Contacts of the helix formed by residues 44 - 78 (chain H) in PDB entry 2ONK
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 44 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H LYS 2.7 12.2 + - - +
41H ALA* 2.9 18.6 + - - +
43H SER* 1.3 73.5 - - - +
45H PRO* 1.3 64.2 - - - +
46H ALA* 2.8 31.8 + - - +
47H VAL* 2.9 29.6 + - + +
48H TRP* 3.5 6.2 - - - -
220H ARG* 2.8 32.8 + - - -
203J GLU* 4.5 0.7 - - - +
204J ARG* 5.4 1.6 + - - -
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Residues in contact with PRO 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H SER 2.7 16.3 - - - +
44H ASP* 1.3 80.4 - - - +
46H ALA* 1.3 64.2 + - - +
47H VAL 3.2 0.4 - - - -
48H TRP* 3.8 14.5 - - + +
49H LYS* 3.0 34.9 + - + +
204J ARG* 5.5 9.0 - - - +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H ASP* 2.8 20.9 + - - +
45H PRO* 1.3 80.4 - - - +
47H VAL* 1.3 62.3 + - - +
49H LYS* 3.2 19.4 + - - +
50H VAL* 3.2 20.3 + - - +
216H LEU* 5.2 5.8 - - + -
220H ARG* 4.6 7.6 - - - +
203J GLU* 4.7 8.7 - - + +
204J ARG* 4.0 24.7 - - - +
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Residues in contact with VAL 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ALA 4.0 9.9 - - - +
44H ASP* 2.9 26.3 + - + +
46H ALA* 1.3 80.5 - - - +
48H TRP* 1.3 69.1 + - + +
50H VAL* 2.9 6.3 + - - +
51H VAL* 2.8 42.3 + - + -
216H LEU* 3.9 26.0 - - + -
220H ARG* 4.2 9.6 - - - +
232H VAL* 4.4 20.9 - - + -
235H ILE* 4.8 17.7 - - + -
236H LEU* 5.4 1.1 - - + -
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Residues in contact with TRP 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ALA 4.8 0.2 + - - -
42H ALA* 2.5 36.0 + - + -
43H SER* 4.1 3.8 - - - +
44H ASP 3.5 24.0 + - - -
45H PRO* 4.1 10.3 - - + +
46H ALA 3.4 0.4 - - - -
47H VAL* 1.3 79.2 - - + +
49H LYS* 1.3 62.5 + - - +
51H VAL* 3.8 16.3 - - + +
52H LEU* 3.1 39.7 + - + +
235H ILE* 4.6 15.0 - - + -
239H LEU* 3.8 33.0 - - + -
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Residues in contact with LYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H PRO* 3.0 28.4 + - - +
46H ALA* 3.3 13.9 - - - +
47H VAL 3.1 1.0 - - - -
48H TRP* 1.3 77.3 - - - +
50H VAL* 1.3 56.6 + - + +
52H LEU* 3.6 5.7 + - - +
53H THR* 2.6 32.3 + - - -
204J ARG* 5.3 9.2 - - - +
206J GLU* 5.7 2.6 + - - -
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Residues in contact with VAL 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ALA 3.2 15.7 - - - +
47H VAL* 2.9 7.5 + - - +
49H LYS* 1.3 75.6 - - + +
51H VAL* 1.3 67.2 + - + +
53H THR* 2.8 6.0 + - - -
54H THR* 2.7 24.3 + - - -
211H MET* 3.2 26.7 - - + +
212H ILE 2.9 11.9 - - - +
213H ALA* 2.7 41.3 - - - +
216H LEU* 4.2 26.0 - - + -
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Residues in contact with VAL 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL* 2.8 35.8 + - + +
48H TRP* 3.8 18.2 - - + +
50H VAL* 1.3 73.4 - - + +
52H LEU* 1.3 71.0 + - + +
54H THR* 3.2 8.5 - - - -
55H TYR* 3.0 42.3 + - + -
213H ALA* 4.8 3.1 - - + -
236H LEU* 3.8 18.2 - - + -
239H LEU* 3.5 36.8 - - + -
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Residues in contact with LEU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H TRP* 3.1 28.7 + - + +
49H LYS* 3.9 5.4 - - - +
51H VAL* 1.3 82.8 - - + +
53H THR* 1.3 68.1 + - - +
55H TYR* 4.0 7.8 - - + +
56H TYR* 2.8 31.4 + - + +
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Residues in contact with THR 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LYS 2.6 24.6 + - - -
