Contacts of ligand A2N1000A in PDB entry 3PKJ
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 A2N1000A
in PDB entry 3PKJ (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
----------------------------------------------------------
20A GLU* 4.5 5.1 + - - -
50A GLY* 3.2 9.5 - - - -
51A ALA* 2.8 36.0 + - - +
52A GLY* 3.3 30.5 + - - -
55A THR* 3.0 29.5 + - + +
56A ALA* 5.3 7.7 + - - +
61A ASP* 3.2 30.7 - - - +
62A PHE* 2.8 63.3 + - + -
63A ARG* 2.7 85.9 + - - +
64A GLY* 4.6 1.8 - - - -
69A TRP* 3.2 30.8 + - + -
111A GLN* 3.0 41.5 + - - +
112A ASN* 4.3 1.4 + - - -
113A VAL* 5.4 10.9 - - + +
131A HIS* 2.8 48.1 + - - +
183A ILE* 6.2 3.4 - - + -
184A LEU* 3.7 20.9 - - - +
185A ASP 5.4 1.7 - - - +
186A TRP* 3.6 27.5 - - + +
212A GLY* 3.1 28.1 - - - +
213A THR* 2.8 24.9 + - - -
214A SER* 2.7 47.4 + - - -
215A LEU 4.1 0.7 + - - -
216A GLN 5.4 0.2 + - - -
217A ILE* 3.4 15.4 - - - +
238A ASN* 2.8 40.9 + - - +
239A LEU* 3.5 38.5 + - + +
240A GLN* 3.0 51.4 + - - +
254A GLY 3.2 20.9 - - - -
255A TYR* 3.4 25.1 - - - +
256A VAL* 2.9 45.4 + - + +
257A ASP 5.4 0.4 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand A2N1000A
and protein in PDB entry 3PKJ
(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 VAL 256A N III 2.9 16.2
3 N3 I LEU 239A N III 3.5 9.3
3 N3 I ASN 238A OD1 II 3.8 4.8
7 N6 I THR 55A OG1 I 3.5 11.1
7 N6 I GLY 52A O II 3.7 2.4
7 N6 I VAL 256A N III 4.1 1.6
7 N6 I ALA 56A N III 5.3 2.6
7 N6 I ASP 257A N III 5.4 0.4
8 N7 I THR 55A OG1 I 3.0 14.5
8 N7 I GLY 52A O II 3.3 0.4
13 O2' I GLN 240A N III 3.4 6.1
13 O2' I GLU 20A OE2 II 4.5 2.4
15 O3' I ASN 238A ND2 III 2.8 16.3
15 O3' I GLN 240A OE1 II 3.0 10.9
19 O5' II SER 214A N III 3.2 3.3
22 OAD I ARG 63A N III 2.8 26.3
22 OAD I PHE 62A N III 2.8 12.5
23 OAE I ALA 51A N III 2.8 25.1
23 OAE I THR 213A OG1 I 4.1 0.3
23 OAE I ASN 112A OD1 II 4.3 0.7
24 OAF I TRP 69A NE1 III 3.2 27.2
24 OAF I ARG 63A NH2 III 3.4 8.0
25 OAI I HIS 131A ND1 I 2.8 15.8
25 OAI I GLN 111A O II 3.0 12.1
25 OAI I ASN 112A OD1 II 5.5 0.2
26 OAJ I SER 214A OG I 2.7 22.2
26 OAJ I ARG 63A NH1 III 2.7 20.8
27 OAK I THR 213A OG1 I 2.8 23.6
27 OAK I SER 214A N III 2.9 7.3
27 OAK I SER 214A OG I 3.5 2.4
