Contacts of ligand NAI 930B in PDB entry 1O0S
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 NAI 930B
in PDB entry 1O0S (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
----------------------------------------------------------
181B ARG* 3.0 41.2 + - - -
183B LEU* 3.7 35.3 - - + +
184B GLY 5.8 0.2 + - - -
275B ASN* 3.2 42.6 + - - -
295B ASP* 3.0 32.9 + - - +
299B THR* 3.2 44.7 + - + -
303B ILE* 6.1 1.3 - - + -
326B PHE* 3.4 37.6 - + - -
327B GLY* 3.6 14.3 - - - -
328B ALA* 3.3 12.6 + - - +
329B GLY* 3.1 36.1 + - - -
330B ALA* 2.9 24.9 + - - +
331B ALA* 3.0 44.7 + - + +
332B SER 4.6 0.3 + - - -
361B ASP* 2.9 50.1 + - - +
362B ILE* 3.0 66.8 + - + +
377B HIS* 5.5 1.4 - - - -
405B ALA* 3.5 47.0 + - - +
406B SER* 3.9 14.2 - - - -
407B THR* 3.9 32.2 + - - +
408B VAL* 3.2 36.4 - - + +
432B LEU* 3.4 31.7 - - + +
433B SER* 3.3 11.8 + - - -
434B ASN* 3.1 63.4 + - - +
459B GLY* 5.3 4.7 - - - -
477B GLY 5.3 7.0 - - - -
479B ASN* 4.2 12.7 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand NAI 930B
and protein in PDB entry 1O0S
(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
------------------------------------------------------------------------
2 O1A I ASN 275B ND2 III 4.6 2.6
3 O2A I ALA 330B N III 2.9 16.1
3 O2A I ASN 275B ND2 III 3.2 15.9
9 O3B I GLY 329B N III 3.2 14.2
9 O3B I ALA 328B N III 3.3 6.2
9 O3B I ALA 328B O II 3.9 0.3
11 O2B I ILE 362B N III 3.3 1.9
11 O2B I ASP 361B OD2 II 4.0 0.2
19 N1A I ILE 362B O II 4.9 1.2
23 O3 II ASN 275B ND2 III 4.3 0.7
23 O3 II THR 407B OG1 I 5.3 1.2
25 O1N I ASN 275B ND2 III 3.2 21.5
25 O1N I ASN 275B OD1 II 4.1 0.9
25 O1N I ARG 181B NH1 III 4.2 10.4
25 O1N I ALA 331B N III 4.2 1.4
26 O2N I ALA 331B N III 3.0 22.9
26 O2N I ALA 330B N III 3.0 2.6
26 O2N I GLY 329B N III 4.4 0.3
26 O2N I SER 332B N III 4.6 0.3
26 O2N I ALA 405B O II 4.6 0.3
32 O3D I ASN 434B N III 3.1 17.8
32 O3D I ASN 434B O II 3.7 5.0
32 O3D I SER 433B OG I 3.8 0.2
32 O3D I THR 407B OG1 I 3.9 7.3
34 O2D I ASN 434B ND2 III 3.1 14.4
34 O2D I ASN 434B O II 4.1 1.4
34 O2D I GLY 184B N III 5.8 0.2
40 O7N II ARG 181B NH1 III 3.0 28.8
40 O7N II ARG 181B NH2 III 3.4 1.6
41 N7N I ASP 295B OD1 II 3.0 21.8
41 N7N I THR 299B OG1 I 3.2 11.7
41 N7N I ASN 479B ND2 III 4.2 5.1
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand NAI 930B
in PDB entry 1O0S (back
to top of page)
Total number of contacts is 168
