Contacts of ligand HEC 402C in PDB entry 2WJM
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 HEC 402C
in PDB entry 2WJM (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
----------------------------------------------------------
77C ILE* 3.7 30.7 - - + -
81C VAL* 3.9 17.7 - - + -
89C TYR* 2.6 30.4 + - + +
90C CYS* 4.5 0.4 - - - -
102C TYR* 2.7 27.3 + - + -
103C PRO* 3.6 35.4 - - + +
106C VAL* 3.4 24.9 - - + -
107C ALA* 4.1 20.9 - - + +
110C MET* 2.4 54.7 - - + +
111C LEU* 3.6 29.6 - - + -
113C MET* 3.6 25.4 - - + -
114C THR* 3.4 35.4 - - + +
117C ILE* 4.5 2.5 - - + -
130C VAL* 4.2 17.0 - - + -
131C THR 3.5 19.7 - - - +
132C CYS* 1.8 57.9 - - + +
135C CYS* 1.8 52.0 - - + -
136C HIS* 2.1 33.6 + + + +
140C PRO* 3.3 24.8 - - + +
141C LEU* 3.3 29.1 - - + +
142C PRO* 3.5 18.2 - - + -
145C VAL* 4.0 21.3 - - + -
277C LEU* 4.1 13.9 - - + -
282C LEU* 4.0 23.3 - - + -
285C LEU* 5.5 2.7 - - + -
289C LEU* 3.5 31.7 - - + +
293C ARG* 2.9 28.1 + - - -
300C ALA* 5.7 0.4 - - + -
301C PRO* 3.7 55.2 - - + +
302C GLN 4.2 4.9 - - - -
303C ALA* 4.5 12.6 - - + +
307C THR* 4.0 10.3 - - + -
308C CYS* 4.2 1.3 - - - -
328C LEU* 4.4 4.9 - - + -
401C HEC 4.0 15.7 - - + -
404C HEC 4.1 17.5 - - + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand HEC 402C
and protein in PDB entry 2WJM
(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
------------------------------------------------------------------------
6 NA I HIS 136C NE2 I 2.9 1.4
15 O1A II TYR 89C OH I 2.6 27.0
15 O1A II TYR 102C OH I 2.7 11.3
15 O1A II ARG 293C NH2 III 3.2 3.6
16 O2A II ARG 293C NE III 2.9 12.5
16 O2A II TYR 102C OH I 3.5 3.1
17 NB I HIS 136C NE2 I 2.9 2.4
25 NC I HIS 136C NE2 I 2.9 1.6
33 ND I HIS 136C NE2 I 3.0 3.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand HEC 402C
in PDB entry 2WJM (back
to top of page)
Total number of contacts is 174
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 FE VI HIS 136C NE2 I 2.1 6.2
1 FE VI MET 110C SD VIII 2.4 2.4
2 CHA IV MET 110C CE IV 3.6 4.3
2 CHA IV HIS 136C CE1 V 3.8 0.7
2 CHA IV VAL 106C CG1 IV 4.0 2.5
3 CHB IV MET 110C CG IV 3.6 3.6
3 CHB IV HIS 136C NE2 I 3.8 0.9*
3 CHB IV VAL 81C CG1 IV 4.1 5.8
3 CHB IV ALA 107C CA VII 4.1 2.0
4 CHC IV CYS 132C CA VII 3.5 5.6
4 CHC IV THR 114C OG1 I 3.6 6.5*
4 CHC IV MET 110C SD VIII 4.0 1.6
5 CHD IV PRO 142C CG IV 3.8 7.9
