Contacts of the helix formed by residues 56 - 85 (chain H) in PDB entry 3WKJ
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 SER 56 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G ARG* 3.5 13.5 - - - +
78G ILE 3.0 12.9 + - - -
79G ILE* 4.0 15.9 - - - -
80G PRO* 3.5 11.5 - - - +
55H ILE* 1.3 78.9 - - - +
57H SER* 1.3 58.1 + - - +
58H LYS* 3.6 4.4 + - - +
59H ALA* 3.0 24.6 + - - +
60H MET* 3.0 28.5 + - - +
166J T 3.7 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H SER* 1.3 69.0 - - - +
58H LYS* 1.3 71.0 + - - +
60H MET* 3.2 8.0 + - - +
61H SER* 3.1 21.5 + - - -
165J A 5.6 0.2 - - - -
166J T 2.8 33.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 5.8 3.4 - - - +
80G PRO* 3.7 22.7 - - + -
103G ALA 5.9 0.4 - - - +
104G GLN* 4.8 20.4 - - + -
56H SER* 3.4 4.1 + - - +
57H SER* 1.3 84.7 + - - +
59H ALA* 1.3 63.3 + - - +
61H SER* 2.7 22.7 + - - -
62H ILE* 2.9 17.5 + - + +
165J A 5.9 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ILE* 3.2 21.3 - - + +
79G ILE 3.9 12.8 - - - -
80G PRO* 3.8 5.7 - - - +
83G LEU* 3.6 18.6 - - + +
55H ILE* 3.6 13.2 - - + -
56H SER* 3.0 19.8 + - - +
58H LYS* 1.3 77.0 - - - +
60H MET* 1.3 58.2 + - - +
62H ILE* 3.4 1.2 + - - -
63H MET* 3.0 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H SER* 2.9 55.4 - - - +
42H ILE* 3.9 20.9 - - + -
43H TYR* 3.9 24.0 - - + +
55H ILE* 4.0 24.0 - - + +
56H SER 3.0 17.5 + - - +
57H SER* 3.5 8.1 - - - +
58H LYS 3.1 0.2 - - - -
59H ALA* 1.3 75.8 - - - +
61H SER* 1.3 61.2 + - - +
63H MET* 3.3 2.2 + - - +
64H ASN* 2.9 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 3.9 23.2 + - - -
100B PHE 5.0 0.9 - - - -
101B GLY 5.5 3.6 - - - -
57H SER 3.1 12.7 + - - -
58H LYS* 2.7 24.9 + - - -
60H MET* 1.3 73.5 - - - +
62H ILE* 1.3 59.9 + - - +
64H ASN* 2.9 9.3 + - - +
65H SER* 2.8 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 3.9 24.2 - - + +
99B GLY* 3.8 23.1 - - - +
80G PRO* 3.7 19.3 - - + -
83G LEU* 3.9 15.3 - - + -
102G ILE* 3.3 36.3 - - + -
103G ALA* 3.7 14.8 - - + +
58H LYS* 2.9 22.8 + - + +
59H ALA* 3.6 5.6 - - - +
61H SER* 1.3 78.6 + - - +
63H MET* 1.3 58.5 + - - +
65H SER* 3.3 2.8 + - - -
66H PHE* 2.9 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G THR* 3.7 40.4 - - + +
62G ILE* 3.7 32.1 - - + -
63G LEU* 4.0 22.2 - - + -
83G LEU* 4.0 17.3 - - + -
42H ILE* 3.8 17.3 - - + -
55H ILE* 4.5 6.3 - - + -
59H ALA 3.0 20.5 + - - +
60H MET* 3.7 5.8 - - - +
61H SER 3.2 0.2 - - - -
62H ILE* 1.3 79.3 - - - +
64H ASN* 1.3 57.8 + - - +
66H PHE* 3.5 17.4 + - + +
67H VAL* 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H GLU 5.2 0.2 + - - -
37H SER* 3.3 27.2 - - - +
38H TYR* 2.9 34.9 + - - +
39H SER* 3.2 12.0 + - - -
42H ILE* 3.9 4.3 - - - +
60H MET* 2.9 13.2 + - + +
61H SER* 2.9 13.8 + - - +
63H MET* 1.3 77.0 - - - +
65H SER* 1.3 57.4 + - - +
67H VAL* 3.2 3.8 + - - +
68H THR* 2.5 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 3.5 23.5 - - - -
99B GLY* 3.2 13.1 + - - -
101B GLY 3.9 1.5 + - - -
102B GLY* 2.8 43.5 + - - +
61H SER 2.8 14.7 + - - -
62H ILE 3.7 5.6 - - - -
64H ASN* 1.3 72.1 - - - +
66H PHE* 1.3 57.3 + - - +
68H THR* 3.4 6.1 + - - -
69H ASP* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 3.4 31.6 - + + -
