Contacts of ligand NDE 400A in PDB entry 1N1E
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 NDE 400A
in PDB entry 1N1E (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
----------------------------------------------------------
22A GLY* 4.3 3.1 - - - -
23A SER* 2.8 34.0 + - - -
24A GLY* 3.3 29.1 + - - -
25A ALA* 2.8 43.0 + - - +
26A PHE* 3.0 66.1 + + + +
27A GLY 4.0 1.9 + - - -
45A HIS* 3.6 16.8 + - - -
46A MET* 3.6 45.9 - - + +
63A PHE* 3.6 41.8 + + - +
92A VAL* 3.1 43.2 + - - +
93A ILE* 5.2 5.4 - - + +
94A PRO* 3.3 42.0 - - - +
97A PHE* 3.4 64.9 - + + +
123A CYS 3.9 9.4 - - - -
124A THR* 3.4 10.9 - - - +
125A LYS* 3.0 74.3 + - - +
153A GLY 3.6 0.9 + - - -
155A SER* 3.3 41.1 + - - -
156A PHE* 3.6 19.2 + - - -
157A ALA* 2.9 43.8 + - - +
210A LYS* 2.7 29.9 + - - -
211A ASN* 3.3 12.5 + - - -
263A ASP* 3.8 4.4 + - - +
266A LEU* 4.5 1.4 - - - +
267A THR* 3.2 12.8 - - - +
272A LEU 3.9 1.4 + - - -
273A SER* 2.6 29.3 + - - -
274A ARG* 2.7 116.4 + - - +
275A ASN* 2.9 31.5 + - - -
297A ALA* 3.3 13.9 - - - +
298A VAL* 2.9 50.1 + - + +
300A GLU* 2.6 45.0 + - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand NDE 400A
and protein in PDB entry 1N1E
(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 O7N II ALA 157A N III 2.9 24.8
3 N7N I ARG 274A NH2 III 3.0 8.3
3 N7N I ARG 274A NH1 III 3.6 1.4
3 N7N I ARG 274A NE III 4.0 0.6
12 O2D I ASN 211A ND2 III 4.2 5.0
14 O3D I GLU 300A OE1 II 2.6 17.7
14 O3D I LYS 125A N III 3.1 14.4
18 O5D II ARG 274A NH2 III 4.3 0.5
20 O1N I ARG 274A NH2 III 2.8 27.4
20 O1N I ARG 274A NH1 III 2.8 5.5
20 O1N I PHE 26A N III 4.1 0.3
21 O2N I PHE 26A N III 3.0 23.2
21 O2N I ALA 25A N III 3.1 7.4
21 O2N I GLY 27A N III 4.0 1.9
21 O2N I VAL 92A O II 4.5 0.3
23 O1A I VAL 298A N III 2.9 30.5
23 O1A I ARG 274A NH1 III 3.8 0.3
24 O3 I ARG 274A NH1 III 3.7 0.5
24 O3 I VAL 298A N III 4.5 0.3
25 O2A I ALA 25A N III 2.8 26.0
25 O2A I ARG 274A NH1 III 3.8 2.9
25 O2A I PHE 63A O II 4.5 0.3
32 O2B I SER 23A OG I 3.5 8.5
32 O2B I HIS 45A ND1 I 3.7 0.3
34 O3B I SER 23A OG I 2.8 15.8
34 O3B I GLY 24A N III 3.3 6.8
34 O3B I SER 23A N III 3.3 5.0
46 O1P I ARG 274A NH2 III 3.1 15.6
46 O1P I ASN 275A ND2 III 3.3 12.8
46 O1P I ARG 274A NE III 3.6 1.0
46 O1P I ASN 211A OD1 II 3.7 3.5
46 O1P I ASN 211A ND2 III 4.3 2.3
46 O1P I VAL 298A O II 4.7 1.0
46 O1P I GLU 300A N III 5.1 1.2
47 O2P I SER 273A OG I 2.6 23.0