50H VAL* 2.8 11.3 + - - -
52H LEU* 1.3 72.7 - - - +
54H THR* 1.3 67.3 + - - +
56H TYR* 4.1 5.3 - - + +
57H ALA* 2.8 25.9 + - - +
128H LEU* 4.3 19.5 - - + +
131H ILE* 4.3 13.9 - - + -
210H PRO* 4.3 11.2 - - + +
211H MET 3.9 16.2 + - - +
212H ILE* 5.5 0.7 - - + -
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Residues in contact with THR 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H VAL 2.7 11.9 + - - -
51H VAL* 3.2 10.1 - - - -
53H THR* 1.3 80.5 - - - +
55H TYR* 1.3 80.1 + - + +
57H ALA* 2.8 11.0 + - - +
58H ALA* 2.9 14.1 + - - +
135H MET* 4.2 4.1 - - + +
197H ILE* 4.1 27.6 - - + +
212H ILE* 3.2 23.9 - - + +
213H ALA* 2.9 35.8 + - + +
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Residues in contact with TYR 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H VAL* 3.0 30.8 + - + +
52H LEU* 4.0 7.9 - - + +
54H THR* 1.3 82.7 - - + +
56H TYR* 1.3 57.5 + - - +
58H ALA* 3.5 0.4 + - - -
59H LEU* 2.9 31.1 + - - +
193H TRP* 3.3 29.4 + + + +
197H ILE* 3.2 33.9 - - + +
236H LEU* 4.9 4.9 + - + +
239H LEU* 3.2 44.5 + - + +
240H SER* 3.7 15.6 + - - -
243H VAL* 3.8 16.6 - - + +
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Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H LEU* 2.8 25.0 + - + +
53H THR* 4.1 3.6 - - + +
55H TYR* 1.3 71.6 - - - +
57H ALA* 1.3 65.9 + - - +
59H LEU* 3.3 16.3 + - + +
60H ILE* 3.3 45.6 + - + +
128H LEU* 3.3 34.7 - - + +
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Residues in contact with ALA 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H THR 2.8 19.8 + - - +
54H THR 2.8 7.0 + - - +
56H TYR* 1.3 74.6 - - - +
58H ALA* 1.3 63.2 + - - +
60H ILE* 3.1 15.3 + - - +
61H SER* 3.3 9.5 + - - -
128H LEU* 3.6 22.2 - - + -
131H ILE* 3.6 31.9 - - + -
132H VAL* 3.6 12.6 - - + +
135H MET* 3.8 3.7 - - - +
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Residues in contact with ALA 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H THR 2.9 13.1 + - - +
55H TYR 3.8 3.8 - - - +
57H ALA* 1.3 74.6 - - - +
59H LEU* 1.3 64.1 + - - +
61H SER* 2.9 22.5 + - - -
62H THR* 3.2 12.3 + - - -
135H MET* 3.3 21.7 - - + -
193H TRP* 3.7 16.0 - - + +
196H GLY* 4.1 4.7 - - - -
197H ILE* 3.8 25.1 - - + +
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Residues in contact with LEU 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H TYR 2.9 18.2 + - - +
56H TYR* 3.5 18.8 - - + +
57H ALA 3.2 0.4 - - - -
58H ALA* 1.3 76.7 - - - +
60H ILE* 1.3 65.8 + - + +
62H THR* 3.6 4.2 + - - -
63H LEU* 3.2 44.0 + - + +
193H TRP* 3.7 23.1 - - + +
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Residues in contact with ILE 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H TYR* 3.3 50.9 - - + +
57H ALA* 3.1 8.4 + - - +
59H LEU* 1.3 80.5 - - + +
61H SER* 1.3 65.2 + - - +
63H LEU* 3.3 9.3 + - + +
64H ILE* 3.0 46.1 + - + +
128H LEU* 4.4 10.8 - - + -
132H VAL* 3.9 16.4 - - + -
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Residues in contact with SER 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ALA 3.3 6.5 + - - -
58H ALA* 2.9 14.3 + - - -
60H ILE* 1.3 77.1 - - - +
62H THR* 1.3 62.9 + - - +
64H ILE* 3.2 2.5 + - - -
65H ALA* 2.8 25.4 + - - +
132H VAL* 4.2 11.1 - - - +
135H MET* 4.1 10.3 - - - +
136H LEU* 3.1 47.8 + - - +
139H SER* 3.8 13.3 + - - -
192H SER 4.8 2.4 + - - -
196H GLY* 5.2 0.7 - - - -
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Residues in contact with THR 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ALA 3.2 11.1 + - - -
