Contacts of the helix formed by residues 47 - 76 (chain A) in PDB entry 1O9R
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 GLN 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY 3.1 0.8 + - - -
46A PRO* 1.3 81.4 - - + +
48A PHE* 1.3 66.2 + - - +
49A ILE 3.3 1.9 + - - -
50A ALA* 3.6 4.9 + - - +
51A VAL* 3.4 25.8 + - + +
103A ILE* 3.5 26.2 - - + +
104A HIS* 4.4 2.9 + - - +
107A LEU* 4.1 18.7 - - - +
157A HIS* 4.3 6.5 + - - -
47D GLN* 6.1 0.4 - - - +
162D SER* 3.7 19.6 + - - +
46F PRO* 2.9 41.1 + - + +
47F GLN* 3.4 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A HIS 4.4 1.3 - - - -
41A TRP 5.1 0.2 - - - -
43A LEU* 3.3 37.1 - - + +
45A GLY 3.0 17.4 + - - +
46A PRO 3.2 3.0 + - - -
47A GLN* 1.3 77.8 - - - +
49A ILE* 1.3 75.4 + - + +
51A VAL* 3.4 1.2 + - - +
52A HIS* 2.9 59.3 + + - +
103A ILE* 3.5 8.9 - - + +
152D TRP* 3.9 17.5 - + - -
153D PHE* 3.5 43.3 - + - -
156D ALA* 3.6 14.1 - - + +
157D HIS* 3.8 26.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN 3.3 0.8 + - - -
48A PHE* 1.3 87.2 - - + +
50A ALA* 1.3 66.5 + - - +
52A HIS* 4.2 2.5 - - + -
53A GLU* 2.9 53.1 + - + +
50D ALA* 3.5 37.2 - - + +
51D VAL 4.6 0.2 - - - +
54D LEU* 4.1 17.9 - - + -
153D PHE* 3.6 37.7 - - + -
157D HIS* 3.6 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN 3.6 5.8 + - - +
48A PHE 3.3 0.6 - - - -
49A ILE* 1.3 83.9 - - - +
51A VAL* 1.3 60.0 + - + +
53A GLU* 3.9 6.1 - - - +
54A LEU* 3.0 30.0 + - - +
50D ALA* 4.3 9.6 - - + +
47F GLN* 4.6 7.0 - - - +
49F ILE* 3.7 23.7 - - + +
50F ALA* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.7 21.5 - - + -
47A GLN* 3.4 29.1 + - + +
48A PHE 3.4 0.8 + - - -
49A ILE 3.3 0.2 - - - -
50A ALA* 1.3 76.1 - - + +
52A HIS* 1.3 65.6 + - - +
54A LEU* 3.2 7.8 + - + +
55A LEU* 3.1 37.8 + - + +
103A ILE* 4.3 17.9 - - + -
107A LEU* 4.5 14.8 - - + -
110A LEU* 5.8 0.4 - - + -
154A LEU* 5.9 0.7 - - + -
157A HIS* 4.1 28.7 - - + +
49F ILE* 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A HIS* 2.7 84.7 + + - -
41A TRP* 4.6 0.4 - + - -
43A LEU* 3.5 12.9 - - + +
48A PHE* 2.9 36.7 + + + +
49A ILE* 3.6 8.3 - - + +
51A VAL* 1.3 76.2 - - - +
53A GLU* 1.3 68.7 + - + +
55A LEU* 3.5 1.3 + - - +
56A ASP* 3.5 6.3 + - - -
71B GLU* 5.4 0.2 - - - -
1163B FE 4.3 6.9 - - - -
152D TRP* 3.7 25.0 - + - -
153D PHE* 3.8 28.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 2.9 47.5 + - + +
50A ALA* 4.0 5.5 - - - +
52A HIS* 1.3 82.2 - - + +
54A LEU* 1.3 65.8 + - - +
56A ASP* 3.1 19.2 + - - +