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
------------------------------------------------------------------------
2 O1A I ASN 275B ND2 III 4.6 2.6
3 O2A I ALA 330B N III 2.9 16.1
3 O2A I ASN 275B ND2 III 3.2 15.9
3 O2A I GLY 329B CA VI 3.4 2.4
4 O5B II GLY 329B CA VI 3.1 4.3
5 C5B VIII GLY 329B CA VI 4.1 0.2
5 C5B VIII ALA 405B O II 4.1 9.0*
5 C5B VIII SER 406B CA VII 4.9 1.8
5 C5B VIII THR 407B OG1 I 5.3 4.9
5 C5B VIII THR 407B CB VI 6.1 0.2
6 C4B VIII GLY 329B N III 3.6 9.0
6 C4B VIII ALA 328B N III 3.9 2.7
6 C4B VIII ALA 405B O II 4.1 3.1*
7 O4B II GLY 327B CA VI 3.6 6.6
7 O4B II SER 406B CB VI 3.9 5.7
8 C3B VI GLY 329B N III 3.8 0.7
8 C3B VI GLY 329B CA VI 4.0 2.0
9 O3B I GLY 329B N III 3.2 14.2
9 O3B I ALA 328B N III 3.3 6.2
9 O3B I ALA 328B C VI 3.4 3.1
9 O3B I ASP 361B CB IV 3.5 6.9*
9 O3B I GLY 329B CA VI 3.7 0.9
9 O3B I ALA 328B O II 3.9 0.3
9 O3B I ALA 328B CB IV 4.3 0.2*
9 O3B I HIS 377B CE1 V 5.5 1.4
10 C2B VI ILE 362B CG2 IV 4.5 0.4
10 C2B VI ILE 362B CD1 IV 4.6 0.9
11 O2B I ILE 362B CG1 IV 3.0 28.6*
11 O2B I ILE 362B N III 3.3 1.9
11 O2B I ASP 361B CB IV 3.4 3.1*
11 O2B I ILE 362B CD1 IV 3.4 2.9*
11 O2B I ASP 361B OD2 II 4.0 0.2
12 C1B VI ILE 362B N III 3.9 1.1
12 C1B VI ASP 361B CA VII 4.0 3.1
12 C1B VI GLY 327B CA VI 4.1 1.6
14 C8A V ILE 362B CG2 IV 3.5 7.4
14 C8A V VAL 408B CG1 IV 4.6 1.8
14 C8A V SER 406B CB VI 4.8 2.0
14 C8A V THR 407B N III 5.2 3.4
14 C8A V THR 407B CB VI 5.8 2.7
15 N7A I ILE 362B CG2 IV 3.4 5.5*
15 N7A I VAL 408B CG1 IV 3.7 8.5*
15 N7A I THR 407B C VI 5.7 0.2
15 N7A I THR 407B CB VI 5.8 0.4
16 C5A V ILE 362B CG2 IV 3.5 3.8
16 C5A V VAL 408B CG1 IV 3.6 4.7
17 C6A V VAL 408B CG1 IV 3.4 4.9
17 C6A V ILE 362B CG2 IV 4.1 4.0
17 C6A V ILE 362B CA VII 4.2 0.4
17 C6A V ILE 362B O II 5.2 0.2
18 N6A I VAL 408B CG1 IV 3.2 16.0*
18 N6A I VAL 408B CB IV 4.3 0.4*
18 N6A I ILE 362B CG2 IV 4.7 1.4*
18 N6A I PHE 326B CZ V 5.0 0.2
19 N1A I PHE 326B CZ V 3.5 9.5
19 N1A I ILE 362B CA VII 4.2 1.0
19 N1A I ILE 362B O II 4.9 1.2
20 C2A V ASP 361B O II 3.2 17.3
20 C2A V PHE 326B CZ V 3.4 21.5
20 C2A V PHE 326B CE1 V 3.6 5.2
20 C2A V ILE 362B CA VII 3.9 0.2
20 C2A V ASP 361B CA VII 4.1 0.2
20 C2A V PHE 326B CE2 V 4.1 0.2
20 C2A V ILE 362B C VI 4.6 0.2
20 C2A V ILE 362B O II 4.8 0.2
21 N3A I ASP 361B C VI 2.9 14.8
21 N3A I ASP 361B CA VII 3.3 4.4
21 N3A I PHE 326B CZ V 4.3 0.8