27 OAK I LEU 215A N III 4.1 0.7
27 OAK I GLN 111A OE1 II 4.5 0.2
27 OAK I GLN 216A N III 5.4 0.2
29 NAS I HIS 131A ND1 I 3.6 4.2
30 OAU II ARG 63A NH1 III 3.3 6.8
31 OAV II ARG 63A NH1 III 3.2 9.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand A2N1000A
in PDB entry 3PKJ (back
to top of page)
Total number of contacts is 175
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 VAL 256A N III 2.9 16.2
1 N1 I TYR 255A CA VII 3.4 3.8
1 N1 I VAL 256A CG2 IV 3.5 0.8*
1 N1 I LEU 239A CD1 IV 4.0 0.2*
2 C2 V GLY 254A O II 3.2 20.9
2 C2 V VAL 256A N III 3.5 4.9
2 C2 V VAL 256A CG1 IV 3.5 14.8
2 C2 V LEU 239A CG IV 3.8 3.6
2 C2 V LEU 239A N III 4.0 2.0
2 C2 V ASN 238A CA VII 4.3 3.1
3 N3 I LEU 239A N III 3.5 9.3
3 N3 I ASN 238A OD1 II 3.8 4.8
3 N3 I ASN 238A CA VII 3.9 0.2
3 N3 I GLY 212A CA VI 4.0 2.4
4 C4 V LEU 239A CD1 IV 3.8 4.3
4 C4 V GLY 52A CA VI 3.9 3.6
5 C5 V GLY 52A O II 3.4 3.6
5 C5 V LEU 239A CD1 IV 3.6 3.8
6 C6 V GLY 52A O II 3.6 4.0
6 C6 V LEU 239A CD1 IV 3.7 4.7
6 C6 V VAL 256A N III 3.9 0.2
6 C6 V VAL 256A CG2 IV 3.9 0.7
7 N6 I THR 55A OG1 I 3.5 11.1
7 N6 I TYR 255A CD1 V 3.6 20.2
7 N6 I GLY 52A O II 3.7 2.4
7 N6 I VAL 256A CG2 IV 4.1 6.1*
7 N6 I VAL 256A N III 4.1 1.6
7 N6 I TYR 255A CB IV 4.2 1.0*
7 N6 I TYR 255A CE1 V 4.5 0.2
7 N6 I ALA 56A N III 5.3 2.6
7 N6 I ASP 257A N III 5.4 0.4
7 N6 I ALA 56A CB IV 5.4 5.1*
8 N7 I THR 55A OG1 I 3.0 14.5
8 N7 I GLY 52A O II 3.3 0.4
8 N7 I THR 55A CG2 IV 3.9 0.6*
8 N7 I THR 55A CB VI 4.0 0.2
8 N7 I LEU 239A CD1 IV 4.0 2.8*
9 C8 V ASP 61A OD1 II 3.2 14.4
9 C8 V GLY 52A CA VI 3.4 8.3
9 C8 V THR 55A OG1 I 4.0 0.9
9 C8 V THR 55A CG2 IV 4.1 2.2
9 C8 V LEU 239A CD1 IV 4.4 3.6
9 C8 V GLU 20A OE2 II 5.3 1.8
11 C1' VI ASN 238A OD1 II 3.1 6.1
11 C1' VI ASN 238A CG VI 3.8 0.2
11 C1' VI LEU 239A N III 4.4 0.2
12 C2' VI ASP 61A OD1 II 3.3 7.6
12 C2' VI GLN 240A OE1 II 3.9 1.6
12 C2' VI GLN 240A CD VI 4.4 0.9
12 C2' VI GLY 64A CA VI 4.6 1.3
12 C2' VI GLU 20A OE2 II 5.2 0.9
13 O2' I GLN 240A CB IV 3.3 19.4*
13 O2' I GLN 240A CG IV 3.3 5.2*
13 O2' I GLN 240A N III 3.4 6.1
13 O2' I GLN 240A CD VI 3.6 0.2
13 O2' I LEU 239A CB IV 4.0 4.0*
13 O2' I GLU 20A OE2 II 4.5 2.4
14 C3' VI GLN 240A OE1 II 3.5 6.3
