Contacts of the helix formed by residues 67 - 98 (chain B) in PDB entry 6BAA
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 LYS 67 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP 3.7 1.3 + - - +
66B LEU* 1.3 79.4 - - - +
68B TRP* 1.3 65.2 + - - +
69B PRO* 3.4 13.0 - - + -
70B HIS* 3.2 27.3 + - + +
71B THR* 3.2 17.2 + - - -
55F SER* 5.1 11.2 + - - -
56F SER* 5.3 15.5 - - - +
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Residues in contact with TRP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.9 34.9 - + - -
158A MET* 6.1 0.2 - - - -
162A ILE* 4.9 12.6 - - + -
66B LEU 3.8 0.4 + - - -
67B LYS* 1.3 72.7 - - - +
69B PRO* 1.3 71.3 - - + +
71B THR* 3.2 7.1 + - + -
72B LEU* 3.0 51.1 + - + +
167B ILE* 3.9 34.1 - - + -
170B LYS* 3.7 49.3 + - + +
171B THR* 4.6 2.5 - - + -
176B ARG* 6.0 3.1 - - - -
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Residues in contact with PRO 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 3.4 13.0 - - + -
68B TRP* 1.3 96.3 - - + +
70B HIS* 1.3 66.2 + - + +
72B LEU* 3.7 11.5 + - + +
73B LEU* 3.1 31.9 + - + +
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Residues in contact with HIS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.4 17.6 - - + +
67B LYS* 3.2 32.0 + - + +
68B TRP 3.2 0.6 - - - -
69B PRO* 1.3 84.4 - - + +
71B THR* 1.3 65.4 + - - +
72B LEU 3.1 1.3 - - - -
73B LEU* 3.8 18.4 - - + +
74B ILE* 3.0 33.4 + - + +
51F TRP* 4.0 18.6 - + - -
52F GLY* 3.9 20.7 + - - -
55F SER* 3.3 28.4 + - - -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.7 15.1 + - + +
66B LEU* 3.8 3.0 + - - +
67B LYS 3.2 10.1 + - - -
68B TRP* 3.2 11.9 + - + -
70B HIS* 1.3 77.0 - - - +
72B LEU* 1.3 63.6 + - + +
74B ILE* 3.5 8.3 + - - +
75B PHE* 3.2 50.6 + - + -
166B CYS* 5.8 0.9 - - + -
167B ILE* 4.1 8.3 - - + -
170B LYS* 3.2 44.0 + - + +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 4.1 32.9 - - + +
162A ILE* 6.3 2.2 - - + -
68B TRP* 3.0 50.3 + - + +
69B PRO* 3.8 9.9 - - + +
71B THR* 1.3 77.2 - - + +
73B LEU* 1.3 57.2 + - + +
75B PHE* 3.8 3.1 - - - +
76B THR* 2.6 40.5 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 3.1 26.3 + - + +
70B HIS* 3.4 21.3 + - + +
72B LEU* 1.3 76.3 - - + +
74B ILE* 1.3 60.0 + - + +
76B THR* 3.7 7.0 - - + +
77B MET* 2.7 42.1 + - + +
48F PHE* 5.2 18.2 - - + -
51F TRP* 5.2 8.1 - - + -
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 3.6 15.5 - - + -
66B LEU* 3.3 34.3 - - + -
70B HIS* 3.0 20.0 + - + +
71B THR* 3.8 5.6 - - - +
73B LEU* 1.3 77.0 - - + +
75B PHE* 1.3 61.6 + - + +
77B MET* 3.3 6.1 + - - +
78B SER* 2.6 49.8 + - - +
45F PRO* 5.0 12.7 - - + +
48F PHE* 4.4 20.9 - - + +
49F ILE* 3.4 27.6 - - + -
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 3.4 27.1 - - + -
63B LEU* 4.9 12.3 - - + -
71B THR* 3.2 41.9 + - + +
72B LEU 4.2 0.2 - - - +
74B ILE* 1.3 84.8 - - + +
76B THR* 1.3 65.6 + - - +
78B SER* 4.0 11.4 - - - -