47 O2P I ASN 275A ND2 III 2.9 18.0
47 O2P I ASN 211A OD1 II 3.3 0.3
47 O2P I ASN 275A N III 3.6 0.7
48 O3P I ARG 274A NE III 2.7 24.9
48 O3P I ARG 274A N III 2.9 11.6
48 O3P I LEU 272A O II 3.9 1.4
49 O1 II LYS 210A NZ III 3.2 6.9
52 O2 II LYS 210A NZ III 2.7 20.4
52 O2 II LYS 125A NZ III 3.0 11.4
54 O31 I SER 155A OG I 3.3 11.4
54 O31 I SER 155A N III 3.3 13.5
54 O31 I LYS 125A NZ III 3.4 5.4
54 O31 I GLY 153A O II 3.6 0.9
54 O31 I PHE 156A N III 3.7 0.2
54 O31 I ASP 263A OD2 II 3.8 4.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand NDE 400A
in PDB entry 1N1E (back
to top of page)
Total number of contacts is 194
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 O7N II ALA 157A N III 2.9 24.8
1 O7N II ALA 157A CB IV 3.5 0.3*
1 O7N II PHE 156A CA VII 3.6 1.9
1 O7N II PHE 156A CD2 V 4.2 2.4
2 C7N VI ALA 157A CB IV 3.8 7.0
2 C7N VI PHE 26A CB IV 4.0 0.2
2 C7N VI ARG 274A NE III 4.7 0.2
3 N7N I ARG 274A NH2 III 3.0 8.3
3 N7N I ARG 274A CZ VI 3.3 5.3
3 N7N I ARG 274A NH1 III 3.6 1.4
3 N7N I ALA 157A CB IV 3.8 11.7*
3 N7N I PHE 26A CB IV 4.0 1.4*
3 N7N I ARG 274A NE III 4.0 0.6
3 N7N I ALA 25A CB IV 4.1 3.4*
3 N7N I ARG 274A CD VII 5.0 0.2
4 C3N V PHE 26A CG V 3.6 2.7
5 C4N V SER 155A O II 3.4 7.2
5 C4N V PHE 26A CD2 V 3.8 1.3
6 C5N V PHE 26A CE1 V 3.3 16.6
6 C5N V LYS 125A NZ III 3.4 6.5
6 C5N V PHE 26A CZ V 3.6 2.5
6 C5N V SER 155A OG I 3.7 0.9
7 C6N V PHE 26A CD1 V 3.3 7.9
7 C6N V PHE 26A CE1 V 3.5 1.6
7 C6N V LYS 125A CE VII 3.6 14.6
7 C6N V CYS 123A O II 3.9 2.7
8 C2N V PHE 26A CB IV 3.3 7.4
8 C2N V ARG 274A NH2 III 3.6 2.5
10 C1D VI CYS 123A O II 3.9 6.7
10 C1D VI LYS 125A N III 4.4 0.2
11 C2D VI GLU 300A CG IV 4.0 4.3
11 C2D VI ARG 274A NH2 III 4.3 6.7
12 O2D I LYS 125A CB IV 3.5 19.2*
12 O2D I GLU 300A CG IV 3.5 9.2*
12 O2D I LYS 125A CD IV 4.1 1.2*
12 O2D I ASN 211A ND2 III 4.2 5.0
13 C3D VI GLU 300A OE1 II 3.3 9.2
13 C3D VI GLU 300A CG IV 3.9 2.9
13 C3D VI PRO 94A CA IV 4.4 2.0
13 C3D VI PRO 94A CB IV 4.8 0.7
13 C3D VI VAL 298A CG1 IV 5.6 0.7
14 O3D I GLU 300A OE1 II 2.6 17.7
14 O3D I LYS 125A N III 3.1 14.4
14 O3D I THR 124A CG2 IV 3.4 5.5*
15 O4D II VAL 92A CG1 IV 3.7 7.4*
16 C4D VIII VAL 92A O II 3.8 5.4*
16 C4D VIII VAL 92A CG1 IV 4.0 4.9
16 C4D VIII THR 124A CA VII 4.3 5.4
16 C4D VIII VAL 92A C VI 4.4 1.1
16 C4D VIII PRO 94A CA IV 4.7 0.4
17 C5D VIII VAL 92A O II 3.1 21.5*
17 C5D VIII VAL 92A CG1 IV 3.9 1.8