14 C3' VI ASP 61A OD1 II 3.7 2.9
14 C3' VI ASP 61A CG VI 4.5 0.4
14 C3' VI SER 214A CB VI 4.6 0.4
14 C3' VI GLY 64A N III 4.7 0.4
14 C3' VI ARG 63A C VI 5.1 0.4
15 O3' I ASN 238A ND2 III 2.8 16.3
15 O3' I GLN 240A OE1 II 3.0 10.9
15 O3' I GLN 240A CB IV 3.6 0.9*
15 O3' I SER 214A CB VI 3.8 8.7
16 C4' VIII ASN 238A OD1 II 3.2 10.1*
16 C4' VIII GLY 212A O II 3.3 2.2*
16 C4' VIII GLY 212A C VI 3.6 0.7
16 C4' VIII SER 214A N III 3.9 2.2
17 O4' II GLY 212A O II 3.1 8.0*
17 O4' II ASN 238A OD1 II 3.2 0.2*
17 O4' II GLY 52A CA VI 3.4 0.3
18 C5' VIII GLY 212A O II 3.1 14.8*
18 C5' VIII GLY 52A N III 3.8 7.9
18 C5' VIII ASP 61A CB IV 4.1 2.9
19 O5' II SER 214A N III 3.2 3.3
20 CAA IV PHE 62A CZ V 4.2 12.8
20 CAA IV PHE 62A CE2 V 4.2 3.4
20 CAA IV LEU 184A O II 5.0 2.9*
20 CAA IV TRP 186A CZ2 V 5.2 6.5
20 CAA IV TRP 69A CZ2 V 5.4 3.6
20 CAA IV TRP 186A CE2 V 5.4 1.6
20 CAA IV VAL 113A CG1 IV 5.6 5.8
20 CAA IV TRP 186A NE1 III 5.7 0.7*
20 CAA IV VAL 113A CG2 IV 5.8 2.0
20 CAA IV ILE 183A CG2 IV 6.2 3.4
21 OAC II LEU 184A O II 3.7 16.8*
21 OAC II HIS 131A CB IV 4.1 11.8*
21 OAC II HIS 131A CG V 4.1 1.4
21 OAC II HIS 131A CD2 V 4.7 0.7
21 OAC II HIS 131A O II 5.1 0.3*
21 OAC II LEU 184A CB IV 5.3 1.2*
21 OAC II ASP 185A O II 5.4 0.7*
21 OAC II VAL 113A CG1 IV 5.4 0.5*
21 OAC II ASP 185A C VI 5.5 1.0
21 OAC II TRP 186A CD2 V 5.9 0.5
21 OAC II TRP 186A CE3 V 5.9 0.2
21 OAC II TRP 186A CA VII 6.1 0.2
22 OAD I ARG 63A N III 2.8 26.3
22 OAD I PHE 62A N III 2.8 12.5
22 OAD I ASP 61A CB IV 3.5 2.1*
22 OAD I ARG 63A CA VII 3.7 1.0
22 OAD I ASP 61A CG VI 3.8 0.3
22 OAD I ARG 63A CB IV 3.9 0.3*
23 OAE I ALA 51A N III 2.8 25.1
23 OAE I GLY 50A CA VI 3.2 9.5
23 OAE I ALA 51A CB IV 3.7 1.7*
23 OAE I THR 213A OG1 I 4.1 0.3
23 OAE I GLN 111A CB IV 4.2 2.6*
23 OAE I ASN 112A OD1 II 4.3 0.7
24 OAF I TRP 69A NE1 III 3.2 27.2
24 OAF I ARG 63A NH2 III 3.4 8.0
24 OAF I PHE 62A CD2 V 3.6 6.6
24 OAF I TRP 186A CH2 V 3.6 2.6
24 OAF I PHE 62A CG V 3.7 0.9
24 OAF I TRP 186A CZ2 V 3.9 0.3
24 OAF I PHE 62A CE2 V 4.0 0.2
25 OAI I HIS 131A ND1 I 2.8 15.8
25 OAI I GLN 111A O II 3.0 12.1
25 OAI I GLN 111A C VI 3.9 0.3
25 OAI I PHE 62A CE1 V 4.1 2.4