5 CHD IV CYS 135C CB IV 4.1 0.2
5 CHD IV MET 110C SD VIII 4.1 0.7
5 CHD IV MET 113C CE IV 4.4 2.0
5 CHD IV LEU 282C CD2 IV 4.5 0.7
5 CHD IV THR 307C CG2 IV 4.9 0.4
6 NA I HIS 136C NE2 I 2.9 1.4
6 NA I MET 110C SD VIII 3.2 2.6
7 C1A V HIS 136C CE1 V 3.4 2.5
7 C1A V VAL 106C CG1 IV 3.6 3.6
8 C2A V VAL 106C CG1 IV 3.4 3.4
8 C2A V HIS 136C CE1 V 4.2 0.2
9 C3A V VAL 106C CG1 IV 3.8 2.5
9 C3A V HIS 136C CE1 V 4.2 1.1
9 C3A V VAL 81C CG1 IV 4.4 0.9
10 C4A V HIS 136C NE2 I 3.5 2.9
10 C4A V HIS 136C CE1 V 3.6 0.9
10 C4A V MET 110C CG IV 3.6 3.4
11 CMA IV PRO 103C O II 3.6 23.6*
11 CMA IV PRO 103C CB IV 4.0 11.7
11 CMA IV HEC 401C CBC IV 4.0 15.5
11 CMA IV ALA 107C CB IV 4.1 1.1
11 CMA IV VAL 81C CG1 IV 4.2 6.3
11 CMA IV CYS 90C SG VI 4.5 0.4
11 CMA IV TYR 89C CE2 V 4.6 2.5
12 CAA IV VAL 106C CG1 IV 3.6 10.8
12 CAA IV VAL 106C CB IV 4.1 2.2
12 CAA IV TYR 102C CE1 V 4.4 5.8
12 CAA IV LEU 289C CD2 IV 4.5 0.7
12 CAA IV PRO 103C CA IV 4.8 0.2
13 CBA IV PRO 140C O II 3.3 11.2*
13 CBA IV PRO 140C C VI 3.9 2.0
13 CBA IV PRO 140C CB IV 4.1 2.0
13 CBA IV TYR 89C OH I 4.4 0.2*
14 CGA VI TYR 102C OH I 3.4 3.8
14 CGA VI ARG 293C NE III 3.5 4.7
14 CGA VI ARG 293C NH2 III 3.6 1.8
14 CGA VI TYR 102C CE1 V 3.7 2.0
15 O1A II TYR 89C OH I 2.6 27.0
15 O1A II TYR 102C OH I 2.7 11.3
15 O1A II ARG 293C NH2 III 3.2 3.6
15 O1A II TYR 102C CE1 V 3.5 1.2
15 O1A II TYR 89C CZ V 3.6 0.7
16 O2A II ARG 293C NE III 2.9 12.5
16 O2A II TYR 102C OH I 3.5 3.1
16 O2A II LEU 289C CD2 IV 3.5 8.1*
17 NB I HIS 136C NE2 I 2.9 2.4
17 NB I MET 110C SD VIII 3.1 2.0
18 C1B V MET 110C CB IV 3.4 3.6
18 C1B V HIS 136C NE2 I 3.6 1.8
18 C1B V VAL 81C CG2 IV 4.0 1.6
19 C2B V CYS 132C SG VI 3.4 0.9
19 C2B V MET 110C CB IV 3.6 2.2
19 C2B V CYS 132C CB IV 3.9 1.6
19 C2B V VAL 81C CG2 IV 3.9 0.4
20 C3B V CYS 132C SG VI 2.7 3.4
20 C3B V CYS 132C CB IV 3.2 0.2
20 C3B V MET 110C CB IV 3.7 0.7
21 C4B V MET 110C CB IV 3.5 3.4
21 C4B V CYS 132C CB IV 3.7 2.7
21 C4B V HIS 136C CD2 V 3.8 0.9
22 CMB IV CYS 132C SG VI 3.6 5.6
22 CMB IV ILE 77C CG2 IV 3.7 26.2
22 CMB IV VAL 81C CG2 IV 4.0 2.7
22 CMB IV ILE 77C CG1 IV 4.1 2.0
22 CMB IV ALA 107C CB IV 4.2 15.0
22 CMB IV HEC 401C CBC IV 4.2 0.2
22 CMB IV ILE 77C CD1 IV 4.2 2.5
22 CMB IV ALA 107C O II 4.4 2.7*
22 CMB IV LEU 111C CG IV 5.0 0.2
23 CAB IV CYS 132C SG VI 1.8 27.1
23 CAB IV CYS 132C CB IV 2.9 0.9
