Contacts of the helix formed by residues 58 - 87 (chain H) in PDB entry 1ID3
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 58 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ARG* 3.5 21.3 - - - +
79G ILE 3.0 18.0 + - - -
80G ILE* 4.1 13.0 - - - -
81G PRO* 3.8 7.6 - - - +
57H ILE* 1.3 75.8 - - - +
59H GLN* 1.3 67.2 + - - +
60H LYS* 3.4 4.0 + - - +
61H SER* 2.9 22.9 + - - -
62H MET* 3.1 19.1 + - - +
165J A 4.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ILE 5.5 0.9 - - - +
58H SER* 1.3 73.2 - - - +
60H LYS* 1.3 68.1 + - - +
62H MET* 3.1 14.2 + - - +
63H SER* 3.1 17.9 + - - -
164J G 5.6 0.9 - - - -
165J A 3.3 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 4.7 3.2 + - - +
99B GLY* 3.7 25.4 - - - +
100B PHE* 4.1 19.9 - - - -
81G PRO* 3.6 16.4 - - + -
104G ALA* 4.0 24.4 - - - +
105G GLN* 3.6 25.0 - - + +
58H SER* 3.4 3.2 + - - +
59H GLN* 1.3 78.3 - - - +
61H SER* 1.3 56.5 + - - +
63H SER* 2.6 28.4 + - - -
64H ILE* 2.7 22.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
79G ILE* 2.7 22.6 + - - -
80G ILE* 3.2 18.4 - - - -
81G PRO* 4.0 0.8 - - - +
84G LEU* 3.8 17.0 - - - +
57H ILE* 3.3 20.0 - - - -
58H SER* 2.9 17.0 + - - -
60H LYS* 1.3 77.3 - - - +
62H MET* 1.3 57.1 + - - +
64H ILE* 3.1 5.9 + - - +
65H LEU* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H SER* 2.9 53.3 + - - +
44H ILE* 3.7 20.2 - - + -
45H TYR* 4.2 15.0 - - + +
57H ILE* 3.4 38.7 - - + +
58H SER 3.1 8.8 + - - +
59H GLN* 3.5 15.0 - - - +
61H SER* 1.3 76.5 - - - +
63H SER* 1.3 64.3 + - - +
65H LEU* 4.4 1.3 - - - +
66H ASN* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY 3.8 23.9 + - - -
100B PHE* 4.6 0.3 - - - -
101B GLY* 4.0 11.4 + - - -
59H GLN* 3.1 11.6 + - - -
60H LYS* 2.6 22.0 + - - -
62H MET* 1.3 73.3 - - - +
64H ILE* 1.3 57.3 + - - -
66H ASN* 3.5 5.9 + - - +
67H SER* 2.9 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 3.5 36.5 - - + +
99B GLY* 3.7 17.3 - - - +
81G PRO* 3.7 37.5 - - + -
84G LEU* 4.0 16.2 - - + -
103G ILE* 4.0 18.2 - - + -
104G ALA 4.0 10.3 - - - +
60H LYS* 2.7 18.1 + - + +
61H SER 3.4 5.6 - - - +
63H SER* 1.3 74.7 - - - +
65H LEU* 1.3 66.5 + - + +
66H ASN 3.0 1.7 + - - -
67H SER* 3.1 3.8 + - - -
68H PHE* 2.9 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G ALA* 5.0 4.3 - - - +
63G ILE* 3.4 36.1 - - + -
64G LEU* 3.8 25.1 - - + +
79G ILE* 5.7 0.9 - - + -
84G LEU* 4.1 18.2 - - + -
44H ILE* 3.9 20.9 - - + -
57H ILE* 3.4 31.9 - - + -
61H SER 2.8 16.5 + - - +
62H MET* 4.1 4.0 - - - +
64H ILE* 1.3 74.8 - - + +
66H ASN* 1.3 60.5 + - - +
68H PHE* 3.5 14.5 + - + +
69H VAL* 3.1 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLY* 5.4 2.2 + - - -
39H THR* 3.8 24.3 - - - +
40H TYR* 2.9 38.7 + - - +
41H SER* 4.2 4.3 + - - +
44H ILE* 5.3 4.0 - - + +
62H MET 3.0 19.1 + - - +
63H SER* 3.6 7.8 + - - +
64H ILE 3.0 0.8 - - - -
65H LEU* 1.3 75.6 - - - +
67H SER* 1.3 61.8 + - - +
69H VAL* 3.2 6.7 + - - +
70H ASN* 2.3 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU 5.0 0.2 - - - -
98B TYR* 3.7 25.6 - - - -
99B GLY 4.3 6.6 + - - -
101B GLY* 3.7 11.0 + - - -
102B GLY* 2.9 28.7 + - - +
63H SER 2.9 13.7 + - - -
64H ILE 3.1 6.6 + - - -