59H LEU* 3.7 10.8 - - - +
60H ILE 3.1 0.4 - - - -
61H SER* 1.3 78.7 + - - +
63H LEU* 1.3 74.4 + - + +
65H ALA* 2.7 15.2 + - + +
66H VAL* 2.8 19.1 + - + +
143H TYR* 5.8 0.2 - - + -
189H ALA* 3.8 28.7 - - + +
192H SER* 2.7 29.2 + - - +
193H TRP* 3.6 18.1 + - + +
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Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LEU* 3.2 34.6 + - + +
60H ILE* 3.3 10.3 + - + +
62H THR* 1.3 84.7 - - + +
64H ILE* 1.3 64.3 + - + +
66H VAL* 3.3 7.7 + - + +
67H ILE* 2.9 41.9 + - + +
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Residues in contact with ILE 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ILE* 3.0 25.9 + - + +
61H SER* 3.4 7.2 - - - +
63H LEU* 1.3 77.5 - - + +
65H ALA* 1.3 62.7 + - - +
67H ILE* 4.5 5.2 - - - -
68H PHE* 3.0 43.6 + - + +
132H VAL* 3.8 26.9 - - + -
136H LEU* 3.9 24.0 - - + -
16I ILE* 5.7 3.1 - - + +
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Residues in contact with ALA 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H SER 2.8 13.0 + - - +
62H THR* 2.7 15.2 + - - +
64H ILE* 1.3 72.5 - - - +
66H VAL* 1.3 60.4 + - - +
68H PHE* 3.0 0.6 + - - -
69H GLY* 2.3 40.6 + - - +
136H LEU* 4.1 10.1 - - + +
139H SER* 5.8 1.1 - - - +
140H VAL* 4.9 13.5 - - + +
143H TYR* 3.9 27.4 - - + -
144H ILE* 6.4 0.2 - - + -
192H SER* 4.9 3.1 - - - +
16I ILE* 5.7 2.7 - - - -
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Residues in contact with VAL 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H THR* 2.8 23.3 + - + +
63H LEU* 3.7 11.0 - - + +
65H ALA* 1.3 75.8 - - - +
67H ILE* 1.3 66.4 + - + +
70H THR* 2.9 32.1 + - - +
71H PRO* 3.9 0.2 - - - +
143H TYR* 3.3 39.9 - - + +
185H ILE* 4.6 10.1 - - + -
189H ALA* 4.2 16.2 - - + -
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Residues in contact with ILE 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H LEU* 2.9 36.6 + - + +
64H ILE* 3.9 4.3 - - - +
66H VAL* 1.3 77.3 - - + +
68H PHE* 1.3 77.3 + - + +
71H PRO* 3.7 5.6 - - - +
12I LEU* 3.5 25.1 - - + +
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Residues in contact with PHE 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H ILE* 3.0 35.5 + - + +
67H ILE* 1.3 97.0 - - + +
69H GLY* 1.3 64.1 + - - +
70H THR 3.5 0.7 - - - -
71H PRO* 3.2 18.2 - - - +
72H LEU 3.8 3.5 + - - -
12I LEU* 3.2 37.9 - - + +
13I SER* 3.9 0.3 - - - -
15I ILE* 3.4 36.8 - - + -
16I ILE* 2.9 35.8 - - + +
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Residues in contact with GLY 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ALA* 2.3 29.0 + - - +
68H PHE* 1.3 68.5 - - - +
70H THR* 1.3 65.4 + - - +
72H LEU* 3.1 6.1 + - - +
73H ALA* 2.9 21.8 + - - +
140H VAL* 5.9 0.4 - - - -
143H TYR* 4.1 5.6 - - - -
144H ILE* 3.8 27.8 - - - +
16I ILE* 4.0 4.4 - - - +
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Residues in contact with THR 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H VAL* 2.9 24.5 + - - +
69H GLY* 1.3 73.8 - - - +
71H PRO* 1.3 73.1 - - + +
73H ALA* 2.7 20.0 + - - +
74H TYR 2.9 10.2 + - - -
143H TYR* 2.5 33.6 + - - -
147H ALA* 4.7 0.8 - - - +
151H PHE* 3.4 30.4 - - + -
173H PHE* 4.3 12.1 - - + -
178H LEU* 4.4 5.8 - - + -
185H ILE* 4.5 6.6 - - + +
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Residues in contact with PRO 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H VAL 3.9 0.2 - - - +
67H ILE 3.7 13.5 - - - +
68H PHE 3.2 21.3 - - - +
