Contacts of the helix formed by residues 5 - 46 (chain A) in PDB entry 1HGZ
Residue contacts within the protein are
derived with the CSU 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.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
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 forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.2 4.9 - - - +
2A ASP* 2.7 32.5 - - - +
4A ASN* 1.4 90.2 - - + +
6A SER* 1.4 56.9 + - - +
8A VAL* 3.3 24.1 - - + +
9A ALA* 3.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ASP* 4.4 7.4 + - - -
3A PHE* 3.5 10.9 + - - -
4A ASN 3.2 1.0 - - - -
5A PRO* 1.4 74.6 - - - +
7A GLU* 1.4 53.7 + - - +
8A VAL 2.8 4.7 - - - -
9A ALA* 2.6 35.3 + - - +
10A SER* 3.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 2.9 39.7 - - + +
4A ASN* 3.6 10.4 - - - +
6A SER* 1.4 75.5 - - - +
8A VAL* 1.3 56.9 + - + +
10A SER* 3.0 32.2 + - - -
11A GLN* 5.4 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASN* 3.1 22.2 + - + +
5A PRO* 3.3 16.6 - - + +
7A GLU* 1.3 76.8 - - + +
9A ALA* 1.3 59.6 + - - +
10A SER 2.7 2.2 - - - -
11A GLN* 2.4 51.3 + - + +
12A VAL* 3.5 11.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO 3.6 4.0 + - - +
6A SER* 2.6 25.7 + - - +
8A VAL* 1.3 73.9 - - - +
10A SER* 1.3 60.1 + - - +
11A GLN 3.3 0.3 + - - -
12A VAL* 3.5 6.3 + - - +
13A THR* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER 3.9 0.4 + - - -
7A GLU* 3.0 20.0 + - - -
8A VAL 2.7 0.6 - - - -
9A ALA* 1.3 79.6 - - - +
11A GLN* 1.3 56.4 + - - -
13A THR* 4.5 4.5 - - - -
14A ASN* 3.1 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU 5.4 0.9 - - - +
8A VAL* 2.4 50.2 + - + +
10A SER* 1.3 68.3 - - - +
12A VAL* 1.3 61.9 + - - +
14A ASN* 5.4 0.9 - - - -
15A TYR* 3.2 58.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.5 14.2 + - + +
9A ALA* 3.5 4.5 + - - +
11A GLN* 1.3 75.1 - - - +
13A THR* 1.3 59.0 + - - +
15A TYR* 2.9 12.6 + - + +
16A ILE* 2.8 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.0 22.0 + - - +
10A SER* 4.1 4.7 - - - -
12A VAL* 1.3 79.6 - - - +
14A ASN* 1.3 64.8 + - - +
16A ILE* 3.3 18.5 + - - +
17A GLN* 3.4 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.1 35.0 + - - +
11A GLN* 5.0 2.0 - - - +
13A THR* 1.3 80.5 - - - +
15A TYR* 1.4 65.5 + - + +
16A ILE 3.4 0.2 + - - -
17A GLN* 3.8 27.0 + - - +
18A ALA 5.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 3.2 44.6 + - + +
12A VAL* 2.9 14.5 + - + +
14A ASN* 1.4 83.3 - - + +
16A ILE* 1.3 51.1 + - + +
17A GLN 3.9 0.2 + - - -
18A ALA* 4.8 0.7 + - - +
19A ILE* 2.4 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 2.8 36.7 + - + +
13A THR* 3.5 12.8 - - - +
14A ASN 3.2 0.4 - - - -
15A TYR* 1.3 82.1 - - + +
17A GLN* 1.4 66.9 + - - +
18A ALA 3.4 1.3 - - - -
19A ILE* 3.7 18.2 - - + -
20A ALA* 2.8 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR 3.4 13.6 + - - +
14A ASN* 3.8 21.1 + - - +
15A TYR 3.8 2.0 - - - -
16A ILE* 1.4 79.0 - - - +
18A ALA* 1.3 62.6 + - + +
20A ALA* 3.9 5.6 + - - +