55G LEU* 5.3 2.2 - - + -
58G LEU* 3.9 34.1 - - + -
59G THR* 4.4 5.6 - - - -
62G ILE* 3.3 34.3 - - + -
93G LEU* 5.6 0.4 - - + -
96G LEU* 4.4 6.7 - - + -
97G LEU* 3.9 21.5 - - + -
62H ILE* 2.9 18.3 + - + +
63H MET* 3.5 16.6 - - + +
65H SER* 1.3 76.5 - - - +
67H VAL* 1.3 74.7 + - + +
69H ASP* 3.3 1.6 + - - +
70H ILE* 3.0 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PHE* 3.9 16.2 - - + -
55G LEU* 3.7 18.9 - - + +
59G THR* 3.7 24.5 - - + +
38H TYR* 3.4 38.4 - - + -
42H ILE* 4.2 14.8 - - + -
63H MET 3.1 18.3 + - - +
64H ASN 3.2 4.4 + - - +
66H PHE* 1.3 82.9 - - + +
68H THR* 1.3 57.8 + - - +
71H PHE* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY 5.6 0.9 + - - -
102B GLY* 5.4 2.6 - - - -
33G LEU* 6.3 1.1 - - + -
38H TYR* 4.0 20.4 - - + +
64H ASN* 2.5 32.0 + - - +
65H SER* 3.4 8.1 + - - -
67H VAL* 1.3 76.1 - - - +
69H ASP* 1.3 55.8 + - - +
71H PHE* 3.4 10.7 - - + +
72H GLU* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 4.2 19.0 + - - +
96B THR* 4.5 3.6 + - + +
98B TYR* 2.5 39.1 + - + +
100G VAL* 3.9 4.3 - - - +
65H SER 2.9 13.7 + - - +
66H PHE 3.6 0.4 - - - +
67H VAL 3.3 0.2 - - - -
68H THR* 1.3 73.3 - - - +
70H ILE* 1.3 67.0 + - - +
72H GLU* 3.0 9.4 + - - +
73H ARG* 2.9 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G LEU* 4.1 10.5 - - + -
58G LEU* 4.0 17.5 - - + -
96G LEU* 4.0 26.9 - - + -
97G LEU* 4.6 2.5 - - + -
66H PHE* 3.0 43.1 + - + +
67H VAL* 5.1 0.2 - - - -
69H ASP* 1.3 76.7 - - - +
71H PHE* 1.3 64.1 + - - +
73H ARG* 4.1 30.7 - - + +
74H ILE* 3.0 48.3 + - + +
103H LEU* 4.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G VAL* 3.9 17.3 - - + -
33G LEU* 4.0 32.8 - - + -
34G LEU* 4.2 9.9 - - + -
39G TYR* 3.9 24.5 - + - -
51G LEU* 3.4 28.5 - - + +
55G LEU* 3.7 30.2 - - + +
38H TYR* 3.9 17.7 - - - +
67H VAL 2.9 20.5 + - - +
68H THR* 3.4 12.3 - - + +
70H ILE* 1.3 77.0 - - - +
72H GLU* 1.3 63.2 + - + +
74H ILE* 4.2 0.9 - - - +
75H ALA* 3.1 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 5.1 16.4 - - - +
80D ARG* 6.2 2.2 - - - -
39G TYR* 3.6 18.8 + - - +
68H THR 2.8 17.3 + - - +
69H ASP* 3.0 7.4 + - - +
71H PHE* 1.3 82.2 - - + +
73H ARG* 1.3 68.7 + - + +
75H ALA* 4.1 0.6 - - - +
76H SER* 2.5 58.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 5.7 2.8 - - - +
96G LEU* 3.1 46.2 + - - +
97G LEU* 4.1 9.3 - - - +
99G ARG* 5.9 3.0 - - - +
100G VAL* 4.1 10.7 - - - +
69H ASP* 2.9 52.6 + - - +
70H ILE* 3.8 17.4 - - + +
72H GLU* 1.3 80.7 - - + +
74H ILE* 1.3 65.3 + - + +
76H SER* 3.7 2.5 - - - -
77H GLU* 3.0 20.3 + - - +
80H ARG* 5.5 0.2 + - - -
102H LEU* 3.5 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU* 3.9 26.7 - - + -
54G VAL* 3.8 26.5 - - + -
55G LEU* 5.1 0.9 - - + -
70H ILE* 3.0 39.2 + - + +
73H ARG* 1.3 77.5 - - - +
75H ALA* 1.3 64.9 + - - +
77H GLU 3.4 0.3 + - - -
78H ALA* 3.0 21.1 + - - +
95H ILE* 4.0 23.8 - - + +
98H ALA* 3.5 16.4 - - + +
99H VAL* 4.0 12.3 - - + -
102H LEU* 3.5 20.0 - - + -
103H LEU* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 4.2 19.1 - - + -
39G TYR* 3.7 35.1 - - + -
51G LEU* 4.8 1.8 - - + +
71H PHE* 3.1 24.6 + - + +
72H GLU 4.1 1.1 - - - +
74H ILE* 1.3 77.7 - - - +
76H SER* 1.3 52.1 + - - +
78H ALA* 3.0 8.5 + - - +