79B PHE* 3.0 36.4 + + + -
159B ILE* 5.9 1.1 - - + -
162B ILE* 5.1 3.1 - - + -
163B MET* 3.7 38.6 - - + -
166B CYS* 3.5 34.1 - - + -
167B ILE* 3.9 15.0 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 6.1 0.2 - - + -
154A ILE* 3.6 40.6 - - + +
158A MET* 5.1 1.3 - - - +
72B LEU* 2.6 27.7 + - - +
73B LEU* 3.7 10.9 - - + +
75B PHE* 1.3 76.9 - - - +
77B MET* 1.3 62.4 + - + +
79B PHE* 3.9 2.1 - - - +
80B LEU* 2.9 36.9 + - + +
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Residues in contact with MET 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 2.7 27.3 + - + +
74B ILE* 3.6 5.6 - - - +
76B THR* 1.3 77.5 - - + +
78B SER* 1.3 60.1 + - - +
80B LEU* 3.7 18.1 - - + +
81B CYS* 2.7 62.2 + - - +
41F PHE* 6.1 0.2 - - + -
44F PHE* 4.0 26.7 - - + -
45F PRO* 5.7 3.8 - - + -
48F PHE* 3.8 31.0 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 2.6 39.9 + - - +
75B PHE* 3.9 12.0 - - - -
76B THR 3.3 0.2 - - - -
77B MET* 1.3 71.8 - - - +
79B PHE* 1.3 64.9 + - - +
81B CYS* 3.9 4.2 - - - +
82B SER* 2.8 32.0 + - - -
159B ILE* 4.8 12.6 - - - +
45F PRO* 4.3 19.7 - - - +
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.5 12.1 - - + -
157A LEU* 3.2 44.4 - - + -
158A MET* 4.2 9.4 - - + -
75B PHE* 3.0 23.9 + + + +
76B THR* 3.9 2.2 - - - +
78B SER* 1.3 79.7 - - - +
80B LEU* 1.3 53.4 + - - +
82B SER* 2.6 21.3 + - - -
83B TRP* 2.7 55.1 + + + -
128B GLN* 5.9 1.8 - - - -
159B ILE* 3.3 34.1 - - + -
160B ASN* 4.0 15.0 - - - -
163B MET* 3.8 21.8 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 4.1 37.7 - - + -
154A ILE* 5.7 0.4 - - + -
76B THR* 2.9 25.6 + - + +
77B MET* 3.7 22.4 - - + +
79B PHE* 1.3 77.0 - - - +
81B CYS* 1.3 57.6 + - - +
83B TRP* 3.3 10.5 + - + +
84B LEU* 2.8 49.3 + - + +
121B PHE* 4.7 4.7 - - + -
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Residues in contact with CYS 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B MET* 2.7 47.0 + - - +
78B SER* 3.9 4.5 - - - +
80B LEU* 1.3 74.2 - - - +
82B SER* 1.3 55.3 + - - +
84B LEU* 3.0 3.3 + - - -
85B LEU* 2.6 39.3 + - - +
41F PHE* 3.4 54.7 - - + +
44F PHE* 4.0 11.2 - - - -
45F PRO* 4.8 2.5 - - + -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER 2.8 17.9 + - - -
79B PHE* 2.6 26.0 + - - -
81B CYS* 1.3 74.4 - - - +
83B TRP* 1.3 63.0 + - - +
85B LEU* 4.2 5.3 - - - +
86B PHE* 3.3 21.1 + - - +
128B GLN* 3.0 32.7 + - - +
155B VAL* 5.4 4.3 - - - -
159B ILE* 3.7 20.6 - - - +
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Residues in contact with TRP 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 4.2 11.0 - - + -
153A ASN* 4.6 9.9 - - + -
154A ILE* 3.8 30.5 - - + -
157A LEU* 5.0 3.4 - - + -
79B PHE* 2.7 56.3 + + + +
80B LEU* 3.7 13.0 - - + +
82B SER* 1.3 73.9 + - - +
84B LEU* 1.3 57.2 + - - +
87B ALA* 3.0 16.8 + - - +
121B PHE* 4.9 4.3 - - + -
124B SER* 2.6 30.3 + - - +
125B ILE* 3.4 37.6 + - + +
128B GLN* 3.2 45.6 - - + +
