Contacts of ligand NAP 402B in PDB entry 4JTR
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 NAP 402B
in PDB entry 4JTR (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
----------------------------------------------------------
22B GLY* 3.4 23.5 - - - -
23B THR 3.2 10.0 + - - -
24B TYR* 3.1 30.2 + - + +
50B ASP* 2.7 25.3 + - - -
55B TYR* 3.2 27.3 - - - -
84B LYS* 3.8 3.8 - - - -
117B HIS* 3.5 11.2 + - - -
166B SER* 2.8 25.5 + - - -
167B ASN* 2.9 21.3 + - - -
190B GLN* 3.0 20.9 + - - -
216B TYR* 3.2 56.1 + + + +
217B SER* 3.3 33.9 + - - -
218B ALA 4.6 1.0 + - - -
219B LEU* 3.1 64.1 + - + +
221B SER* 3.1 37.8 + - - +
222B HIS* 3.3 55.4 + + - +
236B LEU* 3.7 24.9 - - + +
251B THR* 5.3 1.4 + - - -
253B ALA* 3.5 13.9 - - + +
268B LEU* 3.6 22.3 + - - +
269B ALA* 3.8 7.3 - - - -
270B LYS* 2.8 126.6 + - - +
271B SER* 2.3 39.0 + - - -
272B TYR* 3.2 16.6 + - - +
273B ASN* 4.0 2.4 - - - +
276B ARG* 2.7 79.8 + - - +
279B GLN* 2.9 28.7 + - - -
280B ASN* 2.8 44.1 + - - -
306B LEU* 3.8 10.3 - - + +
401B IZP 3.0 44.7 + - - +
405B EDO 4.3 3.6 - - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand NAP 402B
and protein in PDB entry 4JTR
(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 LEU 219B N III 3.1 24.3
2 O1A I SER 221B N III 3.1 9.7
3 O2A I LYS 270B N III 3.2 16.3
3 O2A I LEU 268B O II 4.2 2.8
3 O2A I LEU 219B N III 4.5 0.3
3 O2A I ALA 218B N III 4.6 1.0
9 O3B I LYS 270B NZ III 3.7 4.5
11 O2B I LYS 270B NZ III 4.1 0.3
15 N7A I ASN 280B ND2 III 3.1 18.4
18 N6A I ASN 280B OD1 II 2.8 24.2
18 N6A I GLN 279B OE1 II 2.9 20.6
19 N1A I GLN 279B OE1 II 4.1 3.2
19 N1A I GLN 279B NE2 III 4.9 0.8
19 N1A I THR 251B OG1 I 5.3 0.2
21 N3A I ARG 276B NE III 4.3 0.2
25 O1N I HIS 222B N III 3.3 16.3
25 O1N I SER 217B OG I 3.4 14.9
25 O1N I HIS 222B NE2 I 4.1 0.7
26 O2N I HIS 222B N III 4.2 1.9
26 O2N I TYR 24B O II 5.2 0.7
27 O5D II SER 217B N III 3.6 5.0
32 O3D I TYR 24B N III 3.1 21.1
32 O3D I THR 23B N III 3.2 6.1
32 O3D I TYR 24B O II 4.1 0.2
34 O2D I ASP 50B OD2 II 2.7 17.3
34 O2D I THR 23B N III 3.5 4.0
34 O2D I ASP 50B O II 3.6 1.7
40 O7N II ASN 167B ND2 III 2.9 21.3
40 O7N II IZP 401B O2 I 3.3 4.7
40 O7N II HIS 117B NE2 I 3.5 0.3
40 O7N II TYR 216B OH I 3.7 0.5
41 N7N I SER 166B OG I 2.8 25.5
41 N7N I GLN 190B OE1 II 3.0 10.7
41 N7N I HIS 117B NE2 I 3.8 8.3
46 O1X I LYS 270B NZ III 2.8 27.2
46 O1X I TYR 272B N III 3.2 15.2
47 O2X I ARG 276B NH2 III 2.8 21.5
47 O2X I TYR 272B N III 4.8 0.2
48 O3X I SER 271B OG I 2.3 31.7
48 O3X I ARG 276B NE III 2.7 20.1
48 O3X I ARG 276B NH2 III 3.4 0.5
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand NAP 402B
