2.0
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand HEM 719A
in PDB entry 1Y28 (back
to top of page)
Total number of contacts is 181
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 TYR 203A CB IV 3.6 6.1
1 CHA IV ILE 215A CD1 IV 4.5 1.8
2 CHB IV HIS 200A CD2 V 4.1 2.2
2 CHB IV ASP 196A OD2 II 4.2 1.3*
2 CHB IV ASP 196A CG VI 4.3 2.5
2 CHB IV ILE 215A CD1 IV 4.6 3.1
2 CHB IV VAL 222A CG1 IV 4.7 2.5
3 CHC IV LEU 236A CD2 IV 3.6 4.9
3 CHC IV MET 192A CE IV 3.9 3.6
3 CHC IV LEU 236A CD1 IV 4.2 0.7
3 CHC IV VAL 188A CG2 IV 4.4 0.2
4 CHD IV ILE 238A CD1 IV 3.6 5.6
4 CHD IV HIS 200A CE1 V 3.8 3.4
4 CHD IV ILE 159A CD1 IV 4.0 2.9
4 CHD IV ILE 238A CG1 IV 4.3 0.2
5 C1A V TYR 203A CD2 V 3.5 3.8
5 C1A V ILE 215A CD1 IV 3.9 3.4
6 C2A V TYR 203A CD2 V 3.2 2.9
6 C2A V ILE 215A CD1 IV 4.1 3.1
7 C3A V TYR 203A CE2 V 3.4 3.4
7 C3A V ILE 215A CD1 IV 4.1 2.7
8 C4A V TYR 203A CD2 V 3.8 3.4
8 C4A V ILE 215A CD1 IV 4.0 3.6
8 C4A V HIS 200A CD2 V 4.1 0.2
9 CMA IV ASP 196A OD1 II 3.5 21.1*
9 CMA IV TYR 203A CE2 V 3.5 3.4
9 CMA IV TYR 203A CZ V 3.8 0.9
9 CMA IV TYR 203A OH I 3.9 0.4*
9 CMA IV ASP 196A CG VI 4.0 1.6
9 CMA IV ASP 196A OD2 II 4.1 0.9*
9 CMA IV ILE 215A CD1 IV 4.9 2.5
9 CMA IV VAL 222A CG1 IV 5.2 6.1
10 CAA IV TYR 203A CG V 3.4 10.8
10 CAA IV TYR 203A CD1 V 3.7 0.2
10 CAA IV TYR 203A CB IV 3.7 1.8
10 CAA IV TYR 203A CA VII 4.8 0.2
10 CAA IV ILE 215A CD1 IV 4.8 1.8
10 CAA IV HIS 214A CB IV 4.9 0.2
10 CAA IV ARG 206A NH1 III 6.2 0.7*
11 CBA IV TYR 203A CD1 V 4.0 7.6
11 CBA IV TYR 203A CE1 V 4.0 2.7
11 CBA IV ILE 215A CD1 IV 5.4 0.4
12 CGA VI HIS 214A ND1 I 3.2 4.9
12 CGA VI HIS 214A CB IV 3.7 0.4
13 O1A I HIS 214A ND1 I 2.8 16.1
13 O1A I HIS 214A CE1 V 3.6 2.4
13 O1A I TYR 203A CD1 V 4.5 4.5
13 O1A I TYR 203A CE1 V 4.7 0.7
13 O1A I ARG 206A NE III 5.0 2.6
13 O1A I ARG 206A CZ VI 5.1 0.7
13 O1A I ARG 206A CD VII 5.2 2.6
13 O1A I ARG 206A NH1 III 5.3 0.3
14 O2A II HIS 214A CB IV 3.0 21.8*
14 O2A II HIS 214A ND1 I 3.1 1.6
14 O2A II HIS 214A CG V 3.4 0.2
14 O2A II HIS 214A C VI 4.6 0.7
14 O2A II HIS 214A O II 4.7 0.7*
14 O2A II ILE 215A CG1 IV 5.0 2.6*
15 C1B V HIS 200A CD2 V 3.9 4.0
15 C1B V LEU 236A CD2 IV 4.1 3.1
15 C1B V VAL 222A CG2 IV 4.5 0.2
16 C2B V VAL 222A CG2 IV 3.8 2.7
16 C2B V MET 192A CE IV 4.0 2.7
17 C3B V MET 192A CE IV 3.6 2.5
17 C3B V VAL 222A CG2 IV 4.1 2.7
18 C4B V LEU 236A CD2 IV 3.5 3.6
18 C4B V MET 192A CE IV 3.5 3.8
19 CMB IV ASP 196A OD2 II 3.4 20.0*
19 CMB IV VAL 222A CG2 IV 3.4 16.8