66H ASN* 1.3 77.7 + - - +
68H PHE* 1.3 54.5 + - - +
70H ASN* 3.6 4.0 - - - +
71H ASP* 2.5 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 3.7 17.2 - + + -
59G LEU* 4.1 26.7 - - + -
60G ALA* 5.3 2.5 - - - -
63G ILE* 3.1 44.4 - - + -
94G LEU* 4.3 5.8 - - + -
97G LEU* 4.2 5.6 - - + -
98G LEU* 3.6 38.4 - - + -
64H ILE* 2.9 13.9 + - + +
65H LEU* 3.5 22.4 - - + +
67H SER* 1.3 76.3 - - - +
69H VAL* 1.3 63.4 + - + +
71H ASP* 3.2 1.0 + - - +
72H ILE* 2.9 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 4.5 6.5 - - + -
56G LEU* 4.0 26.8 - - + +
60G ALA* 4.8 9.2 - - + -
40H TYR* 3.5 39.0 - - + +
44H ILE* 3.9 22.2 - - + -
65H LEU* 3.1 17.2 + - + +
66H ASN 3.2 6.0 + - - +
68H PHE* 1.3 82.7 - - + +
70H ASN* 1.3 51.0 + - - +
72H ILE* 3.3 5.3 + - - +
73H PHE* 2.6 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLY* 4.0 19.9 + - - +
34G LEU* 5.8 1.7 - - - +
40H TYR* 3.3 19.6 + - - -
66H ASN* 2.3 56.0 + - - +
67H SER* 3.7 5.5 - - - +
69H VAL* 1.3 73.8 - - - +
71H ASP* 1.3 67.4 + - - +
73H PHE* 3.4 8.1 - - - +
74H GLU* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 4.2 20.3 + - - +
96B THR* 3.8 5.0 + - - +
98B TYR* 2.2 42.7 + - + +
102B GLY 5.4 0.4 + - - -
101G VAL* 3.7 8.1 - - - +
67H SER 2.5 20.2 + - - +
68H PHE 3.3 3.4 - - - +
70H ASN* 1.3 75.3 - - - +
72H ILE* 1.3 58.9 + - + +
74H GLU* 3.4 5.1 + - - +
75H ARG* 2.7 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G LEU* 4.4 6.3 - - + -
59G LEU* 3.8 25.4 - - + -
97G LEU* 4.2 12.1 - - + -
98G LEU* 4.4 1.3 - - + -
68H PHE* 2.9 47.4 + - + +
69H VAL* 3.8 2.7 - - - +
71H ASP* 1.3 74.1 - - - +
73H PHE* 1.3 70.1 + - - +
75H ARG* 2.9 39.1 + - + +
76H ILE* 2.8 43.0 + - + +
104H ILE* 5.0 2.0 - - + -
105H LEU* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G VAL* 3.8 15.7 - - + -
34G LEU* 3.9 31.4 - - + -
35G LEU* 4.0 15.9 - - + -
40G TYR* 3.3 23.8 - + - -
52G LEU* 3.5 29.3 - - + +
56G LEU* 3.9 21.0 - - + +
40H TYR* 3.8 17.0 - - - +
69H VAL 2.6 22.6 + - - +
70H ASN* 3.4 10.3 - - - +
72H ILE* 1.3 75.5 - - - +
74H GLU* 1.3 64.3 - - + +
76H ILE* 3.3 3.8 + - - +
77H ALA* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 6.2 5.6 - - - -
40G TYR* 3.0 38.6 + - - -
70H ASN 3.0 8.7 + - - +
71H ASP* 3.6 8.5 - - - +
73H PHE* 1.3 83.4 - - + +
75H ARG* 1.3 67.6 + - - +
77H ALA 4.5 0.2 - - - +
78H THR* 2.7 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TYR* 4.6 0.6 + - - -
97G LEU* 2.5 46.5 + - - +
98G LEU* 4.3 3.0 - - - +
101G VAL* 5.1 3.6 - - - +
71H ASP* 2.7 69.5 + - - +
72H ILE* 2.9 23.8 + - + +
74H GLU* 1.3 78.2 - - - +
76H ILE* 1.3 60.4 + - - +
78H THR* 3.7 4.0 - - - -
79H GLU* 3.1 21.3 + - - +
104H ILE* 4.2 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 3.6 25.6 - - + -
55G VAL* 3.8 29.6 - - + -
56G LEU* 4.9 1.8 - - + -
59G LEU* 5.2 0.2 - - + -
72H ILE* 2.8 39.3 + - + +
73H PHE 3.7 3.1 - - - +
75H ARG* 1.3 69.0 - - + +
77H ALA* 1.3 68.4 + - - +
78H THR 3.0 1.7 + - - -
79H GLU 3.0 1.9 + - - -
80H ALA* 2.9 23.7 + - - +
97H ILE* 4.3 9.9 - - + +
100H ALA* 3.7 20.6 - - + +
101H VAL* 4.1 20.0 - - + -
104H ILE* 4.4 17.7 - - + -
105H LEU* 5.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 4.4 13.0 - - + -