in PDB entry 4JTR (back
to top of page)
Total number of contacts is 170
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 LEU 219B N III 3.1 24.3
2 O1A I SER 221B N III 3.1 9.7
2 O1A I SER 217B CA VII 3.3 5.7
3 O2A I LYS 270B N III 3.2 16.3
3 O2A I ALA 269B CA VII 3.8 7.3
3 O2A I LEU 219B CG IV 4.2 6.1*
3 O2A I LEU 268B O II 4.2 2.8
3 O2A I LEU 219B CD1 IV 4.2 0.2*
3 O2A I LEU 219B N III 4.5 0.3
3 O2A I ALA 218B N III 4.6 1.0
4 O5B II LEU 219B CB IV 3.7 3.1*
4 O5B II LEU 219B CD1 IV 4.0 1.0*
5 C5B VIII SER 221B O II 3.2 20.4*
5 C5B VIII SER 221B C VI 3.3 2.0
5 C5B VIII SER 221B N III 4.0 0.9
5 C5B VIII LEU 219B CB IV 4.1 5.2
5 C5B VIII LEU 219B O II 4.5 1.8*
6 C4B VIII SER 221B O II 4.0 3.4*
6 C4B VIII HIS 222B CA VII 4.4 1.6
7 O4B II LEU 219B CD1 IV 3.9 2.1*
7 O4B II LEU 219B CB IV 4.3 1.4*
7 O4B II LEU 219B O II 5.0 0.3*
7 O4B II LEU 236B CD1 IV 5.1 1.4*
8 C3B VI LYS 270B O II 3.4 8.5
8 C3B VI LYS 270B CD IV 4.0 3.1
9 O3B I LYS 270B CD IV 3.6 11.8*
9 O3B I LYS 270B NZ III 3.7 4.5
9 O3B I HIS 222B CA VII 4.1 11.3
9 O3B I HIS 222B CB IV 4.2 2.1*
10 C2B IV LYS 270B O II 3.3 1.6*
11 O2B I LYS 270B NZ III 4.1 0.3
12 C1B VI ARG 276B NE III 5.0 0.2
14 C8A V LYS 270B O II 3.0 22.0
14 C8A V LEU 219B CD1 IV 3.4 8.5
14 C8A V SER 271B CB VI 3.7 2.9
14 C8A V ASN 280B ND2 III 4.0 0.9
15 N7A I ASN 280B ND2 III 3.1 18.4
15 N7A I LEU 219B CD1 IV 3.4 2.4*
15 N7A I ARG 276B CB IV 3.8 4.0*
16 C5A V ARG 276B CD VII 3.6 2.2
16 C5A V LEU 219B CD1 IV 3.7 4.9
17 C6A V ALA 253B CB IV 3.5 5.6
17 C6A V ARG 276B CD VII 3.6 4.9
18 N6A I ASN 280B OD1 II 2.8 24.2
18 N6A I GLN 279B OE1 II 2.9 20.6
18 N6A I ALA 253B CB IV 3.5 3.2*
18 N6A I GLN 279B CD VI 3.5 4.0
18 N6A I ASN 280B CG VI 3.8 0.6
18 N6A I ARG 276B CB IV 3.8 5.5*
19 N1A I ARG 276B CD VII 3.5 3.6
19 N1A I ALA 253B CB IV 3.7 5.1*
19 N1A I ARG 276B CG IV 4.0 0.4*
19 N1A I GLN 279B OE1 II 4.1 3.2
19 N1A I GLN 279B CD VI 4.8 0.2
19 N1A I GLN 279B NE2 III 4.9 0.8
19 N1A I THR 251B OG1 I 5.3 0.2
19 N1A I THR 251B CB VI 5.6 1.2
20 C2A V ARG 276B CD VII 3.6 7.9
20 C2A V LEU 236B CD1 IV 3.7 17.5
21 N3A I ARG 276B CD VII 3.7 3.2
21 N3A I LEU 236B CD1 IV 3.9 5.7*
21 N3A I ARG 276B NE III 4.3 0.2
22 C4A V ARG 276B CD VII 3.6 4.7
22 C4A V LEU 219B CD1 IV 4.0 2.5
22 C4A V LEU 236B CD1 IV 4.5 0.2
23 O3 II SER 221B CA VII 3.5 0.7
23 O3 II SER 217B CA VII 3.8 0.2
25 O1N I HIS 222B N III 3.3 16.3
25 O1N I SER 217B OG I 3.4 14.9
25 O1N I SER 221B CA VII 3.5 0.2
25 O1N I HIS 222B CD2 V 3.6 13.3
25 O1N I SER 221B CB VI 4.0 0.5
25 O1N I HIS 222B NE2 I 4.1 0.7
26 O2N I LYS 270B CB IV 3.4 14.0*
26 O2N I LYS 270B CD IV 4.1 2.1*
