Contacts of ligand NAD 336P in PDB entry 3DBV
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 NAD 336P
in PDB entry 3DBV (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
----------------------------------------------------------
6P ASN* 4.1 4.7 + - - -
7P GLY* 3.4 6.7 - - - -
8P PHE 3.9 1.6 + - - -
9P GLY* 3.0 36.2 - - - -
10P ARG* 2.9 78.4 + - - +
11P ILE* 2.9 44.1 + - + +
12P GLY 4.7 0.2 + - - -
13P ARG* 5.0 1.4 + - - -
31P ASN* 3.2 30.2 + - - -
32P ASP* 3.1 53.5 + - - -
33P THR* 3.9 25.5 + - - -
76P GLU 3.5 15.9 + - - -
77P ARG* 3.0 42.0 + - + +
79P PRO* 6.1 0.2 - - - +
95P SER* 3.0 43.6 + - - +
96P THR* 3.4 48.6 - - + +
97P GLY* 3.1 28.8 + - - -
98P ARG* 3.3 33.8 + - - +
99P PHE* 3.5 21.0 - + - -
100P THR* 4.8 2.4 - - - +
119P SER* 3.0 39.3 + - - +
120P ALA* 3.5 24.0 - - + +
121P PRO* 6.0 0.2 - - + -
147P ALA 5.0 0.7 - - - -
148P SER* 5.0 3.1 - - - -
149P CYS* 3.7 30.1 - - - -
176P HIS* 5.1 0.2 - - - -
179P THR* 4.3 20.8 - - - +
180P ASN* 3.3 29.1 + - - +
313P ASN* 3.2 44.2 + - - +
314P GLU* 3.9 7.5 + - - +
317P TYR* 3.9 22.9 - + - -
338P SO4 3.1 48.2 + - - -
185Q LEU* 5.9 1.4 - - - +
186Q ASP 4.7 2.4 + - - -
187Q ALA* 5.4 4.3 - - - +
188Q SER* 5.8 5.5 + - - -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand NAD 336P
and protein in PDB entry 3DBV
(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
------------------------------------------------------------------------
3 O2A I ARG 10P N III 3.0 18.7
3 O2A I ASN 180P ND2 III 3.3 8.0
3 O2A I ASP 186Q O II 4.7 2.4
9 O3B I ASP 32P OD2 II 3.1 13.2
9 O3B I ASP 32P OD1 II 3.7 0.9
9 O3B I PHE 8P O II 3.9 1.6
9 O3B I ARG 13P NH1 III 5.0 1.4
9 O3B I SER 188Q N III 5.9 1.0
11 O2B I ASP 32P OD1 II 3.3 11.3
11 O2B I THR 33P OG1 I 4.4 5.0
15 N7A I THR 33P OG1 I 4.4 1.2
15 N7A I ARG 98P NH1 III 4.8 0.8
18 N6A I ARG 77P O II 3.0 21.4
18 N6A I ARG 98P NH1 III 5.0 2.4
19 N1A I GLU 76P O II 3.5 13.9
19 N1A I ASN 31P ND2 III 3.7 1.0
19 N1A I ARG 77P O II 3.9 0.6
19 N1A I THR 33P OG1 I 4.3 0.4
19 N1A I ASN 6P OD1 II 4.5 0.2
19 N1A I ASN 6P ND2 III 4.9 0.2
21 N3A I THR 33P N III 3.9 0.2
21 N3A I ASN 31P O II 3.9 2.8
25 O1N I SO4 338P O3 I 4.2 6.4
25 O1N I ASN 180P ND2 III 4.7 1.9
25 O1N I ASN 180P N III 5.0 1.0
26 O2N I ARG 10P N III 2.9 26.0
26 O2N I ILE 11P N III 2.9 9.9
26 O2N I SER 95P O II 4.4 0.5
26 O2N I GLY 12P N III 4.7 0.2
27 O5D II SO4 338P O3 I 4.4 0.7
30 O4D II SER 119P OG I 3.4 3.3
32 O3D I GLY 97P O II 4.4 0.5
