Contacts of ligand 3ES1635A in PDB entry 2XY9
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 3ES1635A
in PDB entry 2XY9 (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
----------------------------------------------------------
70A ASN* 6.0 2.2 - - - -
143A GLU* 5.3 2.9 - - - -
277A ASN* 5.2 8.3 - - - -
281A GLN* 3.0 20.9 + - - -
282A THR* 4.2 32.9 - - + +
351A VAL* 6.4 0.7 - - + -
353A HIS* 2.6 41.9 + + + +
354A ALA* 3.1 28.5 - - + +
355A SER* 3.2 20.5 - - - -
356A ALA 2.9 36.2 + - - +
357A TRP* 6.0 0.9 - + - -
358A ASP* 6.0 0.4 - - + -
360A TYR* 5.0 4.9 - - - -
376A GLU* 3.5 44.2 - - + -
379A VAL* 4.8 16.7 - - + +
380A VAL* 3.6 34.8 + - + +
383A HIS* 3.1 51.3 + + + +
384A GLU* 2.7 33.3 + - - +
387A HIS* 3.1 38.0 + + - -
391A PHE* 3.7 28.3 - + - -
394A TYR* 4.6 3.4 - - - -
402A ARG 5.5 0.7 - - - -
403A GLU* 4.7 14.4 - - + -
404A GLY 5.4 0.2 - - - -
407A PRO* 5.6 5.4 - - + -
410A HIS* 3.4 35.0 - + + -
411A GLU* 3.3 10.0 + - - +
415A ASP* 3.7 16.5 + - - -
453A ASP* 5.1 11.0 - - - -
454A LYS* 4.2 5.4 + - - -
457A PHE* 3.7 20.0 - + + -
511A LYS* 2.7 20.5 + - - -
512A PHE* 3.7 29.6 - + + -
513A HIS* 2.8 31.4 + - - +
516A SER* 5.7 0.7 - - - -
518A VAL* 3.6 30.1 - - + -
520A TYR* 2.6 31.9 + - - +
522A ARG* 5.0 15.3 + - - -
523A TYR* 2.6 75.0 + + + +
526A SER* 6.1 0.2 - - - -
527A PHE* 3.4 38.4 - + - -
1628A ZN 2.0 46.4 - - - -
1636A 3ES 3.5 116.7 - + + -
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand 3ES1635A
and protein in PDB entry 2XY9
(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 OAB II ALA 356A N III 2.9 24.9
3 OBJ II ARG 522A NH1 III 5.3 1.0
11 OAD I TYR 523A OH I 2.6 29.3
11 OAD I GLU 411A OE1 II 3.3 0.2
13 OAG I GLU 384A OE2 II 2.7 25.5
13 OAG I HIS 387A NE2 I 3.1 3.1
15 NBI I GLU 411A OE2 II 4.1 3.4
15 NBI I TYR 523A OH I 4.4 0.4
15 NBI I ARG 522A NH1 III 5.5 0.8
26 OBK II HIS 383A ND1 I 3.4 1.6
27 NBG I HIS 383A ND1 I 4.4 0.2
27 NBG I VAL 380A N III 4.7 0.2
27 NBG I ASP 415A OD1 II 4.7 0.8
38 OAC II HIS 353A NE2 I 2.6 21.1
38 OAC II HIS 513A NE2 I 2.8 11.6
42 O II TYR 520A OH I 2.6 22.0
42 O II LYS 511A NZ III 2.7 18.9
42 O II GLN 281A NE2 III 3.0 1.7
50 OH I ASP 415A OD2 II 3.8 5.0
50 OH I LYS 454A NZ III 4.2 5.4
50 OH I ASP 415A OD1 II 4.4 1.0
51 OXT II GLN 281A NE2 III 3.8 4.3
51 OXT II LYS 511A NZ III 4.0 1.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand 3ES1635A
in PDB entry 2XY9 (back
to top of page)
Total number of contacts is 218
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 CBM VI HIS 387A NE2 I 3.8 2.7