26 O2N I HIS 222B N III 4.2 1.9
26 O2N I HIS 222B CB IV 4.3 4.0*
26 O2N I HIS 222B CD2 V 4.5 1.4
26 O2N I TYR 24B O II 5.2 0.7
27 O5D II SER 217B N III 3.6 5.0
28 C5D VIII LYS 270B CB IV 3.8 6.3
28 C5D VIII LYS 270B N III 4.0 2.5
28 C5D VIII SER 217B N III 4.3 4.3
28 C5D VIII LEU 268B CB IV 4.7 5.6
29 C4D VIII GLY 22B CA VI 3.9 8.3
29 C4D VIII LEU 268B CD1 IV 4.4 3.8
29 C4D VIII LEU 268B CB IV 4.4 0.9
30 O4D II TYR 216B CB IV 3.4 8.1*
30 O4D II LEU 268B CD1 IV 3.6 3.1*
31 C3D VI TYR 24B CB IV 4.2 5.8
31 C3D VI TYR 24B CD2 V 5.6 0.7
31 C3D VI HIS 222B CD2 V 5.9 0.2
32 O3D I TYR 24B N III 3.1 21.1
32 O3D I THR 23B N III 3.2 6.1
32 O3D I GLY 22B C VI 3.4 2.9
32 O3D I LYS 270B CB IV 3.5 5.4*
32 O3D I TYR 24B CB IV 3.7 1.2*
32 O3D I LYS 270B CG IV 3.8 1.0*
32 O3D I TYR 24B O II 4.1 0.2
33 C2D VI TYR 55B OH I 3.5 10.5
33 C2D VI TYR 55B CE2 V 3.9 5.2
33 C2D VI TYR 55B CZ V 4.0 0.7
33 C2D VI TYR 24B CB IV 4.4 0.2
34 O2D I ASP 50B OD2 II 2.7 17.3
34 O2D I GLY 22B CA VI 3.4 12.3
34 O2D I THR 23B N III 3.5 4.0
34 O2D I ASP 50B O II 3.6 1.7
34 O2D I ASP 50B CG VI 3.7 0.2
34 O2D I TYR 55B CE2 V 3.9 0.9
35 C1D VI ASP 50B OD2 II 3.6 6.1
35 C1D VI LEU 268B CD1 IV 3.8 6.1
35 C1D VI TYR 216B CB IV 3.9 0.2
36 N1N I TYR 216B CB IV 3.5 0.2*
37 C2N V GLN 190B OE1 II 3.0 9.6
37 C2N V TYR 55B OH I 3.2 10.1
37 C2N V TYR 216B CD2 V 3.7 2.5
38 C3N V IZP 401B O2 I 3.0 3.1
38 C3N V TYR 216B CD2 V 3.3 2.2
39 C7N VI IZP 401B O2 I 3.2 6.1
39 C7N VI TYR 216B CE2 V 3.3 7.0
39 C7N VI HIS 117B NE2 I 3.7 1.6
40 O7N II ASN 167B ND2 III 2.9 21.3
40 O7N II IZP 401B O2 I 3.3 4.7
40 O7N II IZP 401B C7 IV 3.4 8.8*
40 O7N II TYR 216B CE2 V 3.5 1.0
40 O7N II HIS 117B NE2 I 3.5 0.3
40 O7N II TYR 216B CZ V 3.7 0.7
40 O7N II TYR 216B OH I 3.7 0.5
40 O7N II LEU 306B CD2 IV 4.8 0.2*
41 N7N I SER 166B OG I 2.8 25.5
41 N7N I GLN 190B OE1 II 3.0 10.7
41 N7N I TYR 216B CE2 V 3.6 1.8
41 N7N I GLN 190B CD VI 3.7 0.6
41 N7N I HIS 117B NE2 I 3.8 8.3
41 N7N I HIS 117B CD2 V 3.8 1.0
41 N7N I LYS 84B CE VII 3.8 3.8
42 C4N V TYR 216B CE1 V 3.2 13.9
42 C4N V IZP 401B O1 II 3.2 9.9
42 C4N V TYR 216B CZ V 3.3 0.2
42 C4N V IZP 401B C1 VI 3.3 1.1
42 C4N V LEU 306B CD2 IV 3.8 4.3
43 C5N V TYR 216B CD1 V 3.2 12.1
43 C5N V IZP 401B O1 II 3.3 8.5
43 C5N V TYR 216B CE1 V 3.4 1.1
43 C5N V LEU 306B CD2 IV 4.1 5.8
43 C5N V EDO 405B O2 I 4.3 3.6
43 C5N V SER 217B OG I 4.3 3.8
43 C5N V HIS 222B NE2 I 5.0 0.9
43 C5N V HIS 222B CE1 V 5.8 0.2
44 C6N V TYR 216B CB IV 3.6 4.3
44 C6N V TYR 216B CD1 V 3.7 0.2
44 C6N V IZP 401B O1 II 4.0 2.5
44 C6N V HIS 222B NE2 I 5.4 1.1
44 C6N V HIS 222B CD2 V 5.5 0.4
44 C6N V TYR 24B CB IV 5.9 0.2