57A THR* 3.4 11.4 + - - -
54D LEU* 5.1 3.5 - - - +
153D PHE* 5.2 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA 3.0 19.2 + - - +
51A VAL* 3.2 9.2 + - + +
53A GLU* 1.3 76.8 - - - +
55A LEU* 1.3 65.4 + - + +
57A THR* 2.9 24.6 + - + +
58A PHE* 3.1 51.4 + - + -
153A PHE* 3.9 22.7 - - + +
154A LEU* 5.3 4.7 - - + -
157A HIS* 4.2 15.9 - - + -
49F ILE* 4.1 33.0 - - + -
53F GLU* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 3.1 28.8 - - + +
37A LYS* 5.8 0.6 - - - +
39A ALA* 4.2 1.8 - - + -
40A HIS* 3.7 38.6 - - + +
43A LEU* 4.1 11.9 - - + -
51A VAL* 3.1 25.5 + - + +
52A HIS 3.8 4.7 - - - +
53A GLU 3.2 0.2 - - - -
54A LEU* 1.3 77.5 - - + +
56A ASP* 1.3 58.1 + - - +
58A PHE* 3.3 25.2 + - + -
59A ARG* 3.0 22.3 + - - +
110A LEU* 3.9 31.9 - - + -
114A TYR* 5.0 0.7 - - + +
154A LEU* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LYS* 2.6 36.4 + - - +
40A HIS* 3.0 30.8 + - - -
52A HIS* 3.5 2.7 + - - +
53A GLU* 3.1 14.1 + - - +
55A LEU* 1.3 74.4 - - - +
57A THR* 1.4 66.4 + - - +
59A ARG* 3.2 5.4 + - - +
60A THR* 3.1 27.0 + - - -
1163B FE 4.2 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU 3.4 8.6 + - - -
54A LEU* 2.9 18.6 + - + +
56A ASP* 1.4 79.9 - - - +
58A PHE* 1.3 66.3 + - + +
60A THR* 3.3 8.7 + - - -
61A GLN* 3.1 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 4.2 0.4 - - + -
54A LEU* 3.1 48.1 + - + -
55A LEU* 3.6 21.1 - - + +
56A ASP 3.3 0.2 - - - -
57A THR* 1.3 80.9 - - + +
59A ARG* 1.3 63.5 + - - +
61A GLN* 3.1 13.8 + - - +
62A LEU* 2.9 28.1 + - + +
114A TYR* 3.3 33.0 - + + +
150A SER* 3.5 44.0 - - - +
153A PHE* 3.9 11.4 - + + -
154A LEU* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 3.0 48.8 + - - +
34A LEU* 4.0 16.6 - - - +
36A THR* 4.0 10.7 - - + +
37A LYS* 3.4 39.4 - - + +
55A LEU 3.0 17.1 + - - +
56A ASP* 3.2 8.9 + - - +
58A PHE* 1.3 75.7 - - - +
60A THR* 1.3 58.2 + - - +
62A LEU* 3.2 3.7 + - - +
63A ASP* 2.8 52.4 + - - +
33B ALA* 6.2 0.4 - - - +
59B ARG* 3.5 23.6 - - - +
63B ASP* 4.0 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP 3.1 13.1 + - - -
57A THR* 3.5 11.8 - - - -
59A ARG* 1.3 77.3 - - - +
61A GLN* 1.3 64.1 + - + +
63A ASP* 3.3 13.2 + - + +
64A ASN* 3.1 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 3.1 37.3 + - + +
58A PHE* 3.1 10.3 + - - +
60A THR* 1.3 78.3 - - + +
62A LEU* 1.4 57.3 + - + +
64A ASN* 3.2 8.9 + - - +
65A HIS* 2.9 39.5 + - + -
146A ASP* 3.8 33.2 + - + +
150A SER* 3.5 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.7 25.1 - - + +