1 CBM VI 3ES 1636A CAO V 3.9 2.7
2 OAB II ALA 356A N III 2.9 24.9
2 OAB II SER 355A CA VII 3.2 2.8
2 OAB II SER 355A CB VI 3.5 0.7
2 OAB II GLU 384A OE1 II 3.8 0.7*
2 OAB II 3ES 1636A CAO V 3.8 0.2
2 OAB II HIS 387A CD2 V 3.9 0.2
3 OBJ II 3ES 1636A CAU V 3.8 1.9
3 OBJ II HIS 387A CE1 V 4.1 0.2
3 OBJ II GLU 411A OE2 II 4.1 0.2*
3 OBJ II ARG 522A NH1 III 5.3 1.0
4 CBB VIII ALA 356A O II 3.7 11.0*
4 CBB VIII 3ES 1636A CAU V 3.8 2.5
4 CBB VIII HIS 387A CG V 3.9 12.3
4 CBB VIII PHE 391A CZ V 4.3 0.7
5 CBP V 3ES 1636A CAU V 4.0 1.3
5 CBP V PHE 391A CZ V 4.2 2.5
5 CBP V 3ES 1636A NBG I 4.2 0.4
5 CBP V HIS 387A ND1 I 4.2 0.4
6 CAQ V HIS 387A ND1 I 3.8 14.8
6 CAQ V HIS 387A CE1 V 3.8 4.3
6 CAQ V HIS 410A ND1 I 3.8 0.2
6 CAQ V GLU 411A OE2 II 4.2 5.6
6 CAQ V 3ES 1636A NBG I 4.7 0.7
6 CAQ V ARG 522A NH1 III 5.1 3.4
7 CAK V HIS 410A CG V 3.4 18.4
7 CAK V HIS 410A CD2 V 3.4 0.4
7 CAK V HIS 410A CB IV 3.8 3.6
7 CAK V 3ES 1636A NBG I 4.7 0.9
7 CAK V GLU 411A OE2 II 4.9 0.7
7 CAK V ARG 522A NH1 III 5.2 5.4
7 CAK V GLY 404A N III 5.4 0.2
7 CAK V PRO 407A O II 5.6 0.9
7 CAK V PRO 407A CA IV 5.7 4.0
7 CAK V ARG 522A CZ VI 5.9 0.2
7 CAK V PRO 407A CB IV 6.0 0.4
8 CAH V HIS 410A CD2 V 3.6 11.9
8 CAH V HIS 410A NE2 I 3.8 0.2
8 CAH V 3ES 1636A OBK II 4.0 5.6
8 CAH V TYR 394A OH I 4.6 1.6
8 CAH V GLU 403A CB IV 4.7 12.8
8 CAH V 3ES 1636A CBS V 4.8 0.2
8 CAH V 3ES 1636A CBC IV 5.4 0.2
8 CAH V GLU 403A OE1 II 5.6 0.9
9 CAL V 3ES 1636A NBG I 3.5 11.0
9 CAL V 3ES 1636A OBK II 3.6 2.9
9 CAL V PHE 391A CE1 V 3.9 10.8
9 CAL V 3ES 1636A CBU V 4.0 1.1
9 CAL V 3ES 1636A CBS V 4.1 2.9
9 CAL V 3ES 1636A CBA V 4.3 0.4
9 CAL V HIS 410A NE2 I 4.3 0.2
9 CAL V TYR 394A OH I 4.7 1.8
9 CAL V 3ES 1636A CBC IV 4.9 1.1
9 CAL V TYR 360A OH I 5.0 4.9
9 CAL V GLU 403A CB IV 5.4 0.7
9 CAL V ARG 402A O II 5.5 0.7
9 CAL V ASP 358A CB IV 6.0 0.2
10 CAR V 3ES 1636A NBG I 3.5 10.8
10 CAR V PHE 391A CZ V 3.7 14.4
10 CAR V 3ES 1636A CAU V 3.8 4.5
10 CAR V 3ES 1636A CBU V 3.8 1.1
10 CAR V 3ES 1636A CBT V 4.0 0.7
10 CAR V ALA 356A O II 4.3 0.2
10 CAR V ASP 358A CB IV 6.0 0.2
11 OAD I TYR 523A OH I 2.6 29.3
11 OAD I ZN 1628A ZN VI 2.7 12.3
11 OAD I TYR 523A CE1 V 3.3 3.1
11 OAD I GLU 411A OE1 II 3.3 0.2
13 OAG I ZN 1628A ZN VI 2.0 32.9
13 OAG I GLU 384A OE2 II 2.7 25.5
13 OAG I HIS 387A NE2 I 3.1 3.1
14 CBX VI ALA 354A O II 3.5 2.7
15 NBI I ZN 1628A ZN VI 3.8 1.2
15 NBI I GLU 411A OE2 II 4.1 3.4
15 NBI I TYR 523A OH I 4.4 0.4
15 NBI I ARG 522A NH1 III 5.5 0.8
16 CBE IV TYR 523A OH I 3.8 8.1*