23 CAB IV CYS 132C CA VII 3.4 1.3
23 CAB IV THR 114C OG1 I 3.6 2.5*
23 CAB IV CYS 132C N III 3.7 0.7*
24 CBB IV CYS 132C SG VI 2.7 7.9
24 CBB IV THR 114C OG1 I 3.4 13.9*
24 CBB IV LEU 111C CD2 IV 3.6 27.8
24 CBB IV MET 110C O II 3.8 7.0*
24 CBB IV LEU 111C CA VII 3.9 1.6
24 CBB IV THR 114C CB VI 4.0 3.6
24 CBB IV LEU 328C CD2 IV 4.4 4.9
24 CBB IV THR 114C CG2 IV 4.5 0.2
25 NC I HIS 136C NE2 I 2.9 1.6
25 NC I MET 110C SD VIII 3.0 2.8
26 C1C V HIS 136C CD2 V 3.6 3.8
26 C1C V MET 110C SD VIII 3.8 2.5
26 C1C V MET 113C CE IV 3.8 1.3
27 C2C V CYS 135C SG VI 3.3 1.6
27 C2C V CYS 135C CB IV 3.5 1.6
27 C2C V MET 113C CE IV 3.6 2.0
28 C3C V CYS 135C SG VI 2.7 2.2
28 C3C V CYS 135C CB IV 3.1 0.2
28 C3C V MET 113C CE IV 3.6 0.7
29 C4C V CYS 135C CB IV 3.6 3.4
29 C4C V HIS 136C NE2 I 3.7 0.7
29 C4C V MET 113C CE IV 3.7 3.6
30 CMC IV CYS 135C SG VI 3.4 7.0
30 CMC IV THR 131C O II 3.5 19.7*
30 CMC IV THR 114C OG1 I 4.1 8.7*
30 CMC IV VAL 130C CG2 IV 4.2 15.9
30 CMC IV MET 113C CE IV 4.2 3.1
30 CMC IV ILE 117C CD1 IV 4.5 1.8
30 CMC IV VAL 130C CB IV 4.6 1.1
30 CMC IV HEC 404C CBC IV 5.2 0.2
31 CAC IV CYS 135C SG VI 1.8 28.3
31 CAC IV CYS 135C CB IV 2.9 1.1
31 CAC IV THR 307C CG2 IV 4.0 4.3
32 CBC IV CYS 135C SG VI 2.8 6.5
32 CBC IV MET 113C CE IV 3.8 12.3
32 CBC IV HEC 404C CBC IV 4.1 16.8
32 CBC IV LEU 277C CD1 IV 4.1 13.9
32 CBC IV CYS 308C SG VI 4.2 1.3
32 CBC IV THR 307C CG2 IV 4.5 4.3
32 CBC IV ALA 303C CB IV 4.5 9.4
32 CBC IV ILE 117C CD1 IV 4.6 0.7
32 CBC IV MET 113C SD VIII 5.0 0.2
32 CBC IV HEC 404C CMC IV 5.2 0.4
32 CBC IV LEU 282C CD1 IV 5.2 0.9
33 ND I HIS 136C NE2 I 3.0 3.2
33 ND I MET 110C SD VIII 3.2 1.2
34 C1D V PRO 142C CG IV 3.5 4.0
34 C1D V MET 110C CE IV 3.8 3.1
35 C2D V PRO 142C CG IV 3.7 2.5
35 C2D V LEU 282C CD2 IV 4.0 3.4
36 C3D V MET 110C CE IV 3.9 2.7
37 C4D V MET 110C CE IV 3.3 4.0
37 C4D V HIS 136C CE1 V 3.8 2.5
38 CMD IV PRO 301C O II 3.8 14.6*
38 CMD IV LEU 282C CD2 IV 4.0 9.0
38 CMD IV LEU 282C CD1 IV 4.0 7.9
38 CMD IV VAL 145C CG1 IV 4.0 21.3
38 CMD IV PRO 301C C VI 4.2 2.5
38 CMD IV GLN 302C C VI 4.2 4.9
38 CMD IV ALA 303C N III 4.6 0.4*
38 CMD IV ALA 303C CB IV 5.0 2.7
38 CMD IV PRO 142C CB IV 5.1 0.2
38 CMD IV THR 307C CG2 IV 5.1 1.3
39 CAD IV PRO 301C O II 4.0 11.4*
39 CAD IV PRO 301C CB IV 4.1 1.1
39 CAD IV PRO 301C CG IV 4.2 1.6
39 CAD IV PRO 301C CD IV 4.2 2.0