21A ALA* 4.0 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN 5.2 1.0 + - - -
15A TYR 4.8 1.0 + - - -
17A GLN* 1.3 79.3 - - + +
19A ILE* 1.3 59.9 + - + +
21A ALA* 2.7 36.3 + - + +
22A ALA* 3.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TYR* 2.4 45.5 - - + +
16A ILE* 3.2 17.0 + - + +
18A ALA* 1.3 75.1 - - + +
20A ALA* 1.3 72.1 + - - +
21A ALA 2.7 1.6 - - - -
22A ALA* 2.7 25.7 + - + +
23A GLY 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 2.8 33.7 + - + +
17A GLN* 4.4 3.4 - - - +
19A ILE* 1.3 76.5 - - - +
21A ALA* 1.3 60.1 + - - +
22A ALA 3.5 0.2 + - - -
23A GLY 4.3 1.9 + - - -
24A VAL* 4.2 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN 4.0 3.7 + - - +
18A ALA* 2.7 21.9 + - + +
20A ALA* 1.3 78.8 - - - +
22A ALA* 1.3 61.6 + - - +
24A VAL* 5.1 1.3 - - - -
25A GLY* 2.2 54.2 + - - +
26A VAL* 3.0 2.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 3.1 5.4 + - - +
19A ILE* 2.7 26.7 + - + +
21A ALA* 1.3 74.7 - - - +
23A GLY* 1.3 61.2 + - - +
26A VAL* 3.7 9.8 + - - +
27A LEU* 3.6 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE 4.5 0.2 + - - -
20A ALA 4.3 2.6 + - - -
21A ALA 3.3 0.2 - - - -
22A ALA* 1.3 78.9 - - - +
24A VAL* 1.3 59.3 + - - +
27A LEU* 2.8 40.4 - - - +
31A ILE* 4.1 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 4.2 10.1 + - - +
21A ALA* 3.5 2.3 + - - -
23A GLY* 1.3 78.1 - - - +
25A GLY* 1.4 59.6 + - - +
26A VAL 3.9 0.2 - - - -
27A LEU* 4.1 0.8 - - - -
28A ALA* 3.3 24.5 + - - +
31A ILE* 5.1 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 2.2 44.2 + - - +
24A VAL* 1.4 68.9 - - - +
26A VAL* 1.3 65.3 + - - +
27A LEU 3.2 0.9 - - - -
28A ALA* 3.6 12.2 + - - +
29A LEU* 4.9 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.0 10.2 + - + +
22A ALA* 3.7 7.7 + - - +
25A GLY* 1.3 71.7 - - - +
27A LEU* 1.3 71.3 + - + +
29A LEU* 2.9 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 3.6 13.0 - - - +
23A GLY* 2.8 33.7 - - - +
25A GLY 3.2 0.2 - - - -
26A VAL* 1.3 84.4 - - + +
28A ALA* 1.3 56.3 + - - +
29A LEU 2.8 2.7 + - - -
30A ALA* 2.9 12.6 + - + +
31A ILE* 2.5 57.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL 3.3 18.3 + - - +
25A GLY* 4.1 7.9 - - - +
26A VAL 3.1 2.2 + - - -
27A LEU* 1.3 76.5 - - - +
29A LEU* 1.4 64.0 + - - +
31A ILE* 4.1 8.7 - - - -
32A GLY* 3.0 20.7 + - - +
33A LEU* 4.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 2.9 30.9 + - + +
27A LEU 2.8 1.0 + - - -
28A ALA* 1.4 75.4 - - - +
30A ALA* 1.4 50.0 + - - +
33A LEU* 2.4 38.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL 4.3 0.6 + - - -
27A LEU* 2.9 14.7 + - + +
29A LEU* 1.4 74.2 - - - +
31A ILE* 1.3 60.4 + - + +
33A LEU* 2.7 28.9 - - - +
34A SER* 3.3 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 4.1 7.9 - - - +
24A VAL* 5.1 8.3 - - + +
27A LEU* 2.5 58.8 + - + +
28A ALA* 4.1 3.6 - - - -
30A ALA* 1.3 69.8 - - + +
32A GLY* 1.3 66.4 + - - +
33A LEU 2.6 5.2 - - - -
34A SER* 2.4 34.4 + - - +
35A ALA* 3.3 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 3.0 18.1 + - - +
31A ILE* 1.3 77.3 - - - +