16 CBE IV ALA 354A O II 3.9 0.7*
16 CBE IV HIS 353A CD2 V 4.2 3.4
16 CBE IV HIS 513A NE2 I 4.4 4.0*
16 CBE IV PHE 512A CE2 V 4.4 0.2
17 CBQ V PHE 512A CE2 V 4.1 2.9
18 CAS V PHE 512A CE2 V 3.7 12.1
18 CAS V SER 355A CB VI 3.7 11.7
18 CAS V PHE 512A CZ V 3.8 1.8
18 CAS V ALA 354A O II 4.1 2.9
18 CAS V HIS 353A CD2 V 4.5 0.2
18 CAS V HIS 353A O II 5.2 1.1
19 CAM V PHE 512A CZ V 3.9 12.6
19 CAM V 3ES 1636A CAO V 4.0 5.4
19 CAM V SER 355A CB VI 4.1 4.7
19 CAM V 3ES 1636A CAJ V 4.3 1.6
19 CAM V SER 355A OG I 4.6 0.7
19 CAM V GLU 143A OE2 II 5.3 2.9
19 CAM V SER 516A CB VI 5.7 0.2
19 CAM V ASN 70A OD1 II 6.0 2.2
19 CAM V TRP 357A CZ2 V 6.0 0.9
19 CAM V VAL 351A CG1 IV 6.4 0.7
20 CAI V 3ES 1636A CAO V 3.6 10.3
20 CAI V 3ES 1636A CAH V 3.7 16.4
20 CAI V 3ES 1636A CAL V 3.9 2.5
20 CAI V 3ES 1636A CAJ V 4.0 1.3
20 CAI V VAL 518A CG2 IV 4.0 2.5
20 CAI V SER 516A CB VI 5.8 0.4
21 CAN V VAL 518A CG2 IV 3.6 9.9
21 CAN V 3ES 1636A CAO V 3.7 8.7
21 CAN V 3ES 1636A CAU V 3.8 4.9
21 CAN V 3ES 1636A CAH V 3.9 8.1
21 CAN V 3ES 1636A CAL V 3.9 0.9
21 CAN V 3ES 1636A CAK V 4.1 1.3
21 CAN V VAL 518A CG1 IV 4.1 1.3
21 CAN V 3ES 1636A CAR V 4.2 0.2
21 CAN V 3ES 1636A CAQ V 4.3 1.8
21 CAN V ARG 522A NH1 III 5.5 0.7
22 CAT V VAL 518A CG1 IV 3.6 16.4
22 CAT V ARG 522A NH1 III 5.0 3.8
23 CBC IV HIS 383A NE2 I 3.4 14.6*
23 CBC IV HIS 383A CD2 V 3.4 2.9
23 CBC IV GLU 384A OE2 II 3.6 2.2*
23 CBC IV HIS 383A CE1 V 4.0 1.1
24 CBS V HIS 383A CD2 V 3.9 0.2
24 CBS V VAL 380A CG1 IV 4.5 4.5
25 CBA V VAL 380A CG2 IV 4.2 3.1
25 CBA V VAL 380A CG1 IV 4.6 0.9
26 OBK II HIS 383A CG V 3.1 16.8
26 OBK II HIS 383A ND1 I 3.4 1.6
26 OBK II HIS 383A CB IV 3.5 0.9*
27 NBG I VAL 380A CG2 IV 3.8 6.3*
27 NBG I HIS 383A CB IV 4.1 6.9*
27 NBG I VAL 380A CA VII 4.2 2.0
27 NBG I HIS 383A ND1 I 4.4 0.2
27 NBG I VAL 380A N III 4.7 0.2
27 NBG I ASP 415A OD1 II 4.7 0.8
27 NBG I VAL 379A CG1 IV 5.0 2.4*
28 CBU V VAL 380A CG2 IV 3.6 2.7
29 CBT V VAL 380A CG2 IV 3.6 2.5
30 CAU V VAL 380A CG2 IV 3.7 9.0
30 CAU V GLN 281A NE2 III 5.6 0.9
31 CAO V GLU 376A CD VI 3.8 13.7
31 CAO V GLU 376A CG IV 3.9 1.1
31 CAO V GLU 376A OE2 II 4.2 1.6
31 CAO V THR 282A OG1 I 4.8 1.8
31 CAO V ASN 277A ND2 III 5.2 7.4
31 CAO V GLN 281A NE2 III 5.6 3.1
32 CAJ V GLU 376A OE1 II 3.5 19.3
32 CAJ V GLU 376A CD VI 3.6 2.7
32 CAJ V GLU 376A CG IV 3.7 0.4
32 CAJ V THR 282A OG1 I 4.2 13.5
32 CAJ V THR 282A CB VI 5.0 0.4
32 CAJ V ASN 277A ND2 III 5.4 0.9
32 CAJ V ASP 453A OD2 II 5.6 0.2
32 CAJ V ASP 453A CG VI 5.9 0.2