19 CMB IV THR 223A O II 3.5 13.7*
19 CMB IV VAL 222A CB IV 3.6 2.9
19 CMB IV MET 192A CB IV 4.1 7.4
19 CMB IV ASP 196A CG VI 4.1 0.2
19 CMB IV THR 223A N III 4.5 0.2*
20 CAB IV MET 234A CE IV 3.7 13.5
20 CAB IV MET 234A SD VIII 3.9 4.0
20 CAB IV LEU 191A O II 3.9 6.1*
20 CAB IV MET 192A CB IV 4.0 3.6
20 CAB IV THR 223A O II 4.1 3.1*
21 CBB IV LEU 191A O II 3.4 19.5*
21 CBB IV LEU 191A CB IV 3.8 15.7
21 CBB IV MET 234A CE IV 3.8 12.3
21 CBB IV MET 234A SD VIII 4.0 3.6
21 CBB IV LEU 191A C VI 4.0 0.7
21 CBB IV MET 192A CE IV 4.2 1.8
21 CBB IV PHE 176A CZ V 4.3 6.7
22 C1C V LEU 236A CD2 IV 3.8 3.6
22 C1C V HIS 200A NE2 I 3.8 2.0
22 C1C V VAL 188A CG2 IV 4.1 1.6
23 C2C V VAL 188A CG2 IV 3.6 2.9
23 C2C V LEU 236A CD1 IV 4.2 3.1
24 C3C V ILE 159A CD1 IV 4.2 2.2
24 C3C V VAL 188A CG2 IV 4.2 0.9
24 C3C V ILE 238A CD1 IV 4.7 1.8
24 C3C V GLY 251A CA VI 4.7 0.9
25 C4C V HIS 200A NE2 I 3.7 2.5
25 C4C V HIS 200A CE1 V 3.8 0.9
25 C4C V ILE 238A CD1 IV 3.9 3.1
25 C4C V ILE 159A CD1 IV 4.4 0.2
26 CMC IV VAL 188A CG2 IV 3.5 15.3
26 CMC IV ILE 157A CD1 IV 3.9 22.0
26 CMC IV ILE 157A CB IV 4.2 0.7
26 CMC IV LEU 236A CD1 IV 4.3 8.1
26 CMC IV GLY 251A CA VI 4.7 1.3
26 CMC IV VAL 253A CG2 IV 5.0 2.5
27 CAC IV ILE 159A CD1 IV 3.5 16.6
27 CAC IV ILE 159A CG1 IV 3.7 1.1
27 CAC IV GLY 251A N III 4.1 2.5*
27 CAC IV ILE 159A CG2 IV 4.2 0.2
27 CAC IV GLY 251A CA VI 4.2 0.9
27 CAC IV PHE 249A O II 4.3 2.7*
27 CAC IV PHE 249A CB IV 4.3 3.8
27 CAC IV THR 250A C VI 4.5 0.4
27 CAC IV THR 250A O II 5.0 0.2*
27 CAC IV ILE 238A CG2 IV 5.0 1.1
28 CBC IV GLY 251A N III 3.1 28.7*
28 CBC IV ILE 157A O II 3.3 13.0*
28 CBC IV GLY 251A CA VI 3.4 0.2
28 CBC IV PHE 249A O II 3.8 7.9*
28 CBC IV ILE 157A C VI 3.8 5.2
28 CBC IV ILE 157A CB IV 4.0 1.6
28 CBC IV ILE 157A CG2 IV 4.0 3.4
28 CBC IV ILE 159A CG2 IV 4.1 3.8
29 C1D V ILE 238A CD1 IV 3.4 2.9
29 C1D V HIS 200A CE1 V 3.7 3.8
30 C2D V ILE 238A CD1 IV 3.9 1.8
30 C2D V ILE 204A CG1 IV 4.0 3.4
31 C3D V ILE 204A CG1 IV 4.2 2.9
31 C3D V ILE 238A CD1 IV 4.3 0.4
32 C4D V HIS 200A NE2 I 4.0 2.0
32 C4D V ILE 238A CD1 IV 4.1 3.1
32 C4D V HIS 200A CE1 V 4.1 1.1
32 C4D V TYR 203A CB IV 4.3 0.4
33 CMD IV PHE 249A CG V 3.5 29.2
33 CMD IV PHE 249A CD1 V 3.6 6.5
33 CMD IV PHE 249A CD2 V 3.8 5.2
33 CMD IV PHE 249A CE1 V 4.0 1.6
33 CMD IV PHE 249A CB IV 4.1 0.4
33 CMD IV PHE 249A CE2 V 4.1 2.2
33 CMD IV ILE 204A CG1 IV 4.1 7.9
33 CMD IV PHE 249A CZ V 4.2 0.7
33 CMD IV ILE 238A CG2 IV 4.2 4.5
33 CMD IV ILE 204A CD1 IV 4.8 0.2