21 N3A I GLY 327B CA VI 4.4 6.1
21 N3A I PHE 326B CE1 V 4.4 0.2
21 N3A I SER 406B CB VI 4.4 0.6
22 C4A V ILE 362B N III 3.3 5.2
22 C4A V SER 406B CB VI 4.3 4.0
23 O3 II ASN 275B ND2 III 4.3 0.7
23 O3 II THR 407B OG1 I 5.3 1.2
25 O1N I ASN 275B ND2 III 3.2 21.5
25 O1N I ALA 330B CB IV 3.8 6.2*
25 O1N I ASN 275B CG VI 4.0 1.0
25 O1N I ASN 275B OD1 II 4.1 0.9
25 O1N I ARG 181B NH1 III 4.2 10.4
25 O1N I ALA 331B N III 4.2 1.4
25 O1N I ALA 331B CB IV 4.7 1.0*
25 O1N I ARG 181B CD VII 5.5 0.3
26 O2N I ALA 331B N III 3.0 22.9
26 O2N I ALA 330B N III 3.0 2.6
26 O2N I GLY 329B C VI 3.5 1.7
26 O2N I ALA 331B CB IV 3.6 1.4*
26 O2N I GLY 329B CA VI 3.7 0.3
26 O2N I GLY 329B N III 4.4 0.3
26 O2N I SER 332B N III 4.6 0.3
26 O2N I ALA 405B O II 4.6 0.3
27 O5D II ALA 331B CB IV 4.2 1.6*
28 C5D VIII ALA 405B O II 3.5 17.9*
28 C5D VIII ALA 405B C VI 3.9 0.7
28 C5D VIII ALA 405B CB IV 4.5 1.1
28 C5D VIII THR 407B OG1 I 4.5 4.9
29 C4D VIII ALA 405B C VI 4.0 11.0
29 C4D VIII SER 433B OG I 4.2 3.8
29 C4D VIII THR 407B OG1 I 4.6 0.2
30 O4D II ALA 331B CB IV 4.0 6.2*
30 O4D II LEU 432B O II 4.1 0.5*
30 O4D II ALA 405B CB IV 4.2 3.8*
31 C3D VI THR 407B OG1 I 4.2 5.8
32 O3D I ASN 434B N III 3.1 17.8
32 O3D I SER 433B CA VII 3.3 4.5
32 O3D I SER 433B CB VI 3.6 3.3
32 O3D I ASN 434B O II 3.7 5.0
32 O3D I SER 433B OG I 3.8 0.2
32 O3D I THR 407B OG1 I 3.9 7.3
32 O3D I THR 407B CA VII 4.5 0.5
32 O3D I THR 407B CB VI 4.7 0.2
32 O3D I THR 407B CG2 IV 5.0 0.2*
33 C2D VI LEU 183B CD1 IV 4.6 4.3
34 O2D I ASN 434B ND2 III 3.1 14.4
34 O2D I ASN 434B CB IV 3.4 8.0*
34 O2D I ASN 434B O II 4.1 1.4
34 O2D I LEU 183B CD1 IV 4.2 8.8*
34 O2D I LEU 183B CG IV 4.7 0.2*
34 O2D I GLY 184B N III 5.8 0.2
35 C1D VI LEU 432B O II 3.4 9.2
37 C2N V ASN 434B ND2 III 4.1 1.3
37 C2N V LEU 183B CD1 IV 4.2 4.7
37 C2N V ALA 331B CB IV 4.6 4.9
38 C3N V THR 299B OG1 I 4.0 0.2
38 C3N V LEU 183B CD2 IV 4.3 2.7
38 C3N V THR 299B CG2 IV 4.5 1.1
38 C3N V ALA 331B CB IV 5.0 1.6
39 C7N VI THR 299B OG1 I 3.8 2.5
39 C7N VI ASP 295B OD1 II 3.8 0.4
39 C7N VI LEU 183B CD1 IV 4.0 6.3
39 C7N VI LEU 183B CD2 IV 4.1 0.2
39 C7N VI ASP 295B O II 4.2 3.4
39 C7N VI ALA 331B CB IV 5.7 0.9
40 O7N II ARG 181B NH1 III 3.0 28.8
40 O7N II ARG 181B NH2 III 3.4 1.6
40 O7N II ARG 181B CZ VI 3.6 0.2
40 O7N II LEU 183B CD1 IV 3.7 0.3*
40 O7N II ASP 295B OD1 II 3.7 0.2*
40 O7N II ASP 295B CB IV 3.9 2.4*