70H THR* 1.3 97.0 - - + +
72H LEU* 1.3 59.6 + - - +
74H TYR* 3.4 6.7 + - + +
75H ILE* 3.1 27.0 + - - +
173H PHE* 5.3 2.0 - - + -
9I LEU* 3.7 46.1 - - + +
12I LEU* 3.7 20.9 - - + -
13I SER* 4.2 2.2 - - - +
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Residues in contact with LEU 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H PHE 4.3 2.7 - - - +
69H GLY 3.1 8.6 + - - +
70H THR 2.9 2.2 + - - -
71H PRO* 1.3 75.4 - - - +
73H ALA* 1.3 61.6 + - - +
75H ILE* 3.3 10.3 + - + +
76H LEU* 2.9 46.8 + - + +
87H VAL* 3.9 24.0 - - + -
91H VAL* 3.6 18.2 - - + -
144H ILE* 3.5 26.7 - - + -
13I SER* 3.4 30.6 - - - +
16I ILE* 4.7 3.4 - - + -
17I LEU* 3.9 22.4 - - + +
----------------------------------------------------------
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Residues in contact with ALA 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H GLY 2.9 9.7 + - - +
70H THR 2.7 13.7 + - - +
72H LEU* 1.3 73.7 - - - +
74H TYR* 1.3 63.2 + - - +
76H LEU* 3.3 1.5 + - - -
77H ALA* 3.1 17.5 + - - +
144H ILE* 3.5 14.1 - - - +
147H ALA* 3.4 20.2 - - + -
148H LYS* 3.4 42.0 - - - +
151H PHE* 3.8 3.8 - - + -
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Residues in contact with TYR 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H THR 2.9 9.8 + - - +
71H PRO* 3.6 8.5 - - + +
73H ALA* 1.3 76.1 - - - +
75H ILE* 1.3 68.8 + - + +
77H ALA* 2.8 15.2 + - - +
78H ARG* 2.9 44.7 + - + +
79H LYS* 5.9 6.7 - - - -
151H PHE* 3.4 40.0 - + + -
159H GLU* 3.0 21.3 + - - +
169H PRO 5.8 0.3 + - - -
172H VAL* 5.4 2.3 - - - +
173H PHE* 3.8 24.4 + + + +
177H SER* 3.7 21.5 + - - -
5I PHE* 5.4 4.0 - + - -
9I LEU* 4.1 20.2 - - + -
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Residues in contact with ILE 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H PRO 3.1 11.5 + - - +
72H LEU* 3.6 14.1 - - + +
74H TYR* 1.3 86.5 - - + +
76H LEU* 1.3 63.0 + - + +
78H ARG* 4.1 1.6 - - - +
79H LYS* 3.3 51.4 + - + +
81H PHE* 3.8 27.1 - - + -
6I SER 5.5 0.7 - - - +
9I LEU* 4.2 11.7 - - + +
10I ALA* 4.2 20.2 - - + +
13I SER* 3.7 23.1 - - - +
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Residues in contact with LEU 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H LEU* 2.9 37.7 + - + +
73H ALA* 3.8 5.2 - - - +
74H TYR 2.9 0.4 + - - -
75H ILE* 1.3 79.7 - - + +
77H ALA* 1.3 62.6 + - - +
78H ARG 3.6 0.2 + - - -
81H PHE* 4.5 5.2 - - + -
84H LYS* 2.7 43.4 + - + +
87H VAL* 4.1 21.5 - - + -
88H GLU* 4.2 23.0 - - + +
91H VAL* 4.5 12.6 - - + -
144H ILE* 4.4 12.8 - - + -
145H ASN* 6.0 0.2 - - - +
148H LYS* 3.9 31.3 - - + +
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Residues in contact with ALA 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H ALA 3.1 15.0 + - - +
74H TYR 2.8 4.7 + - - +
76H LEU* 1.3 77.4 - - - +
78H ARG* 1.3 73.0 + - - +
84H LYS* 5.2 0.5 + - - -
148H LYS* 3.7 16.6 - - + +
151H PHE* 3.8 8.3 - - + -
152H ALA* 3.6 36.0 - - + +
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Residues in contact with ARG 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H TYR* 2.9 41.9 + - + +
75H ILE* 5.0 0.4 - - - -
76H LEU 4.7 0.2 - - - +
77H ALA* 1.3 94.6 + - + +
79H LYS* 1.3 74.7 + - + +
80H SER* 3.7 3.5 + - - -
84H LYS* 4.8 1.6 + - - -
151H PHE* 2.6 34.8 + - - +
152H ALA* 4.3 6.1 + - - +
154H VAL* 2.7 28.6 + - - +
156H VAL* 4.0 27.6 - - - +
159H GLU* 3.2 37.4 + - - -
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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