25 OAI I PHE 62A CZ V 4.5 0.2
25 OAI I ASN 112A CA VII 5.2 0.5
25 OAI I VAL 113A CG1 IV 5.5 1.0*
25 OAI I ASN 112A OD1 II 5.5 0.2
25 OAI I VAL 113A CG2 IV 6.1 0.2*
26 OAJ I SER 214A OG I 2.7 22.2
26 OAJ I ARG 63A NH1 III 2.7 20.8
26 OAJ I ARG 63A CD VII 3.4 6.4
26 OAJ I SER 214A CB VI 3.4 0.9
26 OAJ I ARG 63A CG IV 3.7 0.2*
26 OAJ I ARG 63A CB IV 3.7 0.2*
27 OAK I THR 213A OG1 I 2.8 23.6
27 OAK I SER 214A N III 2.9 7.3
27 OAK I THR 213A CA VII 3.3 1.0
27 OAK I SER 214A OG I 3.5 2.4
27 OAK I LEU 215A N III 4.1 0.7
27 OAK I GLN 111A OE1 II 4.5 0.2
27 OAK I GLN 216A N III 5.4 0.2
28 CAO VIII GLN 111A OE1 II 3.1 24.5*
28 CAO VIII GLN 111A CD VI 3.8 1.6
28 CAO VIII GLN 111A CB IV 4.0 0.2
28 CAO VIII ARG 63A NH1 III 4.3 0.7
28 CAO VIII ILE 217A CG1 IV 4.5 2.7
28 CAO VIII ILE 217A CB IV 4.7 0.2
29 NAS I HIS 131A ND1 I 3.6 4.2
29 NAS I HIS 131A CE1 V 4.1 1.6
29 NAS I TRP 186A CZ3 V 5.4 0.4
29 NAS I ILE 217A CG2 IV 5.6 1.0*
30 OAU II ARG 63A NH1 III 3.3 6.8
31 OAV II ARG 63A NH1 III 3.2 9.2
31 OAV II ILE 217A CG1 IV 3.4 2.9*
32 OAX II ALA 51A CB IV 3.5 9.2*
32 OAX II PHE 62A CD1 V 3.7 4.7
33 CAY VI HIS 131A ND1 I 4.3 1.6
33 CAY VI HIS 131A CG V 4.5 0.7
33 CAY VI HIS 131A CB IV 4.6 1.8
33 CAY VI TRP 186A CZ2 V 5.4 2.9
33 CAY VI TRP 186A CH2 V 5.4 0.4
33 CAY VI VAL 113A CG1 IV 5.5 1.3
33 CAY VI TRP 186A CE2 V 5.6 0.4
33 CAY VI TRP 186A CZ3 V 5.6 1.1
33 CAY VI TRP 186A CD2 V 5.9 0.7
33 CAY VI TRP 186A CE3 V 5.9 0.2
34 CBC VI ARG 63A NH2 III 3.8 5.6
34 CBC VI TRP 186A CH2 V 4.0 8.5
34 CBC VI ILE 217A CG1 IV 4.1 3.8
34 CBC VI TRP 186A CZ3 V 4.6 0.2
34 CBC VI ILE 217A CG2 IV 5.3 0.2
35 CBF VI PHE 62A CE1 V 3.5 15.5
36 CBH VIII HIS 131A CE1 V 3.7 8.3
36 CBH VIII ILE 217A CG1 IV 4.0 4.5
37 CBI VI PHE 62A CZ V 3.8 4.3
------------------------------------------------------------------------
Table V
Complementarity values for the ligand A2N1000A
in PDB entry 3PKJ (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 815
Actual value (Å2) 501
Normalised complementarity 0.61
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand A2N1000A
in PDB entry 3PKJ (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 |
0.61 |
0.61
|
0.57 |
0.58
|
0.62 |
0.62