40 O7N II ASP 295B O II 4.3 0.5*
40 O7N II ALA 331B CB IV 5.7 0.3*
41 N7N I ASP 295B OD1 II 3.0 21.8
41 N7N I THR 299B OG1 I 3.2 11.7
41 N7N I ASP 295B CA VII 3.5 4.2
41 N7N I LEU 183B CD2 IV 4.2 5.5*
41 N7N I ASN 479B ND2 III 4.2 5.1
41 N7N I ASN 479B CG VI 5.0 0.4
42 C4N V THR 299B OG1 I 3.4 14.1
42 C4N V THR 299B CG2 IV 3.6 2.2
42 C4N V ASN 479B OD1 II 4.6 4.9
42 C4N V ASN 434B ND2 III 4.7 0.4
42 C4N V LEU 183B CD2 IV 4.9 2.2
42 C4N V ASN 479B CG VI 5.2 0.2
43 C5N V THR 299B CG2 IV 3.8 12.1
43 C5N V ASN 434B ND2 III 4.0 3.8
43 C5N V ASN 479B OD1 II 5.0 2.0
43 C5N V LEU 432B CB IV 5.1 2.5
43 C5N V LEU 432B CG IV 5.3 2.5
43 C5N V GLY 477B O II 5.3 7.0
43 C5N V GLY 459B CA VI 5.5 4.0
43 C5N V ILE 303B CD1 IV 6.1 1.3
44 C6N V ASN 434B ND2 III 3.2 11.2
44 C6N V LEU 432B O II 3.4 9.2
44 C6N V LEU 432B CB IV 4.4 7.6
44 C6N V THR 299B CG2 IV 4.8 0.7
44 C6N V ALA 331B CB IV 5.0 2.5
44 C6N V LEU 432B CG IV 5.0 0.2
44 C6N V GLY 459B CA VI 5.3 0.7
------------------------------------------------------------------------
Table V
Complementarity values for the ligand NAI 930B
in PDB entry 1O0S (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 897
Actual value (Å2) 446
Normalised complementarity 0.50
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand NAI 930B
in PDB entry 1O0S (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 |
|---|
| 2 | O1A
| I |
0.50 |
0.50
|
0.49 |
0.49
|
0.50 |
0.50
|
0.49 |
0.50
|
| 3 | O2A
| I |
0.50 |
0.50
|
0.43 |
0.43
|
0.50 |
0.50
|
0.43 |
0.50
|
| 4 | O5B
| II |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 5 | C5B
| VIII |
0.52 |
0.50
|
0.51 |
0.49
|
0.52 |
0.52
|
0.51 |
0.50
|
| 6 | C4B
| VIII |
0.50 |
0.50
|
0.48 |
0.47
|
0.50 |
0.50
|
0.48 |
0.50
|
| 7 | O4B
| II |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 8 | C3B
| VI |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 9 | O3B
| I |
0.50 |
0.50
|
0.45 |
0.47
|
0.51 |
0.51
|
0.47 |
0.51
|
| 10 | C2B
| VI |
0.49 |
0.49
|
0.49 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 11 | O2B
| I |
0.50 |
0.50
|
0.49 |
0.57
|
0.57 |
0.57
|
0.57 |
0.57
|
| 12 | C1B
| VI |
0.50 |
0.50
|
0.49 |
0.49
|
0.50 |
0.50
|
0.49 |
0.50
|
| 14 | C8A
| V |
0.48 |
0.48
|
0.47 |
0.49
|
0.50 |
0.50
|
0.49 |
0.50
|
| 15 | N7A
| I |
0.50 |
0.50
|
0.50 |
0.53
|
0.53 |
0.53
|
0.53 |
0.53
|
| 16 | C5A
| V |
0.48 |
0.48
|