32 O3D I SER 119P OG I 4.7 0.5
34 O2D I SO4 338P O2 I 3.1 14.0
34 O2D I SO4 338P O4 I 3.1 10.4
34 O2D I SO4 338P O3 I 3.2 0.3
36 N1N I SO4 338P O2 I 3.8 0.2
40 O7N II ASN 313P ND2 III 3.2 26.0
41 N7N I GLU 314P OE2 II 4.8 0.8
41 N7N I ASN 313P ND2 III 4.9 0.2
41 N7N I ASN 180P N III 5.7 0.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand NAD 336P
in PDB entry 3DBV (back
to top of page)
Total number of contacts is 173
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 180P CB IV 4.2 9.4*
2 O1A I ASN 180P CG VI 4.6 0.5
3 O2A I ARG 10P N III 3.0 18.7
3 O2A I ARG 10P CG IV 3.3 13.0*
3 O2A I ASN 180P ND2 III 3.3 8.0
3 O2A I GLY 9P CA VI 3.5 3.1
3 O2A I GLY 9P C VI 3.6 0.3
3 O2A I ARG 10P CD VII 4.1 0.3
3 O2A I ASP 186Q O II 4.7 2.4
3 O2A I ALA 187Q CB IV 5.4 2.6*
4 O5B II GLY 9P CA VI 3.0 8.7
5 C5B VIII THR 96P O II 3.7 16.6*
5 C5B VIII SER 95P O II 3.7 11.0*
5 C5B VIII GLY 9P CA VI 3.9 0.2
6 C4B VIII GLY 9P N III 3.7 11.0
6 C4B VIII GLY 7P CA VI 4.0 4.0
7 O4B II THR 96P CA VII 3.4 9.0
7 O4B II GLY 7P CA VI 3.4 2.3
8 C3B VI GLY 9P CA VI 4.1 0.2
9 O3B I ASP 32P OD2 II 3.1 13.2
9 O3B I GLY 9P CA VI 3.5 12.0
9 O3B I ASP 32P OD1 II 3.7 0.9
9 O3B I ASP 32P CG VI 3.9 0.2
9 O3B I PHE 8P O II 3.9 1.6
9 O3B I ARG 13P NH1 III 5.0 1.4
9 O3B I SER 188Q N III 5.9 1.0
9 O3B I ALA 187Q CB IV 6.0 1.6*
9 O3B I SER 188Q CB VI 6.1 0.9
9 O3B I ALA 187Q CA VII 6.1 0.2
11 O2B I ASP 32P OD1 II 3.3 11.3
11 O2B I THR 33P OG1 I 4.4 5.0
11 O2B I THR 33P CB VI 4.4 3.5
11 O2B I SER 188Q CB VI 5.8 3.6
12 C1B VI ASP 32P OD2 II 3.8 5.6
12 C1B VI GLY 7P CA VI 4.0 0.2
12 C1B VI ASP 32P OD1 II 4.0 0.2
14 C8A V ARG 98P CD VII 3.8 11.2
14 C8A V THR 96P CB VI 4.0 4.9
14 C8A V THR 96P O II 4.2 3.8
14 C8A V THR 33P OG1 I 4.6 1.8
15 N7A I ARG 98P CD VII 3.3 16.6
15 N7A I ARG 98P CG IV 4.1 0.8*
15 N7A I THR 33P OG1 I 4.4 1.2
15 N7A I ARG 98P NH1 III 4.8 0.8
16 C5A V THR 96P CG2 IV 3.9 3.4
16 C5A V THR 33P OG1 I 4.0 3.6
17 C6A V ARG 77P CA VII 4.1 1.8
17 C6A V PHE 99P CE2 V 4.1 5.2
17 C6A V ARG 77P CG IV 4.2 2.0
17 C6A V THR 33P OG1 I 4.2 1.3
18 N6A I ARG 77P O II 3.0 21.4
18 N6A I ARG 77P CG IV 3.3 14.1*
18 N6A I PHE 99P CZ V 3.5 13.7
18 N6A I ARG 77P CD VII 4.4 0.2
18 N6A I ARG 98P CD VII 4.6 2.0
18 N6A I ARG 98P NH1 III 5.0 2.4
19 N1A I GLU 76P O II 3.5 13.9
19 N1A I ASN 31P ND2 III 3.7 1.0
19 N1A I ARG 77P CA VII 3.8 2.0
19 N1A I ARG 77P O II 3.9 0.6
19 N1A I THR 33P OG1 I 4.3 0.4
19 N1A I THR 96P CG2 IV 4.4 0.8*