33 CAP V GLU 376A CG IV 4.4 3.8
33 CAP V THR 282A OG1 I 4.6 3.4
33 CAP V VAL 380A CG2 IV 4.8 0.2
33 CAP V THR 282A CG2 IV 5.0 2.9
33 CAP V ASP 453A OD2 II 5.1 10.1
33 CAP V GLU 376A O II 5.1 1.1
33 CAP V VAL 379A CG1 IV 5.2 3.6
33 CAP V ASP 453A CG VI 5.3 0.4
33 CAP V VAL 379A CB IV 5.6 0.2
33 CAP V GLU 376A CA VII 5.6 0.4
34 CAV V VAL 380A CG2 IV 4.2 3.4
34 CAV V VAL 379A CG1 IV 4.8 7.4
35 CBF IV ALA 354A O II 3.1 17.3*
35 CBF IV GLU 384A OE2 II 3.2 4.9*
35 CBF IV HIS 353A NE2 I 3.7 2.7*
35 CBF IV HIS 353A CD2 V 3.9 0.4
35 CBF IV ALA 354A C VI 3.9 0.9
35 CBF IV ALA 354A CB IV 4.2 0.9
36 CBV IV HIS 353A NE2 I 3.8 2.7*
36 CBV IV HIS 353A CD2 V 4.4 0.2
36 CBV IV ALA 354A CB IV 4.8 3.1
37 CBN VI HIS 353A NE2 I 3.4 0.4
38 OAC II HIS 353A NE2 I 2.6 21.1
38 OAC II HIS 513A NE2 I 2.8 11.6
38 OAC II HIS 353A CD2 V 3.6 0.2
40 CA VI HIS 513A NE2 I 3.7 8.3
40 CA VI TYR 523A CZ V 3.7 2.7
40 CA VI TYR 520A OH I 3.9 0.2
41 C VI HIS 513A CE1 V 3.4 5.4
41 C VI GLN 281A NE2 III 3.6 4.7
41 C VI LYS 511A NZ III 3.7 0.4
42 O II TYR 520A OH I 2.6 22.0
42 O II LYS 511A NZ III 2.7 18.9
42 O II GLN 281A NE2 III 3.0 1.7
42 O II HIS 513A CE1 V 3.4 2.1
43 CB IV TYR 520A OH I 3.5 9.6*
43 CB IV TYR 523A CD1 V 3.5 14.4
43 CB IV TYR 523A CG V 3.6 3.1
43 CB IV PHE 457A CZ V 3.7 1.3
44 CG V PHE 457A CZ V 3.8 2.2
45 CD1 V PHE 457A CE1 V 3.7 16.2
45 CD1 V PHE 457A CZ V 3.7 0.2
45 CD1 V GLN 281A NE2 III 3.9 6.1
46 CD2 V TYR 523A CD1 V 3.8 13.7
46 CD2 V TYR 523A CE1 V 4.2 0.2
46 CD2 V PHE 527A CE1 V 4.2 3.6
46 CD2 V HIS 383A CE1 V 4.4 2.9
47 CE1 V PHE 527A CZ V 3.8 8.5
47 CE1 V THR 282A CG2 IV 4.4 10.5
48 CE2 V PHE 527A CE1 V 3.6 10.3
48 CE2 V ASP 415A OD2 II 3.7 9.4
48 CE2 V HIS 383A ND1 I 4.3 2.9
48 CE2 V HIS 383A CE1 V 4.4 0.2
48 CE2 V SER 526A OG I 6.1 0.2
49 CZ V PHE 527A CZ V 3.5 5.4
50 OH I PHE 527A CZ V 3.4 10.6
50 OH I ASP 415A OD2 II 3.8 5.0
50 OH I LYS 454A NZ III 4.2 5.4
50 OH I ASP 415A OD1 II 4.4 1.0
50 OH I ASP 415A CG VI 4.5 0.2
50 OH I VAL 379A CG1 IV 5.3 3.1*
50 OH I THR 282A CG2 IV 5.4 0.3*
51 OXT II GLN 281A NE2 III 3.8 4.3
51 OXT II HIS 353A CE1 V 3.9 9.4
51 OXT II LYS 511A NZ III 4.0 1.2
------------------------------------------------------------------------
Table V
Complementarity values for the ligand 3ES1635A
in PDB entry 2XY9 (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 957
Actual value (Å2) 808
Normalised complementarity 0.84
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand 3ES1635A
in PDB entry 2XY9 (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 | CBM