32A LEU* 3.9 23.8 - - + -
33A ALA* 3.8 30.5 - - + +
36A THR* 3.6 13.7 - - - +
58A PHE* 2.9 19.0 + - + +
59A ARG* 3.7 4.5 - - - +
61A GLN* 1.4 72.2 - - + +
63A ASP* 1.3 61.3 + - - +
65A HIS* 4.5 6.5 - - + +
66A GLY* 2.9 28.4 + - - -
114A TYR* 3.5 26.9 - - + +
147A LEU* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 4.3 4.3 - - - +
59A ARG* 2.8 52.2 + - - +
60A THR* 3.4 14.0 - - + +
61A GLN 3.2 0.2 - - - -
62A LEU* 1.3 77.4 - - - +
64A ASN* 1.3 61.9 + - - +
66A GLY* 3.9 0.8 - - - -
67A ASP* 2.9 39.2 + - - +
59B ARG* 4.1 14.0 + - - -
63B ASP* 4.4 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.1 32.4 + - - +
61A GLN* 3.6 9.8 - - - +
63A ASP* 1.3 77.8 - - - +
65A HIS* 1.3 64.6 + - + +
67A ASP* 3.3 11.0 + - - +
68A THR* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 5.2 4.7 - - + -
61A GLN* 2.9 30.5 + - + +
62A LEU* 4.3 7.6 - - + +
64A ASN* 1.3 77.1 - - + +
66A GLY* 1.3 60.3 + - - +
68A THR* 3.2 8.9 + - - +
69A ILE* 2.9 38.0 + - + +
139A ILE* 4.7 3.3 + - - +
142A ALA* 3.6 16.1 - - + +
143A ALA* 3.5 44.9 + - + +
146A ASP* 2.7 36.5 + - + +
147A LEU* 6.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.4 22.2 - - - +
29A VAL* 3.9 16.9 - - - +
30A ILE* 5.8 1.6 - - - -
62A LEU 2.9 18.1 + - - -
63A ASP* 4.0 0.7 - - - -
65A HIS* 1.3 76.1 - - - +
67A ASP* 1.4 63.1 + - - +
69A ILE* 3.3 3.8 + - - -
70A ALA* 2.9 21.4 + - - +
41B TRP* 4.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASP* 2.9 26.6 + - - +
64A ASN* 3.5 10.3 - - - +
66A GLY* 1.4 74.9 - - - +
68A THR* 1.4 58.6 + - - +
70A ALA* 3.8 0.7 - - - +
71A GLU* 2.9 38.6 + - - +
1163A FE 4.5 10.1 - - - -
37B LYS* 2.7 38.1 + - - +
41B TRP* 3.4 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 3.0 18.9 + - - -
65A HIS* 3.2 10.3 + - - +
67A ASP* 1.4 78.5 - - - +
69A ILE* 1.3 61.5 + - - +
71A GLU* 3.5 12.9 + - - +
72A ARG* 3.1 22.2 + - - +
75A GLN* 5.2 0.7 + - - -
139A ILE* 3.6 26.3 - - + +
145C ARG* 3.5 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.3 42.7 - - + +
25A SER* 4.5 1.8 - - - -
26A LEU* 4.0 14.6 - - + +
29A VAL* 4.4 22.2 - - + -
65A HIS* 2.9 28.5 + - + +
66A GLY* 3.7 5.2 - - - +
68A THR* 1.3 76.6 - - - +
70A ALA* 1.3 62.1 + - - +
72A ARG* 3.1 12.6 + - - +
73A VAL* 3.2 13.9 + - + +
121A ILE* 4.5 5.4 - - + -
139A ILE* 4.0 17.9 - - + -
140A PHE* 4.0 25.4 - - + -
143A ALA* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.9 18.8 - - + -
66A GLY 2.9 14.3 + - - +
69A ILE* 1.3 77.5 - - - +
71A GLU* 1.4 64.4 + - - +
73A VAL* 3.2 20.2 + - - +