129B VAL* 3.2 30.8 - - + +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 2.8 37.6 + - + +
81B CYS 3.7 1.8 - - - +
83B TRP* 1.3 75.4 - - - +
85B LEU* 1.3 66.2 + - - +
87B ALA* 3.1 13.9 + - - +
88B MET* 3.2 18.1 + - + +
117B PHE* 3.9 26.0 - - + -
121B PHE* 3.4 22.4 - - + -
41F PHE* 3.8 29.3 - - + -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B CYS 2.6 21.6 + - - +
82B SER* 4.2 4.9 - - - +
84B LEU* 1.3 74.5 - - - +
86B PHE* 1.3 72.7 + - + +
88B MET* 3.5 11.2 + - + +
89B VAL* 3.6 14.9 + - + +
34F VAL* 5.3 1.1 - - + +
37F VAL* 4.3 7.2 - - + -
38F PHE* 3.4 56.8 - - + +
41F PHE* 3.7 24.1 - - + -
42F ILE* 5.4 3.1 - - + +
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 3.3 13.4 + - - +
84B LEU 3.2 0.2 - - - -
85B LEU* 1.3 86.3 - - + +
87B ALA* 1.3 65.0 + - - +
89B VAL* 3.0 27.1 + - + +
90B TRP* 3.0 17.3 + - + -
128B GLN* 3.5 19.3 - - - -
148B ILE* 4.8 13.2 - - + -
151B VAL* 3.8 23.6 - - + -
152B GLN* 3.2 54.7 - - + +
155B VAL* 3.9 27.1 - - + -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP 3.0 20.2 + - - +
84B LEU* 3.1 10.5 + - - +
86B PHE* 1.3 77.6 - - - +
88B MET* 1.3 60.9 + - - +
90B TRP* 3.2 7.8 + - - +
91B TRP* 3.0 22.9 + - - +
117B PHE* 4.3 6.3 - - + -
120B ALA* 4.1 4.5 - - - +
121B PHE* 3.7 27.6 - - + +
124B SER* 3.6 19.5 + - - -
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.2 11.3 + - + +
85B LEU* 3.6 10.8 - - - +
86B PHE 3.2 0.2 - - - -
87B ALA* 1.3 77.8 - - - +
89B VAL* 1.3 66.1 + - + +
91B TRP* 3.2 33.4 + - + +
92B LEU* 2.9 24.1 + - + +
117B PHE* 4.0 23.4 - - + -
30F ALA 5.2 1.8 - - - +
33F VAL* 3.6 33.7 - - + -
34F VAL* 4.8 13.5 - - + -
37F VAL* 4.1 29.4 - - + -
41F PHE* 6.4 0.4 - - + -
112F MET* 5.6 1.1 - - - -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.6 16.6 + - + +
86B PHE* 3.0 20.3 + - + +
88B MET* 1.3 79.8 - - + +
90B TRP* 1.3 62.1 + - - +
92B LEU* 3.2 9.7 + - + +
93B ILE* 3.0 22.4 + - + +
148B ILE* 3.5 37.9 - - + -
34F VAL* 6.1 6.7 - - + -
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Residues in contact with TRP 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 3.0 26.1 + - + +
87B ALA* 3.2 11.4 + - - +
89B VAL* 1.3 76.4 - - - +
91B TRP* 1.3 62.7 + - - +
93B ILE* 3.2 20.5 - - + +
94B ALA* 3.2 20.8 + - - +
111B VAL* 3.7 29.0 - - + +
114B ILE* 5.6 1.3 - - + +
120B ALA* 4.6 10.0 - - + +
123B PHE* 3.4 38.4 - + + -
124B SER* 4.5 4.0 - - - -
138B VAL* 4.6 4.0 - - + -
145B ALA* 3.2 41.5 - - + -
148B ILE* 3.7 24.4 - - + +
149B LEU* 3.9 21.3 - - + -
152B GLN* 2.6 28.7 + - - -
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Residues in contact with TRP 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA 3.0 12.6 + - - +
88B MET* 3.2 34.5 + - - +
90B TRP* 1.3 76.2 - - - +
92B LEU* 1.3 72.6 + - + +
94B ALA* 3.2 10.2 + - + +
95B PHE* 3.0 34.8 + + - +
100B LEU* 4.2 19.0 - - + +
114B ILE* 5.3 1.8 - - + -
116B SER* 4.3 6.7 - - - +
117B PHE* 3.9 43.5 - + + +
120B ALA* 3.8 15.0 - - + +