19 N1A I PHE 99P CE2 V 4.5 2.2
19 N1A I ASN 6P OD1 II 4.5 0.2
19 N1A I ASN 6P ND2 III 4.9 0.2
19 N1A I PRO 79P CG IV 6.1 0.2*
20 C2A V ASN 31P ND2 III 3.2 25.1
20 C2A V ASP 32P CA VII 3.9 9.9
20 C2A V GLU 76P O II 3.9 1.8
20 C2A V ASN 31P O II 4.1 1.3
20 C2A V ASN 6P OD1 II 4.1 4.3
20 C2A V THR 33P N III 4.1 3.4
20 C2A V THR 96P CG2 IV 4.2 1.6
20 C2A V ASP 32P C VI 4.2 0.2
20 C2A V THR 33P OG1 I 4.3 0.2
20 C2A V GLU 76P C VI 4.9 0.2
20 C2A V THR 33P CA VII 5.1 0.2
21 N3A I ASP 32P CA VII 3.7 12.1
21 N3A I THR 33P N III 3.9 0.2
21 N3A I THR 96P CG2 IV 3.9 3.0*
21 N3A I ASN 31P O II 3.9 2.8
21 N3A I GLY 7P CA VI 4.0 0.2
22 C4A V THR 96P CG2 IV 3.7 4.0
22 C4A V THR 33P OG1 I 3.9 4.7
23 O3 II ASN 180P CB IV 4.3 5.0*
23 O3 II THR 96P O II 5.3 0.2*
25 O1N I ARG 10P CB IV 3.6 5.4*
25 O1N I ARG 10P CG IV 4.0 2.1*
25 O1N I SO4 338P O3 I 4.2 6.4
25 O1N I ASN 180P ND2 III 4.7 1.9
25 O1N I ASN 180P CB IV 4.8 3.1*
25 O1N I ASN 180P N III 5.0 1.0
26 O2N I ARG 10P N III 2.9 26.0
26 O2N I ILE 11P N III 2.9 9.9
26 O2N I GLY 9P C VI 3.9 0.2
26 O2N I GLY 9P CA VI 4.1 0.5
26 O2N I SER 95P O II 4.4 0.5
26 O2N I GLY 12P N III 4.7 0.2
27 O5D II SO4 338P O3 I 4.4 0.7
28 C5D VIII SER 95P O II 3.0 20.4*
28 C5D VIII GLY 97P N III 4.4 1.8
28 C5D VIII SER 95P CA VII 4.4 0.7
28 C5D VIII THR 96P C VI 4.4 1.1
28 C5D VIII SER 95P CB VI 4.5 1.8
28 C5D VIII ILE 11P CB IV 4.5 1.8
28 C5D VIII THR 96P O II 4.7 0.2*
29 C4D VIII SER 95P O II 3.6 6.3*
29 C4D VIII SER 119P OG I 3.6 9.6
29 C4D VIII SER 95P C VI 4.0 2.9
29 C4D VIII GLY 97P N III 4.1 0.2
30 O4D II SER 119P O II 3.3 3.8*
30 O4D II SER 119P OG I 3.4 3.3
30 O4D II ILE 11P CG1 IV 3.8 3.5*
31 C3D VI GLY 97P CA VI 3.4 12.6
32 O3D I GLY 97P CA VI 3.1 13.7
32 O3D I ALA 120P CB IV 3.5 15.1*
32 O3D I GLY 97P O II 4.4 0.5
32 O3D I SER 119P OG I 4.7 0.5
32 O3D I THR 100P CG2 IV 4.8 2.4*
33 C2D VI SO4 338P O3 I 3.6 5.6
34 O2D I SO4 338P O2 I 3.1 14.0
34 O2D I SO4 338P O4 I 3.1 10.4
34 O2D I SO4 338P O3 I 3.2 0.3
34 O2D I ALA 120P CB IV 4.4 3.1*
35 C1D VI SER 119P O II 3.1 6.1
35 C1D VI ALA 120P CB IV 4.1 1.6
36 N1N I SO4 338P O2 I 3.8 0.2
37 C2N V ILE 11P CG1 IV 3.4 5.2
37 C2N V SO4 338P O2 I 3.7 6.1
38 C3N V ILE 11P CG1 IV 3.3 4.0
38 C3N V SO4 338P O2 I 4.2 1.8
39 C7N VI ILE 11P CD1 IV 3.7 9.4
39 C7N VI GLU 314P CG IV 4.3 1.6
39 C7N VI THR 179P CG2 IV 4.6 4.3
39 C7N VI CYS 149P SG VI 5.1 0.4
40 O7N II ASN 313P ND2 III 3.2 26.0
40 O7N II ASN 313P O II 3.6 4.9*