| VI |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 2 | OAB
| II |
0.85 |
0.84
|
0.79 |
0.79
|
0.85 |
0.85
|
0.79 |
0.84
|
| 3 | OBJ
| II |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 4 | CBB
| VIII |
0.87 |
0.84
|
0.87 |
0.84
|
0.87 |
0.87
|
0.87 |
0.84
|
| 5 | CBP
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 6 | CAQ
| V |
0.84 |
0.83
|
0.84 |
0.79
|
0.84 |
0.84
|
0.84 |
0.83
|
| 7 | CAK
| V |
0.83 |
0.82
|
0.82 |
0.83
|
0.84 |
0.84
|
0.83 |
0.84
|
| 8 | CAH
| V |
0.82 |
0.80
|
0.82 |
0.83
|
0.84 |
0.84
|
0.84 |
0.83
|
| 9 | CAL
| V |
0.84 |
0.83
|
0.84 |
0.80
|
0.84 |
0.84
|
0.84 |
0.84
|
| 10 | CAR
| V |
0.84 |
0.84
|
0.84 |
0.82
|
0.84 |
0.84
|
0.84 |
0.84
|
| 11 | OAD
| I |
0.84 |
0.84
|
0.84 |
0.78
|
0.84 |
0.84
|
0.84 |
0.84
|
| 13 | OAG
| I |
0.84 |
0.79
|
0.84 |
0.78
|
0.84 |
0.84
|
0.84 |
0.79
|
| 14 | CBX
| VI |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 15 | NBI
| I |
0.84 |
0.84
|
0.84 |
0.83
|
0.84 |
0.84
|
0.84 |
0.84
|
| 16 | CBE
| IV |
0.87 |
0.87
|
0.87 |
0.84
|
0.87 |
0.87
|
0.87 |
0.87
|
| 17 | CBQ
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 18 | CAS
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 19 | CAM
| V |
0.84 |
0.83
|
0.84 |
0.83
|
0.84 |
0.84
|
0.84 |
0.83
|
| 20 | CAI
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 21 | CAN
| V |
0.82 |
0.82
|
0.82 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 22 | CAT
| V |
0.81 |
0.81
|
0.80 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 23 | CBC
| IV |
0.88 |
0.87
|
0.88 |
0.84
|
0.88 |
0.88
|
0.88 |
0.87
|
| 24 | CBS
| V |
0.83 |
0.83
|
0.83 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 25 | CBA
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 26 | OBK
| II |
0.84 |
0.84
|
0.84 |
0.84
|
0.85 |
0.85
|
0.85 |
0.85
|
| 27 | NBG
| I |
0.84 |
0.84
|
0.84 |
0.87
|
0.88 |
0.88
|
0.87 |
0.87
|
| 28 | CBU
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 29 | CBT
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 30 | CAU
| V |
0.83 |
0.83
|
0.82 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 31 | CAO
| V |
0.84 |
0.84
|
0.82 |
0.81
|
0.84 |
0.84
|
0.82 |
0.84
|
| 32 | CAJ
| V |
0.84 |
0.80
|
0.84 |
0.77
|
0.84 |
0.84
|
0.84 |
0.80
|
| 33 | CAP
| V |
0.82 |
0.80
|
0.82 |
0.81
|
0.84 |
0.84
|
0.84 |
0.82
|
| 34 | CAV
| V |
0.82 |
0.82
|
0.82 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 35 | CBF
| IV |
0.89 |
0.85
|
0.89 |
0.84
|
0.90 |
0.90
|
0.90 |
0.85
|
| 36 | CBV
| IV |