39 CAD IV MET 110C CE IV 4.8 1.1
39 CAD IV LEU 289C CD1 IV 5.0 4.7
39 CAD IV LEU 282C CD2 IV 5.2 1.6
39 CAD IV LEU 285C CD1 IV 5.5 2.7
39 CAD IV ALA 300C CB IV 5.7 0.4
40 CBD IV PRO 301C CG IV 3.7 18.8
40 CBD IV PRO 301C CB IV 3.8 2.7
40 CBD IV LEU 141C CD1 IV 3.8 7.9
40 CBD IV PRO 142C CD IV 3.8 3.6
41 CGD VI LEU 141C CD1 IV 3.8 5.2
41 CGD VI ARG 293C NE III 4.3 2.2
41 CGD VI ARG 293C CD VII 4.3 1.3
41 CGD VI PRO 301C CG IV 4.5 0.4
42 O1D II LEU 141C CD1 IV 3.3 14.0*
42 O1D II PRO 140C O II 3.3 9.5*
42 O1D II LEU 141C CA VII 3.3 1.7
42 O1D II LEU 141C CB IV 3.8 0.3*
43 O2D II LEU 289C CD2 IV 3.5 15.2*
43 O2D II LEU 289C CD1 IV 4.0 2.9*
43 O2D II ARG 293C CD VII 4.0 1.9
------------------------------------------------------------------------
Table V
Complementarity values for the ligand HEC 402C
in PDB entry 2WJM (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 798
Actual value (Å2) 483
Normalised complementarity 0.61
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand HEC 402C
in PDB entry 2WJM (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 | FE
| VI |
0.61 |
0.60
|
0.61 |
0.59
|
0.61 |
0.61
|
0.61 |
0.60
|
| 2 | CHA
| IV |
0.59 |
0.59
|
0.59 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 3 | CHB
| IV |
0.58 |
0.58
|
0.58 |
0.61
|
0.61 |
0.61
|
0.60 |
0.61
|
| 4 | CHC
| IV |
0.62 |
0.62
|
0.61 |
0.61
|
0.62 |
0.62
|
0.61 |
0.62
|
| 5 | CHD
| IV |
0.58 |
0.58
|
0.58 |
0.61
|
0.61 |
0.61
|
0.61 |
0.60
|
| 6 | NA
| I |
0.61 |
0.60
|
0.61 |
0.60
|
0.61 |
0.61
|
0.61 |
0.60
|
| 7 | C1A
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 8 | C2A
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 9 | C3A
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 10 | C4A
| V |
0.60 |
0.60
|
0.60 |
0.60
|
0.61 |
0.61
|
0.61 |
0.61
|
| 11 | CMA
| IV |
0.58 |
0.52
|
0.58 |
0.61
|
0.66 |
0.66
|
0.66 |
0.61
|
| 12 | CAA
| IV |
0.57 |
0.57
|
0.57 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 13 | CBA
| IV |
0.63 |
0.60
|
0.63 |
0.61
|
0.63 |
0.63
|
0.63 |
0.61
|
| 14 | CGA
| VI |
0.61 |
0.61
|
0.59 |
0.58
|
0.61 |
0.61
|
0.59 |
0.61
|
| 15 | O1A
| II |
0.61 |
0.61
|
0.60 |
0.50
|
0.61 |
0.61
|
0.60 |
0.61
|
| 16 | O2A
| II |
0.61 |
0.61
|
0.57 |
0.59
|
0.63 |
0.63
|
0.59 |
0.63
|
| 17 | NB
| I |
0.61 |
0.60
|
0.61 |
0.60
|
0.61 |
0.61
|
0.61 |
0.60