33 CMD IV ILE 204A CG2 IV 5.0 0.2
34 CAD IV TYR 203A O II 3.6 19.3*
34 CAD IV TYR 207A CB IV 3.9 3.6
34 CAD IV TYR 203A C VI 4.0 1.6
34 CAD IV ILE 204A CA VII 4.0 1.3
35 CBD IV TYR 207A CG V 3.6 17.9
35 CBD IV ILE 216A CD1 IV 3.8 7.4
35 CBD IV ILE 216A CG1 IV 3.9 0.4
36 CGD VI HIS 214A N III 3.6 3.6
36 CGD VI ILE 215A N III 3.9 2.7
36 CGD VI ILE 216A CG1 IV 4.0 0.2
36 CGD VI PRO 213A CA IV 4.1 5.4
36 CGD VI TYR 207A CG V 4.2 1.1
36 CGD VI ILE 215A CB IV 4.6 0.7
37 O1D II ILE 216A N III 3.0 29.1
37 O1D II ILE 215A N III 3.0 6.4
37 O1D II HIS 214A N III 3.2 3.1
37 O1D II ILE 216A CG1 IV 3.2 4.2*
37 O1D II ILE 216A CB IV 3.6 0.7*
37 O1D II PRO 213A CA IV 3.7 0.5*
37 O1D II ILE 215A CA VII 3.7 0.3
37 O1D II ILE 215A CB IV 3.9 0.2*
38 O2D II HIS 214A N III 3.3 13.2
38 O2D II HIS 214A CB IV 3.7 9.0*
38 O2D II PRO 213A CA IV 4.1 1.0*
38 O2D II TYR 207A CB IV 4.3 3.5*
38 O2D II HIS 214A CG V 4.3 1.6
38 O2D II ARG 206A NH1 III 4.3 5.4
39 NA I HIS 200A NE2 I 3.4 2.0
39 NA I ILE 215A CD1 IV 3.9 2.2*
40 NB I HIS 200A NE2 I 3.2 2.4
40 NB I LEU 236A CD2 IV 3.5 1.8*
41 NC I HIS 200A NE2 I 3.0 2.2
41 NC I LEU 236A CD2 IV 3.8 2.0*
42 ND I HIS 200A NE2 I 3.1 2.0
42 ND I ILE 238A CD1 IV 3.6 2.0*
43 FE VI HIS 200A NE2 I 2.4 2.6
43 FE VI LEU 236A CD2 IV 3.9 1.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand HEM 719A
in PDB entry 1Y28 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 825
Actual value (Å2) 357
Normalised complementarity 0.43
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand HEM 719A
in PDB entry 1Y28 (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 |
0.41 |
0.41
|
0.41 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 2 | CHB
| IV |
0.42 |
0.42
|
0.42 |
0.43
|
0.44 |
0.44
|
0.44 |
0.43
|
| 3 | CHC
| IV |
0.41 |
0.41
|
0.41 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 4 | CHD
| IV |
0.41 |
0.41
|
0.41 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 5 | C1A
| V |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 6 | C2A
| V |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 7 | C3A
| V |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 8 | C4A
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 9 | CMA
| IV |
0.47 |
0.41
|
0.47 |
0.43
|
0.49 |
0.49
|
0.49 |
0.43
|
| 10 | CAA
| IV |
0.43 |
0.43
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 11 | CBA
| IV |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 12 | CGA
| VI |
0.43 |
0.43
|
0.43 |
0.42
|