|
0.57 |
0.62
|
| 2 | C2
| V |
0.57 |
0.52
|
0.54 |
0.55
|
0.61 |
0.61
|
0.59 |
0.56
|
| 3 | N3
| I |
0.61 |
0.60
|
0.59 |
0.58
|
0.61 |
0.61
|
0.59 |
0.60
|
| 4 | C4
| V |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 5 | C5
| V |
0.61 |
0.60
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 6 | C6
| V |
0.60 |
0.59
|
0.60 |
0.60
|
0.61 |
0.61
|
0.61 |
0.60
|
| 7 | N6
| I |
0.61 |
0.61
|
0.60 |
0.60
|
0.64 |
0.64
|
0.63 |
0.64
|
| 8 | N7
| I |
0.61 |
0.61
|
0.61 |
0.59
|
0.62 |
0.62
|
0.62 |
0.62
|
| 9 | C8
| V |
0.60 |
0.56
|
0.60 |
0.57
|
0.61 |
0.61
|
0.61 |
0.58
|
| 11 | C1'
| VI |
0.61 |
0.60
|
0.61 |
0.60
|
0.61 |
0.61
|
0.61 |
0.60
|
| 12 | C2'
| VI |
0.61 |
0.59
|
0.61 |
0.59
|
0.61 |
0.61
|
0.61 |
0.59
|
| 13 | O2'
| I |
0.61 |
0.61
|
0.60 |
0.66
|
0.68 |
0.68
|
0.67 |
0.68
|
| 14 | C3'
| VI |
0.61 |
0.59
|
0.61 |
0.59
|
0.61 |
0.61
|
0.61 |
0.59
|
| 15 | O3'
| I |
0.61 |
0.59
|
0.57 |
0.55
|
0.62 |
0.62
|
0.58 |
0.59
|
| 16 | C4'
| VIII |
0.64 |
0.61
|
0.64 |
0.61
|
0.64 |
0.64
|
0.64 |
0.61
|
| 17 | O4'
| II |
0.63 |
0.61
|
0.63 |
0.61
|
0.63 |
0.63
|
0.63 |
0.61
|
| 18 | C5'
| VIII |
0.64 |
0.61
|
0.62 |
0.60
|
0.65 |
0.65
|
0.63 |
0.61
|
| 19 | O5'
| II |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 20 | CAA
| IV |
0.60 |
0.59
|
0.59 |
0.61
|
0.62 |
0.62
|
0.62 |
0.62
|
| 21 | OAC
| II |
0.66 |
0.61
|
0.66 |
0.65
|
0.69 |
0.69
|
0.69 |
0.65
|
| 22 | OAD
| I |
0.61 |
0.61
|
0.52 |
0.53
|
0.62 |
0.62
|
0.52 |
0.62
|
| 23 | OAE
| I |
0.61 |
0.61
|
0.55 |
0.56
|
0.63 |
0.63
|
0.56 |
0.62
|
| 24 | OAF
| I |
0.61 |
0.61
|
0.53 |
0.53
|
0.61 |
0.61
|
0.53 |
0.61
|
| 25 | OAI
| I |
0.61 |
0.58
|
0.61 |
0.55
|
0.62 |
0.62
|
0.62 |
0.59
|
| 26 | OAJ
| I |
0.61 |
0.61
|
0.55 |
0.51
|
0.62 |
0.62
|
0.55 |
0.62
|
| 27 | OAK
| I |
0.61 |
0.61
|
0.59 |
0.53
|
0.61 |
0.61
|
0.59 |
0.61
|
| 28 | CAO
| VIII |
0.67 |
0.61
|
0.67 |
0.61
|
0.67 |
0.67
|
0.67 |
0.61
|
| 29 | NAS
| I |
0.61 |
0.61
|
0.61 |
0.61
|
0.62 |
0.62
|
0.62 |
0.62
|
| 30 | OAU
| II |
0.61 |
0.61
|
0.60 |
0.60
|
0.61 |
0.61
|
0.60 |
0.61
|
| 31 | OAV
| II |
0.61 |
0.61
|
0.59 |
0.60
|
0.62 |
0.62
|
0.60 |
0.62
|
| 32 | OAX
| II |
0.61 |
0.61