|
| 18 | C1B
| V |
0.59 |
0.59
|
0.59 |
0.60
|
0.61 |
0.61
|
0.61 |
0.61
|
| 19 | C2B
| V |
0.59 |
0.59
|
0.59 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 20 | C3B
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 21 | C4B
| V |
0.59 |
0.59
|
0.59 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 22 | CMB
| IV |
0.49 |
0.48
|
0.49 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 23 | CAB
| IV |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 24 | CBB
| IV |
0.57 |
0.56
|
0.57 |
0.61
|
0.66 |
0.66
|
0.65 |
0.64
|
| 25 | NC
| I |
0.61 |
0.60
|
0.61 |
0.60
|
0.61 |
0.61
|
0.61 |
0.60
|
| 26 | C1C
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.60
|
| 27 | C2C
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 28 | C3C
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 29 | C4C
| V |
0.59 |
0.59
|
0.59 |
0.60
|
0.61 |
0.61
|
0.61 |
0.61
|
| 30 | CMC
| IV |
0.62 |
0.57
|
0.62 |
0.61
|
0.68 |
0.68
|
0.68 |
0.63
|
| 31 | CAC
| IV |
0.59 |
0.59
|
0.59 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 32 | CBC
| IV |
0.46 |
0.46
|
0.46 |
0.61
|
0.61 |
0.61
|
0.61 |
0.60
|
| 33 | ND
| I |
0.61 |
0.60
|
0.61 |
0.60
|
0.61 |
0.61
|
0.61 |
0.60
|
| 34 | C1D
| V |
0.59 |
0.59
|
0.59 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 35 | C2D
| V |
0.59 |
0.59
|
0.59 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 36 | C3D
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 37 | C4D
| V |
0.59 |
0.59
|
0.59 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 38 | CMD
| IV |
0.54 |
0.50
|
0.54 |
0.61
|
0.64 |
0.64
|
0.64 |
0.61
|
| 39 | CAD
| IV |
0.60 |
0.57
|
0.60 |
0.61
|
0.63 |
0.63
|
0.63 |
0.61
|
| 40 | CBD
| IV |
0.52 |
0.52
|
0.52 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 41 | CGD
| VI |
0.59 |
0.59
|
0.58 |
0.60
|
0.61 |
0.61
|
0.60 |
0.61
|
| 42 | O1D
| II |
0.63 |
0.61
|
0.62 |
0.64
|
0.66 |
0.66
|
0.66 |
0.64
|
| 43 | O2D
| II |
0.61 |
0.61
|
0.60 |
0.65
|
0.65 |
0.65
|
0.65 |
0.65
|
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 FME 1
2. Oxygen ("hydroxy" or "carbonyl")
3 O1 10 O
3. Nitrogen ("hydrophilic")
1 N
Ligand HEC 401
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 HEC 402
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 HEC 403
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 HEC 404
