Contacts of the helix formed by residues 33 - 62 (chain E) in PDB entry 1Q0K
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 ASP 33 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ASN* 2.8 27.3 + - - +
32E ASP* 1.3 76.6 - - - +
34E LEU* 1.3 60.4 + - - +
35E HIS* 3.1 24.6 + - - +
36E PHE* 3.2 11.3 + - + +
37E GLN* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.3 16.8 - - + -
37C GLN* 5.2 8.7 - - + -
32E ASP 3.2 6.2 + - - -
33E ASP* 1.3 71.8 + - - +
35E HIS* 1.3 78.1 + - + +
37E GLN* 3.0 7.9 + - - +
38E ILE* 2.9 51.0 + - + +
34F LEU* 4.1 34.8 - - + -
38F ILE* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C MET* 3.5 5.1 - - + +
37C GLN* 2.6 33.4 + - + +
41C THR* 3.6 23.7 - - + +
44C LYS* 6.3 0.4 - - - -
90C ALA 5.9 3.4 - - - +
92C THR* 3.4 30.4 - - + +
33E ASP* 3.1 10.8 + - - +
34E LEU* 1.3 95.8 - - + +
36E PHE* 1.3 63.1 + - - +
38E ILE* 3.3 10.2 + - + +
39E ARG* 3.1 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.9 35.0 - - + -
27E LYS* 3.4 45.5 - - + -
28E MET* 4.0 7.0 - - - -
31E ASN* 3.5 48.0 - - + +
33E ASP* 3.2 15.0 + - + +
34E LEU 3.2 0.6 - - - -
35E HIS* 1.3 77.4 - - - +
37E GLN* 1.3 60.7 + - - +
39E ARG* 3.3 11.5 + - - +
40E ALA* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E MET* 3.1 41.5 + - - +
31E ASN 2.7 26.1 + - - +
32E ASP* 4.1 17.6 + - - +
33E ASP 2.8 20.5 + - - +
34E LEU* 3.3 11.4 - - - +
36E PHE* 1.3 79.9 - - - +
38E ILE* 1.3 53.4 + - - +
40E ALA* 4.5 2.2 - - - -
41E THR* 2.6 37.6 + - - -
92E THR* 4.6 0.9 - - - +
34F LEU* 5.1 7.9 - - + -
35F HIS* 2.5 38.2 + - + +
38F ILE* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLN* 4.3 6.1 - - + +
38C ILE* 3.8 41.1 - - + +
41C THR* 3.8 31.0 - - + +
34E LEU* 2.9 39.4 + - + +
35E HIS* 3.6 10.3 - - + +
37E GLN* 1.3 74.5 - - - +
39E ARG* 1.3 64.0 + - - +
41E THR* 3.3 2.8 + - - -
42E VAL* 3.0 36.9 + - + +
38F ILE* 3.8 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP 2.9 24.2 + - - -
4B LEU* 2.8 37.3 + - + +
41C THR* 3.5 20.4 - - + -
45C GLU* 2.8 39.0 + - - +
86C SER 5.1 0.6 + - - -
89C LYS* 3.4 26.6 + - - +
90C ALA* 3.4 31.0 - - - +
35E HIS* 3.1 20.6 + - - +
36E PHE* 3.8 9.7 - - - +
38E ILE* 1.3 72.8 - - - +
40E ALA* 1.3 65.2 + - - +
42E VAL* 3.3 6.3 + - - +
43E ILE* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.8 18.3 - - + +
24E ILE* 3.6 13.4 - - + +
28E MET* 3.6 33.4 - - + -
36E PHE* 2.9 23.5 + - + +
37E GLN 4.0 0.2 - - - +
39E ARG* 1.3 77.0 - - - +
41E THR* 1.3 57.3 + - - +
43E ILE* 3.8 0.8 - - - -