|
0.61 |
0.64
|
0.64 |
0.64
|
0.64 |
0.64
|
| 33 | CAY
| VI |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 34 | CBC
| VI |
0.60 |
0.60
|
0.59 |
0.60
|
0.61 |
0.61
|
0.60 |
0.61
|
| 35 | CBF
| VI |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 36 | CBH
| VIII |
0.60 |
0.60
|
0.60 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
| 37 | CBI
| VI |
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
0.61 |
0.61
|
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 A2N 1000
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 4 C4 5 C5
9 C8 11 C1' 12 C2' 14 C3' 16 C4' 34 CBC
37 CBI 35 CBF 36 CBH
2. Oxygen ("hydroxy" or "carbonyl")
13 O2' 15 O3' 21 OAC 24 OAF 25 OAI
3. Nitrogen ("hydrophilic")
1 N1 3 N3 7 N6 8 N7 10 N9 29 NAS
Ligand A2N 1000
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 4 C4 5 C5
9 C8 11 C1' 12 C2' 14 C3' 16 C4' 34 CBC
37 CBI 35 CBF 36 CBH
2. Oxygen ("hydroxy" or "carbonyl")
13 O2' 15 O3' 21 OAC 24 OAF 25 OAI
3. Nitrogen ("hydrophilic")
1 N1 3 N3 7 N6 8 N7 10 N9 29 NAS
Ligand A2N 1000
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 4 C4 5 C5
9 C8 11 C1' 12 C2' 14 C3' 16 C4' 34 CBC
37 CBI 35 CBF 36 CBH
2. Oxygen ("hydroxy" or "carbonyl")
13 O2' 15 O3' 21 OAC 24 OAF 25 OAI
3. Nitrogen ("hydrophilic")
1 N1 3 N3 7 N6 8 N7 10 N9 29 NAS
Ligand A2N 1000
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 4 C4 5 C5
9 C8 11 C1' 12 C2' 14 C3' 16 C4' 34 CBC
37 CBI 35 CBF 36 CBH
2. Oxygen ("hydroxy" or "carbonyl")
13 O2' 15 O3' 21 OAC 24 OAF 25 OAI
3. Nitrogen ("hydrophilic")
1 N1 3 N3 7 N6 8 N7 10 N9 29 NAS
Ligand A2N 1000
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 4 C4 5 C5
9 C8 11 C1' 12 C2' 14 C3' 16 C4' 34 CBC
37 CBI 35 CBF 36 CBH
2. Oxygen ("hydroxy" or "carbonyl")
13 O2' 15 O3' 21 OAC 24 OAF 25 OAI
3. Nitrogen ("hydrophilic")
1 N1 3 N3 7 N6 8 N7 10 N9 29 NAS
Ligand A2N 1000
1. Carbon (in rings)
2 C2 4 C4 5 C5 6 C6 4 C4 5 C5
9 C8 11 C1' 12 C2' 14 C3' 16 C4' 34 CBC
37 CBI 35 CBF 36 CBH
2. Oxygen ("hydroxy" or "carbonyl")
13 O2' 15 O3' 21 OAC 24 OAF 25 OAI
3. Nitrogen ("hydrophilic")
1 N1 3 N3 7 N6 8 N7 10 N9 29 NAS
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il