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 DGA 405
2. Oxygen ("hydroxy" or "carbonyl")
13 OA1 32 OB1
Ligand BCB 301
1. Carbon (in rings)
2 CHA 38 C4D 37 C3D 40 CAD 42 CBD 7 C1A
8 C2A 9 C3A 10 C4A 18 C1B 19 C2B 20 C3B
21 C4B 27 C1C 28 C2C 29 C3C 30 C4C 35 C1D
36 C2D 37 C3D 38 C4D
2. Oxygen ("hydroxy" or "carbonyl")
15 O1A 24 OBB 41 OBD 44 O1D
3. Nitrogen ("hydrophilic")
6 NA 17 NB 26 NC 34 ND
Ligand BCB 302
1. Carbon (in rings)
2 CHA 38 C4D 37 C3D 40 CAD 42 CBD 7 C1A
8 C2A 9 C3A 10 C4A 18 C1B 19 C2B 20 C3B
21 C4B 27 C1C 28 C2C 29 C3C 30 C4C 35 C1D
36 C2D 37 C3D 38 C4D
2. Oxygen ("hydroxy" or "carbonyl")
15 O1A 24 OBB 41 OBD 44 O1D
3. Nitrogen ("hydrophilic")
6 NA 17 NB 26 NC 34 ND
Ligand BPB 303
1. Carbon (in rings)
24 C1A 31 C2A 37 C3A 41 C4A 26 C1B 33 C2B
38 C3B 42 C4B 27 C1C 34 C2C 39 C3C 43 C4C
28 C1D 35 C2D 40 C3D 44 C4D 40 C3D 44 C4D
58 CHA 53 CBD 48 CAD
2. Oxygen ("hydroxy" or "carbonyl")
25 O1A 29 O1D 51 OBB 54 OBD
3. Nitrogen ("hydrophilic")
10 NA 11 NB 12 NC 13 ND
Ligand MPG 304
2. Oxygen ("hydroxy" or "carbonyl")
21 O2 23 O3 24 O4
Ligand MPG 305
2. Oxygen ("hydroxy" or "carbonyl")
21 O2 23 O3 24 O4
Ligand BCB 401
1. Carbon (in rings)
2 CHA 38 C4D 37 C3D 40 CAD 42 CBD 7 C1A
8 C2A 9 C3A 10 C4A 18 C1B 19 C2B 20 C3B
21 C4B 27 C1C 28 C2C 29 C3C 30 C4C 35 C1D
36 C2D 37 C3D 38 C4D
2. Oxygen ("hydroxy" or "carbonyl")
15 O1A 24 OBB 41 OBD 44 O1D
3. Nitrogen ("hydrophilic")
6 NA 17 NB 26 NC 34 ND
Ligand BCB 402
1. Carbon (in rings)
2 CHA 38 C4D 37 C3D 40 CAD 42 CBD 7 C1A
8 C2A 9 C3A 10 C4A 18 C1B 19 C2B 20 C3B
21 C4B 27 C1C 28 C2C 29 C3C 30 C4C 35 C1D
36 C2D 37 C3D 38 C4D
2. Oxygen ("hydroxy" or "carbonyl")
15 O1A 24 OBB 41 OBD 44 O1D
3. Nitrogen ("hydrophilic")
6 NA 17 NB 26 NC 34 ND
Ligand BPB 403
1. Carbon (in rings)
21 C1A 27 C2A 33 C3A 37 C4A 23 C1B 29 C2B
34 C3B 38 C4B 24 C1C 30 C2C 35 C3C 39 C4C
25 C1D 31 C2D 36 C3D 40 C4D 36 C3D 40 C4D
54 CHA 49 CBD 44 CAD
2. Oxygen ("hydroxy" or "carbonyl")
22 O1A 26 O1D 47 OBB 50 OBD
3. Nitrogen ("hydrophilic")
10 NA 11 NB 12 NC 13 ND
Ligand MQ7 404
1. Carbon (in rings)
1 C1 3 C2 5 C3 6 C4 8 C5 13 C10
8 C5 9 C6 10 C7 11 C8 12 C9 13 C10
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 7 O4
Please E-mail any questions and/or suggestions
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Vladimir.Sobolev@weizmann.ac.il