40G TYR* 3.5 38.3 - - + +
52G LEU* 5.0 2.9 - - + +
73H PHE* 2.9 31.6 + - + +
74H GLU 4.0 0.7 - - - +
76H ILE* 1.3 74.6 - - - +
78H THR* 1.3 57.7 + - - +
80H ALA* 3.5 7.9 - - - +
81H SER* 2.9 26.2 + - - -
92H ILE* 5.2 0.3 - - - +
97H ILE* 4.9 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G TYR* 4.0 4.1 - - + -
74H GLU* 2.7 52.3 + - - +
75H ARG* 3.7 4.7 - - - -
77H ALA* 1.3 70.9 - - - +
79H GLU* 1.3 67.0 + - - +
80H ALA 3.0 1.8 - - - -
81H SER* 3.0 17.2 + - - -
82H LYS* 3.0 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 2.9 27.5 + - - -
92F ARG* 3.8 18.5 - - + +
75H ARG 3.1 8.3 + - - +
76H ILE 3.0 5.5 + - - +
78H THR* 1.3 75.8 - - - +
80H ALA* 1.3 58.2 + - - +
82H LYS* 2.9 37.8 + - - +
83H LEU* 2.9 33.0 + - - +
100H ALA* 4.1 5.2 - - + -
103H LEU* 3.3 18.5 - - + +
104H ILE* 3.6 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ILE 2.9 16.3 + - - +
77H ALA* 3.5 9.2 - - - +
79H GLU* 1.3 74.7 - - - +
81H SER* 1.3 67.1 + - - +
83H LEU* 2.9 24.5 + - - +
84H ALA* 3.1 11.4 + - - +
92H ILE* 3.5 20.9 - - + +
96H GLU* 4.2 12.0 - - + +
97H ILE* 4.3 13.2 - - + -
100H ALA* 4.0 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN* 5.0 2.8 + - - +
40G TYR* 2.4 44.3 + - - +
77H ALA 2.9 15.6 + - - -
78H THR* 3.2 14.1 - - - -
80H ALA* 1.3 76.9 - - - +
82H LYS* 1.3 58.7 + - - +
84H ALA* 3.9 1.9 - - - +
85H ALA* 3.0 29.9 + - - +
92H ILE* 3.8 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D GLU* 6.0 2.0 - - - +
91F LYS* 6.6 0.7 - - + -
92F ARG* 5.7 3.6 - - - +
78H THR* 3.0 29.8 + - + +
79H GLU* 2.9 49.4 + - - +
80H ALA 3.1 0.2 - - - -
81H SER* 1.3 75.0 - - - +
83H LEU* 1.3 56.9 + - - +
85H ALA* 3.4 6.4 - - - +
86H TYR* 2.7 71.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 3.4 36.3 - - + -
75F HIS* 4.3 17.9 - - + +
79H GLU* 2.9 24.8 + - - +
80H ALA* 2.9 12.5 + - - +
82H LYS* 1.3 74.0 - - - +
84H ALA* 1.3 56.6 + - - +
86H TYR* 2.7 32.3 + - + +
87H ASN* 3.0 16.6 + - - +
96H GLU* 3.7 26.0 - - + +
99H THR* 3.7 34.3 - - + -
100H ALA* 3.7 9.6 - - - +
103H LEU* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ALA* 5.2 4.7 - - + -
80H ALA 3.1 10.1 + - - +
81H SER* 3.9 2.9 - - - +
83H LEU* 1.3 76.9 - - - +
85H ALA* 1.3 68.3 + - - +
87H ASN* 2.7 15.6 + - - +
89H LYS* 3.3 35.1 + - + +
91H THR 3.4 26.2 - - - +
92H ILE* 4.1 9.2 - - + -
96H GLU* 4.2 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H SER* 3.0 17.9 + - - +
82H LYS* 3.4 9.2 - - - +
84H ALA* 1.3 80.6 - - - +
86H TYR* 1.3 68.1 + - + +
87H ASN 3.0 0.5 + - - -
88H LYS* 3.3 12.9 + - - +
89H LYS 4.2 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR* 4.0 26.1 + + - -
88F TYR* 3.0 67.7 + + + +
91F LYS* 5.4 7.3 - - - +
82H LYS* 2.7 58.1 + - + +
83H LEU* 2.7 19.3 + - + +
85H ALA* 1.3 74.5 - - + +
87H ASN* 1.3 66.4 + - - +
88H LYS* 3.7 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR 5.7 0.6 + - - -
75F HIS* 3.5 29.8 + - + +
76F ALA* 4.0 23.8 - - - +
78F ARG* 5.4 1.9 + - - -
83H LEU* 3.0 20.6 + - - +
84H ALA* 2.7 13.7 + - - +
86H TYR* 1.3 81.8 - - - +
88H LYS* 1.3 56.0 + - - +
89H LYS* 2.5 32.4 + - + +
----------------------------------------------------------
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