17 C5D VIII VAL 92A C VI 4.1 0.4
17 C5D VIII PRO 94A CG IV 4.3 9.6
17 C5D VIII PRO 94A CD IV 4.4 0.2
18 O5D II ARG 274A NH2 III 4.3 0.5
18 O5D II PRO 94A CG IV 4.4 1.6*
18 O5D II VAL 298A CB IV 5.2 1.7*
20 O1N I ARG 274A NH2 III 2.8 27.4
20 O1N I ARG 274A NH1 III 2.8 5.5
20 O1N I PHE 26A N III 4.1 0.3
21 O2N I PHE 26A N III 3.0 23.2
21 O2N I ALA 25A N III 3.1 7.4
21 O2N I GLY 24A C VI 3.4 4.3
21 O2N I GLY 24A CA VI 3.4 3.6
21 O2N I PHE 26A CB IV 3.7 0.9*
21 O2N I PHE 26A CA VII 3.8 0.2
21 O2N I GLY 27A N III 4.0 1.9
21 O2N I VAL 92A O II 4.5 0.3
22 PA VI PHE 63A CD2 V 3.9 0.3
23 O1A I VAL 298A N III 2.9 30.5
23 O1A I ALA 297A CA VII 3.3 10.4
23 O1A I ALA 297A CB IV 3.6 1.4*
23 O1A I VAL 298A CG2 IV 3.8 0.3*
23 O1A I ARG 274A NH1 III 3.8 0.3
23 O1A I PHE 63A CD2 V 4.5 1.9
24 O3 I ARG 274A NH1 III 3.7 0.5
24 O3 I VAL 298A N III 4.5 0.3
24 O3 I VAL 298A CB IV 4.5 2.3*
25 O2A I ALA 25A N III 2.8 26.0
25 O2A I ALA 25A CB IV 3.5 6.2*
25 O2A I GLY 24A CA VI 3.6 0.3
25 O2A I ARG 274A NH1 III 3.8 2.9
25 O2A I PHE 63A CB IV 4.1 6.1*
25 O2A I PHE 63A CD2 V 4.1 1.0
25 O2A I PHE 63A O II 4.5 0.3
25 O2A I ALA 297A CB IV 4.7 2.1*
26 O5B II GLY 24A CA VI 3.3 5.7
26 O5B II PHE 63A CD2 V 3.8 2.4
27 C5B VIII PHE 63A CE2 V 4.0 8.7
27 C5B VIII VAL 298A CG2 IV 4.1 9.6
27 C5B VIII PRO 94A CG IV 4.1 0.7
28 C4B VIII PRO 94A CG IV 3.8 9.9
28 C4B VIII PRO 94A CD IV 3.8 2.5
28 C4B VIII GLY 24A CA VI 4.2 2.2
28 C4B VIII GLY 24A N III 4.3 0.2
28 C4B VIII VAL 92A O II 5.5 0.2*
29 O4B II PRO 94A CG IV 3.3 11.1*
30 C1B VI PRO 94A CD IV 4.4 2.5
30 C1B VI ILE 93A CG2 IV 5.9 0.7
31 C2B VI PHE 63A CZ V 3.6 10.8
32 O2B I SER 23A OG I 3.5 8.5
32 O2B I HIS 45A CE1 V 3.6 16.5
32 O2B I HIS 45A ND1 I 3.7 0.3
32 O2B I PHE 63A CE1 V 3.8 0.3
32 O2B I PHE 63A CZ V 3.9 0.2
32 O2B I MET 46A CE IV 4.6 6.4*
32 O2B I MET 46A SD VIII 4.9 1.2
32 O2B I MET 46A CG IV 4.9 0.7*
33 C3B VI SER 23A OG I 3.6 4.7
33 C3B VI GLY 24A N III 3.7 5.8
33 C3B VI PHE 63A CE1 V 3.8 5.6
34 O3B I SER 23A OG I 2.8 15.8
34 O3B I GLY 24A N III 3.3 6.8
34 O3B I SER 23A N III 3.3 5.0
34 O3B I GLY 22A C VI 4.3 0.5
34 O3B I GLY 22A CA VI 4.6 2.6
34 O3B I PRO 94A CD IV 4.9 0.9*
34 O3B I ILE 93A CA VII 5.7 0.2
34 O3B I ILE 93A CG1 IV 6.0 0.5*
36 C8A V PHE 97A CE1 V 3.9 5.4
36 C8A V MET 46A CE IV 5.0 1.6
36 C8A V VAL 298A CG2 IV 5.0 3.6
36 C8A V PHE 63A CZ V 5.1 3.8
36 C8A V PHE 63A CE2 V 5.4 0.2