0.43 |
0.43
|
0.43 |
0.43
|
| 13 | O1A
| I |
0.43 |
0.43
|
0.42 |
0.39
|
0.43 |
0.43
|
0.42 |
0.43
|
| 14 | O2A
| II |
0.44 |
0.43
|
0.44 |
0.49
|
0.49 |
0.49
|
0.49 |
0.49
|
| 15 | C1B
| V |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 16 | C2B
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 17 | C3B
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 18 | C4B
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 19 | CMB
| IV |
0.45 |
0.37
|
0.45 |
0.43
|
0.52 |
0.52
|
0.51 |
0.43
|
| 20 | CAB
| IV |
0.41 |
0.38
|
0.41 |
0.43
|
0.46 |
0.46
|
0.46 |
0.42
|
| 21 | CBB
| IV |
0.41 |
0.35
|
0.41 |
0.43
|
0.48 |
0.48
|
0.48 |
0.42
|
| 22 | C1C
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 23 | C2C
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 24 | C3C
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 25 | C4C
| V |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 26 | CMC
| IV |
0.32 |
0.32
|
0.32 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 27 | CAC
| IV |
0.39 |
0.38
|
0.38 |
0.43
|
0.45 |
0.45
|
0.44 |
0.44
|
| 28 | CBC
| IV |
0.53 |
0.48
|
0.46 |
0.43
|
0.55 |
0.55
|
0.48 |
0.50
|
| 29 | C1D
| V |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 30 | C2D
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 31 | C3D
| V |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 32 | C4D
| V |
0.42 |
0.42
|
0.42 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 33 | CMD
| IV |
0.40 |
0.40
|
0.40 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 34 | CAD
| IV |
0.47 |
0.42
|
0.47 |
0.43
|
0.48 |
0.48
|
0.48 |
0.43
|
| 35 | CBD
| IV |
0.41 |
0.41
|
0.41 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
| 36 | CGD
| VI |
0.42 |
0.42
|
0.40 |
0.42
|
0.43 |
0.43
|
0.42 |
0.43
|
| 37 | O1D
| II |
0.43 |
0.43
|
0.34 |
0.35
|
0.45 |
0.45
|
0.35 |
0.45
|
| 38 | O2D
| II |
0.43 |
0.43
|
0.39 |
0.42
|
0.47 |
0.47
|
0.42 |
0.47
|
| 39 | NA
| I |
0.43 |
0.43
|
0.43 |
0.43
|
0.44 |
0.44
|
0.44 |
0.44
|
| 40 | NB
| I |
0.43 |
0.43
|
0.43 |
0.43
|
0.44 |
0.44
|
0.44 |
0.44
|
| 41 | NC
| I |
0.43 |
0.43
|
0.43 |
0.43
|
0.44 |
0.44
|
0.44 |
0.44
|
| 42 | ND
| I |
0.43 |
0.43
|
0.43 |
0.43
|
0.44 |
0.44
|
0.44 |
0.44
|
| 43 | FE
| VI |
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
0.43 |
0.43
|
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 HEM 719
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
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il