44E LYS* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E MET* 3.6 15.7 - - - +
37E GLN 2.6 24.1 + - - -
38E ILE 3.6 4.5 - - - -
40E ALA* 1.3 77.2 - - - +
42E VAL* 1.3 62.5 + - - +
44E LYS* 3.8 12.3 + - - +
45E GLU* 3.0 25.5 + - + +
35F HIS* 3.7 15.2 - - + +
38F ILE* 3.6 26.0 - - + +
39F ARG* 3.6 30.3 - - + +
42F VAL* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 5.8 0.7 - - + -
42C VAL* 3.6 39.9 - - + +
45C GLU* 5.2 13.0 - - + -
38E ILE* 3.0 23.4 + - + +
39E ARG* 3.6 7.6 - - - +
41E THR* 1.3 76.8 - - - +
43E ILE* 1.3 64.2 + - + +
45E GLU* 3.3 8.7 - - - +
46E GLN* 3.2 39.0 + - + +
38F ILE* 4.9 0.4 - - + -
42F VAL* 3.8 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B CYS* 3.3 46.2 - - + +
4B LEU* 3.4 39.5 - - + +
45C GLU* 3.8 24.7 - - + +
24E ILE* 3.7 9.2 - - + -
39E ARG* 2.9 19.3 + - - +
40E ALA* 4.1 2.9 - - - +
42E VAL* 1.3 76.9 - - + +
44E LYS* 1.3 66.1 + - - +
46E GLN* 3.2 15.9 + - - +
47E ARG* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E VAL* 4.0 20.9 - - + +
24E ILE* 3.7 19.8 - - + +
25E GLN* 3.6 25.8 - - + +
28E MET* 3.7 26.0 - - - +
40E ALA 2.9 17.2 + - - +
41E THR* 3.8 12.4 + - - +
43E ILE* 1.3 75.3 - - - +
45E GLU* 1.3 63.9 + - - +
47E ARG* 3.3 2.2 + - - +
48E ALA* 2.9 24.6 + - - +
88E ALA 3.3 9.0 + - - +
89E LYS* 2.7 33.3 + - - +
91E SER 3.0 21.6 + - - +
92E THR* 5.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D CYS 5.0 0.5 - - - +
3D ASP* 4.3 1.4 - - - +
41E THR* 3.0 15.0 + - + +
42E VAL* 3.3 13.0 - - - +
44E LYS* 1.3 77.4 - - - +
46E GLN* 1.3 58.8 + - + +
49E GLU* 3.1 27.9 + - - +
89E LYS* 3.1 40.8 + - + +
39F ARG* 2.9 50.1 + - - +
42F VAL* 5.1 11.4 - - + -
43F ILE* 3.9 20.1 - - + +
46F GLN* 5.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B CYS 5.7 0.5 - - - +
45C GLU* 6.0 2.6 - - - +
46C GLN* 5.7 8.7 - - - +
42E VAL* 3.2 26.6 - - + +
43E ILE* 3.2 24.1 + - - +
45E GLU* 1.3 75.3 - - + +
47E ARG* 1.3 79.2 + - - +
49E GLU* 3.4 6.1 + - - +
50E LEU* 3.0 28.2 + - + +
46F GLN* 5.7 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B HIS* 3.1 19.2 + - - -
2B CYS* 3.5 29.7 - - + +
7002B THJ 2.5 42.8 + - - -
17E GLU* 3.0 45.5 + - - +
20E SER* 4.3 5.6 - - - -
21E VAL* 3.9 15.7 - - + -
24E ILE* 4.1 10.8 - - + -
43E ILE* 2.9 28.6 + - + +
44E LYS 3.3 0.6 + - - +
46E GLN* 1.3 86.8 + - - +
48E ALA* 1.3 61.6 + - - +
50E LEU* 3.3 18.0 + - - +
51E ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E VAL* 3.5 20.1 - - + +
44E LYS 2.9 17.5 + - - +
47E ARG* 1.3 73.9 - - - +
49E GLU* 1.3 60.7 + - - +
51E ALA* 3.2 6.2 + - - +
52E LYS* 2.9 33.5 + - - +