0.48 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 17 | C6A
| V |
0.48 |
0.48
|
0.48 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 18 | N6A
| I |
0.50 |
0.50
|
0.50 |
0.54
|
0.54 |
0.54
|
0.54 |
0.54
|
| 19 | N1A
| I |
0.50 |
0.49
|
0.49 |
0.49
|
0.50 |
0.50
|
0.49 |
0.49
|
| 20 | C2A
| V |
0.50 |
0.46
|
0.50 |
0.46
|
0.50 |
0.50
|
0.50 |
0.46
|
| 21 | N3A
| I |
0.50 |
0.50
|
0.49 |
0.50
|
0.50 |
0.50
|
0.49 |
0.50
|
| 22 | C4A
| V |
0.50 |
0.50
|
0.49 |
0.49
|
0.50 |
0.50
|
0.49 |
0.50
|
| 23 | O3
| II |
0.50 |
0.50
|
0.50 |
0.49
|
0.50 |
0.50
|
0.50 |
0.50
|
| 25 | O1N
| I |
0.50 |
0.50
|
0.42 |
0.44
|
0.51 |
0.51
|
0.44 |
0.51
|
| 26 | O2N
| I |
0.50 |
0.50
|
0.44 |
0.44
|
0.50 |
0.50
|
0.44 |
0.50
|
| 27 | O5D
| II |
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 28 | C5D
| VIII |
0.53 |
0.49
|
0.53 |
0.49
|
0.54 |
0.54
|
0.54 |
0.50
|
| 29 | C4D
| VIII |
0.50 |
0.50
|
0.50 |
0.49
|
0.50 |
0.50
|
0.50 |
0.50
|
| 30 | O4D
| II |
0.50 |
0.50
|
0.50 |
0.52
|
0.52 |
0.52
|
0.52 |
0.52
|
| 31 | C3D
| VI |
0.50 |
0.50
|
0.50 |
0.48
|
0.50 |
0.50
|
0.50 |
0.50
|
| 32 | O3D
| I |
0.50 |
0.49
|
0.45 |
0.43
|
0.50 |
0.50
|
0.45 |
0.49
|
| 33 | C2D
| VI |
0.49 |
0.49
|
0.49 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 34 | O2D
| I |
0.50 |
0.49
|
0.46 |
0.50
|
0.54 |
0.54
|
0.50 |
0.53
|
| 35 | C1D
| VI |
0.50 |
0.48
|
0.50 |
0.48
|
0.50 |
0.50
|
0.50 |
0.48
|
| 37 | C2N
| V |
0.48 |
0.48
|
0.47 |
0.49
|
0.50 |
0.50
|
0.49 |
0.50
|
| 38 | C3N
| V |
0.49 |
0.49
|
0.49 |
0.50
|
0.50 |
0.50
|
0.50 |
0.50
|
| 39 | C7N
| VI |
0.48 |
0.47
|
0.48 |
0.48
|
0.50 |
0.50
|
0.50 |
0.49
|
| 40 | O7N
| II |
0.50 |
0.50
|
0.43 |
0.44
|
0.51 |
0.51
|
0.44 |
0.50
|
| 41 | N7N
| I |
0.50 |
0.45
|
0.48 |
0.42
|
0.51 |
0.51
|
0.49 |
0.46
|
| 42 | C4N
| V |
0.49 |
0.48
|
0.49 |
0.45
|
0.50 |
0.50
|
0.50 |
0.49
|
| 43 | C5N
| V |
0.46 |
0.44
|
0.45 |
0.47
|
0.50 |
0.50
|
0.49 |
0.48
|
| 44 | C6N
| V |
0.47 |
0.45
|
0.45 |
0.45
|
0.50 |
0.50
|
0.47 |
0.48
|
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 TTN 810
2. Oxygen ("hydroxy" or "carbonyl")
4 O1 5 O2 6 O3 7 O4 8 O5
Ligand NAI 920
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 TTN 815
2. Oxygen ("hydroxy" or "carbonyl")
4 O1 5 O2 6 O3 7 O4 8 O5
Ligand NAI 930
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
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il