46 O1X I LYS 270B NZ III 2.8 27.2
46 O1X I TYR 272B N III 3.2 15.2
46 O1X I SER 271B CA VII 3.2 1.2
46 O1X I TYR 272B CB IV 4.6 1.0*
47 O2X I ARG 276B NH2 III 2.8 21.5
47 O2X I ARG 276B CZ VI 3.7 0.2
47 O2X I ASN 273B CB IV 4.5 2.3*
47 O2X I TYR 272B N III 4.8 0.2
47 O2X I TYR 272B C VI 5.6 0.2
48 O3X I SER 271B OG I 2.3 31.7
48 O3X I ARG 276B NE III 2.7 20.1
48 O3X I SER 271B CB VI 3.1 3.1
48 O3X I ARG 276B NH2 III 3.4 0.5
48 O3X I ARG 276B CD VII 3.6 0.7
48 O3X I ASN 273B CB IV 4.0 0.2*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand NAP 402B
in PDB entry 4JTR (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 913
Actual value (Å2) 643
Normalised complementarity 0.71
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand NAP 402B
in PDB entry 4JTR (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 |
0.71 |
0.71
|
0.62 |
0.63
|
0.71 |
0.71
|
0.62 |
0.71
|
| 3 | O2A
| I |
0.71 |
0.70
|
0.65 |
0.67
|
0.72 |
0.72
|
0.66 |
0.71
|
| 4 | O5B
| II |
0.71 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
| 5 | C5B
| VIII |
0.74 |
0.69
|
0.74 |
0.70
|
0.75 |
0.75
|
0.75 |
0.71
|
| 6 | C4B
| VIII |
0.71 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
| 7 | O4B
| II |
0.71 |
0.71
|
0.71 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 8 | C3B
| VI |
0.70 |
0.68
|
0.70 |
0.69
|
0.71 |
0.71
|
0.71 |
0.69
|
| 9 | O3B
| I |
0.71 |
0.71
|
0.67 |
0.73
|
0.74 |
0.74
|
0.70 |
0.74
|
| 10 | C2B
| IV |
0.71 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
| 11 | O2B
| I |
0.71 |
0.71
|
0.70 |
0.70
|
0.71 |
0.71
|
0.70 |
0.71
|
| 12 | C1B
| VI |
0.71 |
0.71
|
0.70 |
0.70
|
0.71 |
0.71
|
0.70 |
0.71
|
| 14 | C8A
| V |
0.69 |
0.64
|
0.68 |
0.65
|
0.71 |
0.71
|
0.70 |
0.66
|
| 15 | N7A
| I |
0.71 |
0.71
|
0.66 |
0.68
|
0.72 |
0.72
|
0.68 |
0.72
|
| 16 | C5A
| V |
0.69 |
0.69
|
0.69 |
0.71
|
0.71 |
0.71
|
0.70 |
0.71
|
| 17 | C6A
| V |
0.69 |
0.69
|
0.68 |
0.71
|
0.71 |
0.71
|
0.69 |
0.71
|
| 18 | N6A
| I |
0.71 |
0.61
|
0.71 |
0.63
|
0.72 |
0.72
|
0.72 |
0.63
|
| 19 | N1A
| I |
0.71 |
0.70
|
0.70 |
0.71
|
0.72 |
0.72
|
0.71 |
0.71
|
| 20 | C2A
| V |
0.67 |
0.67
|
0.65 |
0.71
|
0.71 |
0.71
|
0.69 |
0.71
|
| 21 | N3A
| I |
0.71 |
0.71
|
0.70 |
0.72
|
0.72 |
0.72
|
0.71 |
0.72
|
| 22 | C4A
| V |
0.70 |
0.70
|
0.69 |
0.71
|
0.71 |
0.71
|
0.69 |
0.71
|
| 23 | O3
| II |
0.71 |
0.71
|
0.70 |
0.71
|
0.71 |
0.71
|
0.70 |
0.71
|
| 25 | O1N
| I |
0.71 |
0.71
|
0.67 |
0.64
|
0.71 |
0.71
|
0.67 |
0.71
|
| 26 | O2N
| I |
0.71 |
0.70
|
0.70 |
0.74
|
0.75 |
0.75
|
0.74 |
0.75
|
| 27 | O5D
| II |
0.71 |
0.71
|
0.69 |
0.69
|
0.71 |
0.71
|
0.69 |
0.71
|
| 28 | C5D