74A VAL* 3.3 6.9 + - - +
80A ALA* 3.7 12.9 - - + +
41B TRP* 3.2 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 2.9 29.3 + - - +
68A THR* 3.9 11.9 + - - +
70A ALA* 1.4 77.1 - - - +
72A ARG* 1.3 57.8 + - - +
74A VAL* 3.0 13.9 - - - +
75A GLN* 2.9 37.7 + - - +
1163A FE 2.0 36.3 - - - -
41B TRP* 4.2 10.5 - - + -
52B HIS* 4.8 0.3 + - - -
149C LYS* 3.0 34.2 + - - +
152C TRP* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN* 4.3 0.2 + - - -
10A LEU* 5.0 1.0 - - - +
22A LEU* 3.7 18.2 - - + -
68A THR 3.1 14.9 + - - +
69A ILE 3.1 9.6 + - - +
71A GLU* 1.3 73.8 - - - +
73A VAL* 1.3 66.6 + - - +
75A GLN* 3.1 30.5 + - - +
76A LEU* 3.2 44.0 + - + +
133A ASP* 3.1 27.7 + - - -
135A THR* 3.4 22.9 - - - +
136A THR* 2.8 25.0 + - - +
139A ILE* 3.8 21.3 - - + -
122C ARG* 4.3 5.1 - - - +
148C ASP* 2.7 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 4.1 13.0 - - + +
22A LEU* 3.4 36.3 - - + +
23A ASN* 3.8 25.1 - - - +
69A ILE* 3.2 9.4 + - + +
70A ALA* 3.2 13.1 + - - +
72A ARG* 1.3 76.2 - - - +
74A VAL* 1.3 62.2 + - - +
76A LEU* 3.2 10.0 + - - +
77A GLY 3.4 0.2 + - - -
78A GLY* 3.0 24.7 + - - -
79A THR 3.4 40.8 - - - +
80A ALA* 3.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A HIS* 5.8 0.2 - - - +
70A ALA 3.3 7.6 + - - +
71A GLU* 3.0 29.2 - - - +
73A VAL* 1.3 73.5 - - - +
75A GLN* 1.3 65.0 + - - +
77A GLY* 2.9 14.4 + - - -
78A GLY 3.6 14.3 - - - +
80A ALA* 3.8 11.9 - - + +
41B TRP* 3.6 13.9 - - + +
42B ASN* 3.6 24.9 - - - +
44B LYS* 4.7 9.9 + - - +
152C TRP* 3.3 46.0 - - + +
159C GLN* 5.6 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 4.1 18.2 + - - +
8A ASN* 4.3 8.8 - - - +
68A THR 5.2 0.6 + - - -
71A GLU* 2.9 40.5 + - - +
72A ARG* 3.1 44.6 + - - +
74A VAL* 1.3 77.0 - - - +
76A LEU* 1.3 60.4 + - + +
77A GLY 3.2 1.3 + - - -
139A ILE* 5.4 0.5 - - - +
145C ARG* 4.6 2.8 + - - +
148C ASP* 3.7 14.8 - - + +
149C LYS* 3.9 21.7 + - - +
152C TRP* 3.6 37.4 - - + +
155C GLU* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 6.0 0.5 - - - +
6A THR* 4.5 3.9 - - - +
8A ASN* 3.9 25.1 - - - +
10A LEU* 4.0 21.8 - - + -
15A LYS* 3.4 32.1 - - + +
18A VAL* 4.0 20.4 - - + -
19A ILE* 3.9 21.2 - - + +
22A LEU* 4.4 5.6 - - + -
72A ARG* 3.2 39.3 + - - +
73A VAL 3.2 4.5 + - - +
74A VAL 3.1 1.0 - - - -
75A GLN* 1.3 75.1 - - - +
77A GLY* 1.3 59.7 + - - +
78A GLY 3.4 1.5 + - - -
133A ASP* 3.9 18.2 - - - +
----------------------------------------------------------
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