40 O7N II ASN 313P C VI 3.7 1.2
40 O7N II ASN 313P CB IV 3.8 1.2*
40 O7N II GLU 314P CG IV 3.9 1.4*
40 O7N II THR 179P CG2 IV 4.4 2.1*
40 O7N II CYS 149P SG VI 4.6 0.7
40 O7N II HIS 176P CE1 V 5.1 0.2
41 N7N I ARG 10P CB IV 4.1 11.9*
41 N7N I THR 179P CG2 IV 4.3 13.1*
41 N7N I GLU 314P CG IV 4.3 3.8*
41 N7N I THR 179P CB VI 4.5 1.2
41 N7N I ARG 10P CG IV 4.8 1.0*
41 N7N I GLU 314P OE2 II 4.8 0.8
41 N7N I ASN 313P ND2 III 4.9 0.2
41 N7N I THR 179P CA VII 5.4 0.2
41 N7N I ASN 180P N III 5.7 0.2
41 N7N I LEU 185Q CD1 IV 5.9 1.4*
42 C4N V ILE 11P CD1 IV 3.6 10.3
42 C4N V ASN 313P O II 3.6 10.8
42 C4N V CYS 149P SG VI 3.7 9.4
43 C5N V CYS 149P SG VI 3.8 13.9
43 C5N V TYR 317P CD2 V 3.9 17.3
43 C5N V TYR 317P CG V 4.0 2.5
43 C5N V TYR 317P CE2 V 4.0 0.4
43 C5N V CYS 149P N III 4.1 4.5
43 C5N V SO4 338P O2 I 4.9 0.2
44 C6N V SER 119P O II 3.0 15.9
44 C6N V TYR 317P CE2 V 4.2 1.6
44 C6N V TYR 317P CZ V 4.3 1.1
44 C6N V SO4 338P O2 I 4.4 2.5
44 C6N V ALA 120P CB IV 4.7 2.9
44 C6N V ALA 120P CA VII 4.7 1.3
44 C6N V CYS 149P N III 4.9 1.1
44 C6N V ALA 147P O II 5.0 0.7
44 C6N V SER 148P CA VII 5.0 1.8
44 C6N V SER 148P CB VI 5.5 1.3
44 C6N V PRO 121P CD IV 6.0 0.2
------------------------------------------------------------------------
Table V
Complementarity values for the ligand NAD 336P
in PDB entry 3DBV (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 849
Actual value (Å2) 434
Normalised complementarity 0.51
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand NAD 336P
in PDB entry 3DBV (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 |
0.51 |
0.51
|
0.51 |
0.53
|
0.53 |
0.53
|
0.53 |
0.53
|
| 3 | O2A
| I |
0.51 |
0.51
|
0.45 |
0.48
|
0.55 |
0.55
|
0.48 |
0.54
|
| 4 | O5B
| II |
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 5 | C5B
| VIII |
0.58 |
0.51
|
0.58 |
0.51
|
0.58 |
0.58
|
0.58 |
0.51
|
| 6 | C4B
| VIII |
0.51 |
0.51
|
0.49 |
0.49
|
0.51 |
0.51
|
0.49 |
0.51
|
| 7 | O4B
| II |
0.51 |
0.51
|
0.49 |
0.51
|
0.51 |
0.51
|
0.49 |
0.51
|
| 8 | C3B
| VI |
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 9 | O3B
| I |
0.51 |
0.47
|
0.51 |
0.47
|
0.51 |
0.51
|
0.51 |
0.48
|
| 11 | O2B
| I |
0.51 |
0.48
|
0.51 |
0.47
|
0.51 |
0.51
|
0.51 |
0.48
|
| 12 | C1B
| VI |
0.51 |
0.50
|
0.51 |
0.50
|
0.51 |
0.51
|
0.51 |
0.50
|
| 14 | C8A
| V |
0.51 |
0.50
|
0.48 |
0.50
|
0.51 |
0.51
|
0.48 |
0.50
|
| 15 | N7A
| I |
0.51 |
0.51
|
0.47 |
0.51
|
0.51 |
0.51
|
0.47 |