30F ALA* 3.9 25.1 - - + -
33F VAL* 5.3 2.9 - - + -
105F HIS* 3.2 41.5 - + - -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 2.9 17.7 + - + +
89B VAL* 3.6 8.7 - - + +
91B TRP* 1.3 81.8 - - + +
93B ILE* 1.3 65.0 + - + +
95B PHE* 2.9 9.1 + - - +
96B ALA* 2.7 30.5 + - + +
27F PHE* 3.5 27.6 - - + -
30F ALA* 4.2 13.9 - - + +
31F LEU* 3.8 25.8 - - + -
34F VAL* 4.1 21.3 - - + -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 3.0 12.6 + - + +
90B TRP* 3.2 40.8 - - + +
92B LEU* 1.3 80.8 - - + +
94B ALA* 1.3 61.8 + - - +
96B ALA* 4.0 6.0 - - + +
97B HIS* 3.2 23.6 + - - +
110B CYS* 5.5 2.4 - - + +
111B VAL* 4.9 5.8 - - + -
142B CYS* 4.4 13.9 - - + -
144B LEU* 3.4 43.7 - - + -
145B ALA* 3.5 21.3 - - + +
148B ILE* 3.5 15.0 - - + -
----------------------------------------------------------
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TRP 3.2 11.7 + - - +
91B TRP 3.2 10.9 + - - +
92B LEU 3.1 0.2 - - - -
93B ILE* 1.3 81.6 - - + +
95B PHE* 1.3 56.1 + - - +
97B HIS* 3.4 1.8 + - - +
98B GLY 2.9 21.0 + - - -
99B ASP* 3.0 34.6 + - - +
100B LEU* 4.3 6.3 - - + -
110B CYS* 6.0 2.0 - - - -
111B VAL* 5.9 3.8 - - + -
114B ILE* 3.8 28.3 - - + -
----------------------------------------------------------
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TRP* 3.0 38.7 + + - +
92B LEU* 2.9 12.7 + - - +
94B ALA* 1.3 76.3 - - - +
96B ALA* 1.3 62.1 + - - +
98B GLY* 2.8 18.4 + - - +
100B LEU* 3.9 19.9 - - + +
6F CYS* 5.5 1.8 - - + -
12F SER* 2.7 42.6 - - - -
13F ALA* 5.0 0.2 - - - -
15F TYR* 4.6 11.7 - - + -
16F ARG* 3.9 4.5 - - + +
26F CYS* 4.5 27.1 - - + -
27F PHE* 4.3 32.1 - + + -
30F ALA* 5.1 4.9 - - + -
105F HIS* 5.8 1.1 - + - -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 2.7 22.0 + - + +
93B ILE* 4.0 10.3 - - + +
95B PHE* 1.3 73.4 - - - +
97B HIS* 1.3 63.7 + - - +
98B GLY 3.2 0.7 + - - -
16F ARG* 3.4 12.6 - - - +
27F PHE* 4.5 20.6 - - + -
----------------------------------------------------------
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Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE 3.2 14.7 + - - +
94B ALA* 3.6 5.6 - - - +
96B ALA* 1.3 80.0 - - - +
98B GLY* 1.3 57.2 + - - +
99B ASP* 3.4 20.0 + - + +
107B ASN* 3.2 23.1 + - - -
108B VAL 3.1 28.4 + - - -
109B PRO* 4.4 0.7 - - + -
110B CYS* 3.3 30.9 - - - -
141B GLU* 4.4 9.9 + - + +
142B CYS* 4.1 5.2 - - - -
16F ARG* 3.9 8.5 - - - +
----------------------------------------------------------
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ALA 2.9 3.3 + - - -
95B PHE* 2.8 20.7 + - - -
97B HIS* 1.3 78.2 - - - +
99B ASP* 1.3 60.0 + - - +
100B LEU* 3.3 3.4 - - - -
102B PRO* 3.2 24.6 - - - +
107B ASN* 4.6 2.8 + - - -
13F ALA* 3.4 16.0 - - - +
16F ARG* 3.4 16.8 - - - -
17F VAL* 5.2 2.1 + - - +
----------------------------------------------------------
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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