37 N7A I PHE 97A CE1 V 3.5 4.8
37 N7A I PHE 97A CZ V 3.8 1.2
37 N7A I MET 46A CE IV 4.7 0.4*
38 C5A V PHE 97A CE1 V 3.4 3.8
38 C5A V MET 46A CE IV 4.1 3.8
39 C6A V PHE 97A CZ V 3.6 4.9
39 C6A V MET 46A CE IV 4.2 4.9
40 N6A I PHE 97A CE2 V 3.5 12.7
40 N6A I PHE 97A CZ V 3.6 1.0
40 N6A I MET 46A CE IV 4.9 0.8*
41 C4A V PHE 97A CD1 V 3.5 3.8
41 C4A V MET 46A CE IV 4.0 3.1
42 N3A I PHE 97A CD1 V 3.7 2.8
42 N3A I MET 46A SD VIII 3.7 5.3
42 N3A I PHE 97A CG V 3.9 0.2
42 N3A I PHE 97A CB IV 4.1 1.0*
42 N3A I ILE 93A CG2 IV 5.2 3.4*
43 C2A V MET 46A SD VIII 3.6 15.3
43 C2A V PHE 97A CG V 3.7 11.4
43 C2A V PHE 97A CB IV 3.8 5.4
43 C2A V ILE 93A CG2 IV 5.6 0.7
44 N1A I PHE 97A CD2 V 3.7 6.5
44 N1A I MET 46A SD VIII 4.1 2.4
46 O1P I ARG 274A NH2 III 3.1 15.6
46 O1P I ASN 275A ND2 III 3.3 12.8
46 O1P I ARG 274A NE III 3.6 1.0
46 O1P I ASN 211A OD1 II 3.7 3.5
46 O1P I ASN 211A CG VI 4.3 1.4
46 O1P I ASN 211A ND2 III 4.3 2.3
46 O1P I ARG 274A CB IV 4.6 0.3*
46 O1P I VAL 298A O II 4.7 1.0
46 O1P I GLU 300A N III 5.1 1.2
46 O1P I GLU 300A CG IV 5.4 0.5*
47 O2P I SER 273A OG I 2.6 23.0
47 O2P I ASN 275A ND2 III 2.9 18.0
47 O2P I THR 267A CG2 IV 3.2 8.5*
47 O2P I ASN 211A OD1 II 3.3 0.3
47 O2P I ASN 275A N III 3.6 0.7
48 O3P I ARG 274A NE III 2.7 24.9
48 O3P I ARG 274A N III 2.9 11.6
48 O3P I SER 273A CA VII 3.3 6.2
48 O3P I ARG 274A CD VII 3.5 0.3
48 O3P I LEU 272A O II 3.9 1.4
48 O3P I PHE 156A CD2 V 4.8 0.2
49 O1 II LYS 210A NZ III 3.2 6.9
49 O1 II THR 267A CG2 IV 3.8 3.6*
49 O1 II PHE 156A CE2 V 4.2 0.2
50 C1 VIII PHE 156A CD2 V 4.0 10.8
50 C1 VIII PHE 156A CE2 V 4.1 0.7
51 C2 VIII LYS 210A NZ III 3.5 2.0
51 C2 VIII ASP 263A OD2 II 4.6 0.2*
51 C2 VIII PHE 156A CD2 V 4.7 0.2
51 C2 VIII THR 267A OG1 I 4.9 0.7
52 O2 II LYS 210A NZ III 2.7 20.4
52 O2 II LYS 125A NZ III 3.0 11.4
52 O2 II LYS 210A CE VII 3.7 0.5
52 O2 II LYS 125A CD IV 3.8 1.4*
53 C3 VI SER 155A O II 3.4 6.1
53 C3 VI SER 155A C VI 3.7 2.0
53 C3 VI PHE 156A N III 4.0 1.8
53 C3 VI PHE 156A CA VII 4.1 0.2
53 C3 VI PHE 156A CD2 V 4.4 0.7
54 O31 I SER 155A OG I 3.3 11.4
54 O31 I SER 155A N III 3.3 13.5
54 O31 I LYS 125A NZ III 3.4 5.4
54 O31 I GLY 153A O II 3.6 0.9
54 O31 I PHE 156A N III 3.7 0.2
54 O31 I ASP 263A OD2 II 3.8 4.2
54 O31 I LEU 266A CD2 IV 4.5 1.4*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand NDE 400A
in PDB entry 1N1E (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 986