| VIII |
0.68 |
0.68
|
0.66 |
0.69
|
0.71 |
0.71
|
0.69 |
0.71
|
| 29 | C4D
| VIII |
0.69 |
0.69
|
0.69 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
| 30 | O4D
| II |
0.71 |
0.71
|
0.71 |
0.73
|
0.73 |
0.73
|
0.73 |
0.73
|
| 31 | C3D
| VI |
0.69 |
0.69
|
0.69 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
| 32 | O3D
| I |
0.71 |
0.70
|
0.65 |
0.66
|
0.72 |
0.72
|
0.66 |
0.72
|
| 33 | C2D
| VI |
0.70 |
0.70
|
0.70 |
0.68
|
0.71 |
0.71
|
0.71 |
0.71
|
| 34 | O2D
| I |
0.71 |
0.66
|
0.70 |
0.65
|
0.71 |
0.71
|
0.70 |
0.66
|
| 35 | C1D
| VI |
0.69 |
0.68
|
0.69 |
0.69
|
0.71 |
0.71
|
0.71 |
0.69
|
| 36 | N1N
| I |
0.71 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
| 37 | C2N
| V |
0.71 |
0.68
|
0.71 |
0.66
|
0.71 |
0.71
|
0.71 |
0.68
|
| 38 | C3N
| V |
0.71 |
0.71
|
0.71 |
0.70
|
0.71 |
0.71
|
0.71 |
0.71
|
| 39 | C7N
| VI |
0.71 |
0.71
|
0.71 |
0.69
|
0.71 |
0.71
|
0.71 |
0.71
|
| 40 | O7N
| II |
0.71 |
0.71
|
0.66 |
0.67
|
0.72 |
0.72
|
0.68 |
0.72
|
| 41 | N7N
| I |
0.71 |
0.68
|
0.70 |
0.61
|
0.71 |
0.71
|
0.70 |
0.68
|
| 42 | C4N
| V |
0.70 |
0.67
|
0.70 |
0.68
|
0.71 |
0.71
|
0.71 |
0.68
|
| 43 | C5N
| V |
0.69 |
0.67
|
0.69 |
0.67
|
0.71 |
0.71
|
0.71 |
0.69
|
| 44 | C6N
| V |
0.70 |
0.69
|
0.70 |
0.70
|
0.71 |
0.71
|
0.71 |
0.70
|
| 46 | O1X
| I |
0.71 |
0.71
|
0.61 |
0.61
|
0.71 |
0.71
|
0.61 |
0.71
|
| 47 | O2X
| I |
0.71 |
0.71
|
0.66 |
0.66
|
0.71 |
0.71
|
0.66 |
0.71
|
| 48 | O3X
| I |
0.71 |
0.71
|
0.66 |
0.59
|
0.71 |
0.71
|
0.66 |
0.71
|
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 IBP 401
1. Carbon (in rings)
8 C8 9 C9 10 C10 11 C11 12 C12 13 C13
2. Oxygen ("hydroxy" or "carbonyl")
14 O1 15 O2
Ligand NAP 402
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 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Ligand EDO 403
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 404
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 405
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand IZP 401
1. Carbon (in rings)
10 C8 11 C9 12 C10 13 C11 14 C12 15 C13
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand NAP 402
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 32 O3D 34 O2D 40 O7N
3. Nitrogen ("hydrophilic")
13 N9A 15 N7A 18 N6A 19 N1A 21 N3A 36 N1N
41 N7N
Ligand EDO 403
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 404
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand EDO 405
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2
Ligand TLA 407
2. Oxygen ("hydroxy" or "carbonyl")
1 O1 2 O11 5 O2 7 O3 9 O4 10 O41
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il