0.51
|
| 16 | C5A
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.51 |
0.51
|
0.51 |
0.51
|
| 17 | C6A
| V |
0.51 |
0.51
|
0.50 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 18 | N6A
| I |
0.51 |
0.46
|
0.50 |
0.49
|
0.54 |
0.54
|
0.53 |
0.49
|
| 19 | N1A
| I |
0.51 |
0.48
|
0.50 |
0.48
|
0.51 |
0.51
|
0.51 |
0.48
|
| 20 | C2A
| V |
0.51 |
0.49
|
0.42 |
0.43
|
0.51 |
0.51
|
0.42 |
0.49
|
| 21 | N3A
| I |
0.51 |
0.50
|
0.48 |
0.51
|
0.52 |
0.52
|
0.49 |
0.51
|
| 22 | C4A
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.51 |
0.51
|
0.51 |
0.51
|
| 23 | O3
| II |
0.51 |
0.51
|
0.51 |
0.52
|
0.52 |
0.52
|
0.52 |
0.52
|
| 25 | O1N
| I |
0.51 |
0.51
|
0.50 |
0.51
|
0.54 |
0.54
|
0.53 |
0.54
|
| 26 | O2N
| I |
0.51 |
0.51
|
0.43 |
0.43
|
0.51 |
0.51
|
0.43 |
0.51
|
| 27 | O5D
| II |
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 28 | C5D
| VIII |
0.56 |
0.51
|
0.55 |
0.51
|
0.56 |
0.56
|
0.55 |
0.51
|
| 29 | C4D
| VIII |
0.53 |
0.51
|
0.53 |
0.49
|
0.53 |
0.53
|
0.53 |
0.51
|
| 30 | O4D
| II |
0.52 |
0.51
|
0.52 |
0.51
|
0.53 |
0.53
|
0.53 |
0.52
|
| 31 | C3D
| VI |
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 32 | O3D
| I |
0.51 |
0.51
|
0.51 |
0.55
|
0.55 |
0.55
|
0.55 |
0.55
|
| 33 | C2D
| VI |
0.51 |
0.51
|
0.51 |
0.50
|
0.51 |
0.51
|
0.51 |
0.51
|
| 34 | O2D
| I |
0.51 |
0.51
|
0.51 |
0.46
|
0.52 |
0.52
|
0.52 |
0.52
|
| 35 | C1D
| VI |
0.51 |
0.49
|
0.51 |
0.50
|
0.51 |
0.51
|
0.51 |
0.50
|
| 36 | N1N
| I |
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 37 | C2N
| V |
0.50 |
0.50
|
0.50 |
0.50
|
0.51 |
0.51
|
0.51 |
0.51
|
| 38 | C3N
| V |
0.50 |
0.50
|
0.50 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 39 | C7N
| VI |
0.48 |
0.48
|
0.48 |
0.51
|
0.51 |
0.51
|
0.51 |
0.51
|
| 40 | O7N
| II |
0.52 |
0.51
|
0.46 |
0.46
|
0.53 |
0.53
|
0.47 |
0.52
|
| 41 | N7N
| I |
0.51 |
0.51
|
0.51 |
0.58
|
0.58 |
0.58
|
0.58 |
0.58
|
| 42 | C4N
| V |
0.49 |
0.46
|
0.49 |
0.49
|
0.51 |
0.51
|
0.51 |
0.49
|
| 43 | C5N
| V |
0.51 |
0.51
|
0.50 |
0.50
|
0.51 |
0.51
|
0.50 |
0.51
|
| 44 | C6N
| V |
0.50 |
0.46
|
0.49 |
0.46
|
0.51 |
0.51
|
0.50 |
0.47
|
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 NAD 336
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 NAD 336
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 NAD 336
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 NAD 336
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