Actual value (Å2) 685
Normalised complementarity 0.69
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand NDE 400A
in PDB entry 1N1E (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 | O7N
| II |
0.69 |
0.69
|
0.64 |
0.64
|
0.69 |
0.69
|
0.64 |
0.69
|
| 2 | C7N
| VI |
0.68 |
0.68
|
0.68 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 3 | N7N
| I |
0.69 |
0.69
|
0.67 |
0.71
|
0.73 |
0.73
|
0.71 |
0.73
|
| 4 | C3N
| V |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 5 | C4N
| V |
0.69 |
0.68
|
0.69 |
0.68
|
0.69 |
0.69
|
0.69 |
0.68
|
| 6 | C5N
| V |
0.69 |
0.69
|
0.68 |
0.68
|
0.69 |
0.69
|
0.68 |
0.69
|
| 7 | C6N
| V |
0.69 |
0.69
|
0.66 |
0.69
|
0.69 |
0.69
|
0.66 |
0.69
|
| 8 | C2N
| V |
0.68 |
0.68
|
0.67 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 10 | C1D
| VI |
0.69 |
0.68
|
0.69 |
0.68
|
0.69 |
0.69
|
0.69 |
0.68
|
| 11 | C2D
| VI |
0.69 |
0.69
|
0.67 |
0.68
|
0.69 |
0.69
|
0.68 |
0.69
|
| 12 | O2D
| I |
0.69 |
0.69
|
0.68 |
0.74
|
0.75 |
0.75
|
0.74 |
0.75
|
| 13 | C3D
| VI |
0.68 |
0.66
|
0.68 |
0.68
|
0.69 |
0.69
|
0.69 |
0.68
|
| 14 | O3D
| I |
0.69 |
0.66
|
0.67 |
0.64
|
0.71 |
0.71
|
0.68 |
0.67
|
| 15 | O4D
| II |
0.69 |
0.69
|
0.69 |
0.71
|
0.71 |
0.71
|
0.71 |
0.71
|
| 16 | C4D
| VIII |
0.69 |
0.68
|
0.68 |
0.69
|
0.71 |
0.71
|
0.69 |
0.69
|
| 17 | C5D
| VIII |
0.71 |
0.67
|
0.71 |
0.69
|
0.74 |
0.74
|
0.74 |
0.69
|
| 18 | O5D
| II |
0.69 |
0.69
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 20 | O1N
| I |
0.69 |
0.69
|
0.63 |
0.63
|
0.69 |
0.69
|
0.63 |
0.69
|
| 21 | O2N
| I |
0.69 |
0.69
|
0.63 |
0.63
|
0.70 |
0.70
|
0.63 |
0.70
|
| 22 | PA
| VI |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 23 | O1A
| I |
0.69 |
0.69
|
0.61 |
0.64
|
0.70 |
0.70
|
0.61 |
0.70
|
| 24 | O3
| I |
0.69 |
0.69
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 25 | O2A
| I |
0.69 |
0.69
|
0.64 |
0.66
|
0.72 |
0.72
|
0.66 |
0.72
|
| 26 | O5B
| II |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 27 | C5B
| VIII |
0.67 |
0.67
|
0.67 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 28 | C4B
| VIII |
0.67 |
0.67
|
0.67 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 29 | O4B
| II |
0.69 |
0.69
|
0.69 |
0.72
|
0.72 |
0.72
|
0.72 |
0.72
|
| 30 | C1B
| VI |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 31 | C2B