33A LEU* 1.3 53.4 + - - +
35A ALA* 2.4 36.6 + - - +
36A ALA* 2.6 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 4.3 1.3 - - - +
29A LEU 2.4 28.9 - - - +
30A ALA* 2.7 21.3 - - - +
32A GLY* 1.3 80.3 - - - +
34A SER* 1.3 50.9 + - - -
35A ALA 3.0 0.2 - - - -
36A ALA* 3.3 24.2 - - + -
37A TRP* 2.2 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 3.7 2.6 + - - -
31A ILE* 2.4 39.3 + - - +
33A LEU* 1.3 73.1 - - - +
35A ALA* 1.4 53.4 + - - -
37A TRP* 3.1 22.9 - - - +
38A LYS* 3.2 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE 3.3 0.6 + - - +
32A GLY* 2.4 29.7 + - - +
34A SER* 1.4 70.2 - - - +
36A ALA* 1.3 51.5 + - - +
37A TRP 2.9 3.8 - - - -
38A LYS* 2.6 40.9 + - + +
39A TYR* 3.1 14.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLY 2.6 9.1 + - - +
33A LEU* 3.3 39.7 - - + +
35A ALA* 1.3 68.8 - - - +
37A TRP* 1.3 66.2 + - - +
38A LYS 3.3 0.2 + - - -
39A TYR* 3.4 16.8 + - - +
40A ALA* 3.3 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 2.2 37.0 + - + +
34A SER* 3.1 19.1 - - - +
36A ALA* 1.3 73.6 - - - +
38A LYS* 1.4 58.4 + - - +
40A ALA* 2.7 37.2 + - + +
41A LYS* 3.1 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER 3.2 13.7 + - - +
35A ALA* 2.6 26.5 + - - +
37A TRP* 1.4 72.6 - - - +
39A TYR* 1.3 83.0 + - + +
40A ALA 2.9 0.7 + - - -
41A LYS* 2.9 15.6 + - - +
42A ARG* 3.1 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 3.1 35.4 - - + -
36A ALA* 3.7 15.7 - - - +
37A TRP 3.3 0.4 - - - -
38A LYS* 1.3 94.2 - - + +
40A ALA* 1.3 61.4 + - - +
41A LYS 3.2 0.3 + - - -
42A ARG* 3.3 35.3 + - - +
43A PHE* 2.6 58.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 3.3 8.6 + - - +
37A TRP* 2.7 34.2 + - + +
39A TYR* 1.3 81.9 - - - +
41A LYS* 1.3 61.1 - - + +
43A PHE* 4.4 3.4 + - - +
44A LEU* 3.0 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TRP* 3.1 47.6 + - + +
38A LYS* 2.9 8.8 + - - +
40A ALA* 1.3 85.0 - - + +
42A ARG* 1.4 49.2 + - + +
43A PHE 3.6 0.4 - - - -
44A LEU* 2.9 21.8 - - + +
45A LYS* 2.8 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.1 42.8 + - + +
39A TYR* 3.3 34.0 + - - +
41A LYS* 1.4 70.0 - - - +
43A PHE* 1.3 66.4 + - + +
44A LEU 2.8 5.6 - - - -
45A LYS* 3.2 20.6 - - + -
46A GLY* 2.5 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 2.6 65.1 - + + +
40A ALA* 4.6 4.5 - - - +
42A ARG* 1.3 84.1 - - + +
44A LEU* 1.3 64.1 + - + +
46A GLY* 4.3 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 3.0 25.1 - - - +
41A LYS* 2.9 26.5 - - + +
42A ARG 2.8 0.2 - - - -
43A PHE* 1.3 84.4 - - + +
45A LYS* 1.4 54.9 + - + -
46A GLY* 3.7 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 2.8 43.7 + - + +
42A ARG* 2.9 19.7 + - + +
44A LEU* 1.4 70.4 - - - +
46A GLY* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 2.5 22.0 + - - +
43A PHE 4.3 3.8 + - - +
44A LEU 3.7 6.5 - - - +
45A LYS* 1.3 77.1 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact 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 heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il