0.84 |
0.84
|
0.84 |
0.84
|
0.85 |
0.85
|
0.85 |
0.85
|
| 37 | CBN
| VI |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 38 | OAC
| II |
0.84 |
0.84
|
0.84 |
0.78
|
0.84 |
0.84
|
0.84 |
0.84
|
| 40 | CA
| VI |
0.84 |
0.84
|
0.84 |
0.83
|
0.84 |
0.84
|
0.84 |
0.84
|
| 41 | C
| VI |
0.84 |
0.84
|
0.83 |
0.83
|
0.84 |
0.84
|
0.83 |
0.84
|
| 42 | O
| II |
0.84 |
0.84
|
0.80 |
0.75
|
0.84 |
0.84
|
0.80 |
0.84
|
| 43 | CB
| IV |
0.86 |
0.86
|
0.86 |
0.84
|
0.86 |
0.86
|
0.86 |
0.86
|
| 44 | CG
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 45 | CD1
| V |
0.84 |
0.84
|
0.83 |
0.83
|
0.84 |
0.84
|
0.83 |
0.84
|
| 46 | CD2
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 47 | CE1
| V |
0.82 |
0.82
|
0.82 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 48 | CE2
| V |
0.84 |
0.82
|
0.84 |
0.82
|
0.84 |
0.84
|
0.84 |
0.82
|
| 49 | CZ
| V |
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
0.84 |
0.84
|
| 50 | OH
| I |
0.84 |
0.83
|
0.83 |
0.83
|
0.85 |
0.85
|
0.84 |
0.84
|
| 51 | OXT
| II |
0.84 |
0.84
|
0.83 |
0.83
|
0.84 |
0.84
|
0.83 |
0.84
|
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 NAG 1
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand NAG 2
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand BMA 3
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O3 9 O4 11 O6
Ligand FUC 4
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
7 O2 8 O3 9 O4
Ligand ACT 1625
2. Oxygen ("hydroxy" or "carbonyl")
2 O 3 OXT
Ligand NAG 1631
1. Carbon (in rings)
1 C1 2 C2 3 C3 4 C4 5 C5
2. Oxygen ("hydroxy" or "carbonyl")
10 O3 11 O4 13 O6 14 O7
3. Nitrogen ("hydrophilic")
9 N2
Ligand EPE 1634
1. Carbon (in rings)
2 C2 3 C3 5 C5 6 C6
2. Oxygen ("hydroxy" or "carbonyl")
9 O8
3. Nitrogen ("hydrophilic")
1 N1 4 N4
Ligand 3ES 1635
1. Carbon (in rings)
5 CBP 6 CAQ 7 CAK 8 CAH 9 CAL 10 CAR
17 CBQ 18 CAS 19 CAM 20 CAI 21 CAN 22 CAT
24 CBS 25 CBA 28 CBU 29 CBT 30 CAU 31 CAO
32 CAJ 33 CAP 34 CAV 44 CG 45 CD1 47 CE1
49 CZ 48 CE2 46 CD2
2. Oxygen ("hydroxy" or "carbonyl")
2 OAB 38 OAC 42 O 50 OH 51 OXT
3. Nitrogen ("hydrophilic")
15 NBI 27 NBG 39 N
Ligand 3ES 1636
1. Carbon (in rings)
5 CBP 6 CAQ 7 CAK 8 CAH 9 CAL 10 CAR
17 CBQ 18 CAS 19 CAM 20 CAI 21 CAN 22 CAT
24 CBS 25 CBA 28 CBU 29 CBT 30 CAU 31 CAO
32 CAJ 33 CAP 34 CAV 44 CG 45 CD1 47 CE1
49 CZ 48 CE2 46 CD2
2. Oxygen ("hydroxy" or "carbonyl")
2 OAB 38 OAC 42 O 50 OH 51 OXT
3. Nitrogen ("hydrophilic")
15 NBI 27 NBG 39 N
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il