79H SER* 2.7 33.6 + - - -
90H ILE* 4.4 2.4 - - - +
95H ILE* 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G TYR* 3.9 8.7 - - - -
72H GLU* 2.5 46.2 + - - -
73H ARG* 3.7 3.1 - - - -
75H ALA* 1.3 72.9 - - - +
77H GLU* 1.3 66.2 + - - +
78H ALA 3.0 1.8 - - - -
79H SER* 3.0 18.0 + - - -
80H ARG* 3.1 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 2.8 41.2 + - - -
92F ARG* 4.0 12.5 + - - +
73H ARG 3.0 16.4 + - - +
76H SER* 1.3 76.6 - - - +
78H ALA* 1.3 56.9 + - - +
80H ARG* 2.6 37.7 + - - +
81H LEU* 3.1 28.2 + - + +
84H TYR* 5.0 0.2 - - - -
98H ALA* 3.7 31.0 - - + +
101H LEU* 3.4 12.4 - - + +
102H LEU* 4.0 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H ILE 3.0 15.2 + - - +
75H ALA* 3.1 13.9 - - - +
76H SER 3.0 0.2 - - - -
77H GLU* 1.3 76.4 - - - +
79H SER* 1.3 63.5 + - - +
81H LEU* 3.5 4.5 + - - +
82H ALA* 3.2 22.5 + - - +
90H ILE* 4.1 10.6 - - + +
94H GLU* 4.0 27.2 - - + +
95H ILE* 3.9 24.9 - - + -
98H ALA* 4.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN* 5.1 2.3 - - - +
38G ASN 4.8 1.2 + - - -
39G TYR* 2.6 41.0 + - - +
75H ALA 2.7 12.7 + - - -
76H SER* 3.3 13.5 - - - -
78H ALA* 1.3 79.4 - - - +
80H ARG* 1.3 63.7 + - - +
82H ALA* 3.3 4.9 + - - +
83H HIS* 3.2 29.1 + - - +
90H ILE* 3.9 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLU* 5.5 4.2 + - - -
72F TYR* 6.0 0.2 - - - -
91F LYS* 6.5 0.9 - - - -
92F ARG* 5.7 1.2 - - - +
73H ARG 5.5 0.2 + - - -
76H SER* 3.1 31.4 + - - +
77H GLU* 2.6 47.4 + - - +
79H SER* 1.3 76.6 - - - +
81H LEU* 1.3 57.3 + - - +
83H HIS* 2.8 30.2 + - - +
84H TYR* 2.8 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 3.4 33.7 - - + +
75F HIS* 3.7 32.9 + - + +
77H GLU* 3.1 24.3 + - - +
78H ALA* 3.6 5.6 - - - +
80H ARG* 1.3 79.0 - - - +
82H ALA* 1.3 58.8 + - - +
84H TYR* 3.4 15.0 + - + +
85H SER* 3.1 17.5 + - - -
94H GLU* 3.6 12.8 - - + +
97H THR* 3.4 40.6 - - + -
98H ALA* 3.6 15.3 - - - +
101H LEU* 4.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G SER* 5.5 3.6 - - - -
78H ALA 3.2 9.6 + - - +
79H SER 3.6 9.0 - - - +
80H ARG 3.1 0.6 - - - -
81H LEU* 1.3 76.2 - - - +
83H HIS* 1.3 65.2 + - + +
85H SER* 3.1 8.9 + - - -
86H LYS 3.1 3.8 + - - -
87H ARG* 2.9 40.0 + - + +
89H THR 4.2 14.8 - - - +
90H ILE* 4.5 8.7 - - + -
94H GLU* 4.1 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS 3.7 19.0 + - - -
37C GLY* 4.3 10.6 - - - -
38C ASN* 2.7 33.7 + - - -
39G TYR 5.3 0.2 - - - -
79H SER* 3.2 22.1 + - - +
80H ARG* 2.8 12.6 + - - +
82H ALA* 1.3 79.1 - - + +
84H TYR* 1.3 68.4 + - + +
86H LYS* 3.2 17.2 + - - +
87H ARG 4.6 9.9 + - - -
88H SER* 6.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 3.9 28.1 + + + -
76F ALA* 6.6 0.2 - - - -
88F TYR* 3.1 70.0 - + + +
91F LYS* 6.2 0.2 - - - +
80H ARG* 2.8 49.0 + - + +
81H LEU* 3.7 15.7 - - + +
82H ALA 3.2 0.4 - - - -
83H HIS* 1.3 82.9 - - + +
85H SER* 1.3 59.9 + - - +
86H LYS* 3.3 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F HIS* 4.0 16.2 - - - -
76F ALA* 5.5 10.1 - - - -
81H LEU 3.1 12.0 + - - -
82H ALA* 3.1 15.3 + - - -
84H TYR* 1.3 77.0 - - - +
86H LYS* 1.3 73.2 + - - +
87H ARG* 3.1 23.7 + - - +
----------------------------------------------------------
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