85E LEU* 4.0 15.5 - - + +
89E LYS* 3.4 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ASP* 4.4 0.9 - - - +
53D HIS* 4.1 21.0 - - - -
57D VAL* 5.8 0.5 - - - +
7004D THJ 4.9 6.3 - - - -
45E GLU 3.1 17.7 + - - +
46E GLN* 3.5 8.7 - - - +
47E ARG 3.2 0.2 - - - -
48E ALA* 1.3 77.8 - - - +
50E LEU* 1.3 64.3 + - + +
52E LYS* 3.2 14.7 + - - +
53E HIS* 3.0 24.2 + - + +
89E LYS* 2.6 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7002B THJ 3.4 26.7 - - - +
7005B THJ 4.9 12.6 - - - +
17E GLU* 3.9 14.6 - - + +
46E GLN* 3.0 15.9 + - + +
47E ARG* 3.5 40.4 - - - +
48E ALA 3.2 0.2 - - - -
49E GLU* 1.3 74.9 - - + +
51E ALA* 1.3 67.1 + - - +
53E HIS* 3.2 11.1 + - + +
54E HIS* 3.0 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ALA* 3.9 15.0 - - + +
17E GLU* 3.8 17.7 - - + +
18E ALA* 4.1 4.7 - - + +
47E ARG 2.9 13.4 + - - +
48E ALA* 3.5 9.6 - - - +
50E LEU* 1.3 77.2 - - - +
52E LYS* 1.3 61.8 + - - +
54E HIS* 3.4 6.7 + - - +
55E LEU* 3.2 26.3 + - - +
85E LEU* 3.6 25.8 - - + -
104E ILE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ASP* 3.1 17.3 + - - +
57D VAL* 6.3 0.6 - - - +
60D SER* 4.0 10.4 + - - -
61D ASP* 2.7 32.7 + - - -
48E ALA 2.9 19.2 + - - +
49E GLU* 3.5 14.5 + - - +
51E ALA* 1.3 76.7 - - - +
53E HIS* 1.3 57.5 + - - +
55E LEU* 3.4 2.8 + - - +
56E ASP* 2.9 39.5 + - - +
82E VAL* 3.9 24.4 - - + +
85E LEU* 3.6 25.4 - - + -
86E SER* 3.0 22.3 + - - +
89E LYS* 4.1 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7005B THJ 2.8 40.9 + - - -
49D GLU* 4.2 17.9 - - - -
53D HIS* 5.6 6.0 + - + -
56D ASP* 5.8 1.8 + - - -
49E GLU* 3.0 16.7 + - + +
50E LEU* 3.2 16.4 + - + +
52E LYS* 1.3 73.9 - - - +
54E HIS* 1.3 75.6 + + - +
56E ASP* 3.2 12.6 + - - +
57E VAL* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 6.0 1.0 + - - -
7005B THJ 3.7 35.4 - - - -
10E ASP 6.0 0.2 - - - +
13E GLN* 3.5 51.9 + - + +
14E ALA* 3.7 21.5 - - + +
17E GLU* 4.1 12.0 + - + +
50E LEU* 3.0 35.6 + - + +
51E ALA 3.4 1.3 + - - +
53E HIS* 1.3 79.8 - + - +
55E LEU* 1.3 62.6 + - - +
57E VAL* 3.3 8.0 + - - +
58E LEU* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E PRO* 5.9 0.9 - - + -
14E ALA* 3.6 20.2 - - + -
51E ALA 3.2 8.5 + - - +
52E LYS 3.7 5.8 - - - +
54E HIS* 1.3 73.8 - - - +
56E ASP* 1.3 67.1 + - - +
58E LEU* 3.0 19.6 + - + +
59E TRP* 2.9 23.9 + - - +
78E VAL* 4.2 8.8 - - + +
81E ALA* 3.8 24.2 - - + -
82E VAL* 4.0 13.7 - - + -
85E LEU* 3.7 29.6 - - + -
104E ILE* 4.2 17.3 - - + -
107E ILE* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASP* 3.6 41.6 - - - +