| VI |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 32 | O2B
| I |
0.69 |
0.69
|
0.69 |
0.69
|
0.71 |
0.71
|
0.71 |
0.71
|
| 33 | C3B
| VI |
0.69 |
0.69
|
0.68 |
0.67
|
0.69 |
0.69
|
0.68 |
0.69
|
| 34 | O3B
| I |
0.69 |
0.69
|
0.67 |
0.64
|
0.70 |
0.70
|
0.67 |
0.70
|
| 36 | C8A
| V |
0.68 |
0.68
|
0.68 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 37 | N7A
| I |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 38 | C5A
| V |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 39 | C6A
| V |
0.68 |
0.68
|
0.68 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 40 | N6A
| I |
0.69 |
0.69
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.70
|
| 41 | C4A
| V |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 42 | N3A
| I |
0.69 |
0.68
|
0.69 |
0.70
|
0.70 |
0.70
|
0.70 |
0.69
|
| 43 | C2A
| V |
0.68 |
0.65
|
0.68 |
0.69
|
0.69 |
0.69
|
0.69 |
0.66
|
| 44 | N1A
| I |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 46 | O1P
| I |
0.69 |
0.69
|
0.63 |
0.62
|
0.70 |
0.70
|
0.63 |
0.69
|
| 47 | O2P
| I |
0.69 |
0.69
|
0.66 |
0.63
|
0.71 |
0.71
|
0.67 |
0.71
|
| 48 | O3P
| I |
0.69 |
0.69
|
0.61 |
0.62
|
0.69 |
0.69
|
0.61 |
0.69
|
| 49 | O1
| II |
0.69 |
0.69
|
0.68 |
0.69
|
0.70 |
0.70
|
0.69 |
0.70
|
| 50 | C1
| VIII |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 51 | C2
| VIII |
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
0.69 |
0.69
|
| 52 | O2
| II |
0.69 |
0.69
|
0.63 |
0.63
|
0.70 |
0.70
|
0.63 |
0.70
|
| 53 | C3
| VI |
0.69 |
0.68
|
0.69 |
0.68
|
0.69 |
0.69
|
0.69 |
0.68
|
| 54 | O31
| I |
0.69 |
0.68
|
0.66 |
0.62
|
0.70 |
0.70
|
0.66 |
0.69
|
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 NDE 400
1. Carbon (in rings)
4 C3N 5 C4N 6 C5N 7 C6N 8 C2N 10 C1D
11 C2D 13 C3D 16 C4D 28 C4B 30 C1B 31 C2B
33 C3B 36 C8A 38 C5A 41 C4A 38 C5A 39 C6A
43 C2A 41 C4A
2. Oxygen ("hydroxy" or "carbonyl")
1 O7N 12 O2D 14 O3D 32 O2B 34 O3B 52 O2
54 O31
3. Nitrogen ("hydrophilic")
3 N7N 9 N1N 35 N9A 37 N7A 40 N6A 42 N3A
44 N1A
Ligand NDE 401
1. Carbon (in rings)
4 C3N 5 C4N 6 C5N 7 C6N 8 C2N 10 C1D
11 C2D 13 C3D 16 C4D 28 C4B 30 C1B 31 C2B
33 C3B 36 C8A 38 C5A 41 C4A 38 C5A 39 C6A
43 C2A 41 C4A
2. Oxygen ("hydroxy" or "carbonyl")
1 O7N 12 O2D 14 O3D 32 O2B 34 O3B 52 O2
54 O31
3. Nitrogen ("hydrophilic")
3 N7N 9 N1N 35 N9A 37 N7A 40 N6A 42 N3A
44 N1A
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il