59D TRP* 3.8 15.6 - - - -
60D SER* 4.7 5.5 + - - -
52E LYS* 2.9 27.0 + - - +
53E HIS* 3.2 13.3 + - - +
55E LEU* 1.3 74.7 - - - +
57E VAL* 1.3 59.1 + - + +
59E TRP* 3.3 10.0 + - - +
60E SER* 2.8 33.3 + - - -
82E VAL* 3.6 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7005B THJ 5.0 1.3 - - - +
49D GLU* 5.6 1.8 - - - +
52D LYS* 6.2 0.9 - - - +
56D ASP* 6.2 0.2 - - - +
1E HIS* 3.6 44.0 - - + +
9E TYR* 4.3 3.3 - - + -
53E HIS* 2.9 44.6 + - + +
54E HIS* 3.6 10.8 - - - +
55E LEU 3.2 0.2 - - - -
56E ASP* 1.3 74.6 - - + +
58E LEU* 1.3 60.8 + - + +
60E SER* 3.7 6.3 - - - +
61E ASP* 2.8 43.6 + - + +
62E TYR 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E TYR* 4.2 15.5 - - + -
10E ASP 4.5 8.5 - - - +
11E PRO* 3.8 32.5 - - + -
14E ALA* 5.6 0.7 - - + -
54E HIS 3.1 17.0 + - - +
55E LEU* 3.0 19.8 + - + +
57E VAL* 1.3 76.5 - - + +
59E TRP* 1.3 58.7 + - - +
62E TYR* 3.0 18.2 + - + +
63E PHE* 3.0 41.7 + - + -
78E VAL* 6.4 0.9 - - + -
107E ILE* 4.3 17.7 - - + -
111E PHE* 4.2 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ASP* 4.1 16.6 - - - -
59D TRP* 3.5 56.7 - + - -
75D HIS 3.7 7.6 - - - -
78D VAL* 3.8 16.8 - - + -
79D ASN* 3.0 65.5 + - + +
82D VAL* 4.4 5.6 - - + -
83D LYS* 3.7 3.6 + - - -
55E LEU 2.9 11.6 + - - +
56E ASP* 3.5 10.3 - - - +
58E LEU* 1.3 80.0 - - - +
60E SER* 1.3 71.0 + - - +
63E PHE* 3.8 10.3 - - - +
68E PHE* 3.6 27.2 - + - -
75E HIS* 2.9 26.2 + - - +
78E VAL* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LYS* 4.2 6.9 + - - -
56D ASP* 4.8 5.6 + - - -
79D ASN* 4.0 4.5 - - - +
82D VAL* 3.4 30.4 - - - +
83D LYS* 2.8 34.4 + - - +
86D SER* 5.3 0.7 + - - -
56E ASP 2.8 22.0 + - - -
57E VAL* 3.7 4.9 + - - +
59E TRP* 1.3 79.7 - - - +
61E ASP* 1.3 81.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LYS* 3.0 19.0 + - - -
83D LYS* 5.4 0.3 - - - -
86D SER* 4.0 3.2 + - - -
1E HIS 4.5 1.0 - - - +
3E ASP* 3.4 36.2 + - - +
9E TYR* 3.5 25.3 + - + +
57E VAL* 2.8 33.4 + - + +
60E SER* 1.3 93.5 + - - +
62E TYR* 1.3 60.4 + - - +
63E PHE 4.6 1.1 - - - -
64E LYS* 3.3 21.3 + - - +
9005E SO4 4.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E TYR* 3.4 44.2 - + + -
57E VAL 3.5 0.4 + - - -
58E LEU* 3.0 16.7 + - + +
61E ASP* 1.3 78.4 - - - +
63E PHE* 1.3 88.8 + + - +
64E LYS* 3.3 20.6 + - - +
67E HIS* 3.9 16.9 + + - -
111E PHE* 3.4 32.5 - + - -
114E THR* 2.6 36.4 + - - -
115E LYS* 3.1 27.3 - - + +
9005E SO4 4.6 6.1 - - - -
----------------------------------------------------------
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