Contacts of the helix formed by residues 70 - 101 (chain B) in PDB entry 2CKD
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL 3.3 5.1 + - - +
67B GLU 3.4 4.6 + - - -
68B ALA 4.7 0.2 - - - -
69B ILE* 1.3 86.8 - - + +
71B ALA* 1.3 69.0 + - - +
72B GLU* 3.4 8.1 + - - +
73B ALA* 3.0 37.7 + - + +
74B ALA* 3.0 12.1 + - - +
233B ARG* 3.0 35.8 + - - -
236B ARG* 4.2 17.0 + - + -
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 3.9 27.6 + - - +
70B ASP* 1.3 75.0 + - - +
72B GLU* 1.3 60.6 + - - +
74B ALA* 3.1 5.6 + - - +
75B ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP* 3.3 7.0 + - - +
71B ALA* 1.3 77.9 - - - +
73B ALA* 1.3 65.8 + - - +
75B ALA* 3.6 7.4 + - + +
76B MET* 3.0 28.1 + - - +
233B ARG* 3.8 32.8 + - - +
293B PRO* 4.1 23.1 - - + +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP* 3.0 30.8 + - + +
72B GLU* 1.3 78.4 - - - +
74B ALA* 1.3 56.0 + - - +
76B MET* 2.8 19.9 + - - +
77B VAL* 2.9 19.0 + - + +
233B ARG* 3.8 23.5 - - + +
234B PHE* 4.7 1.2 - - + -
237B VAL* 3.7 29.8 - - + -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 5.3 0.7 - - - +
63B VAL 5.4 0.4 - - - +
66B VAL* 3.5 28.7 - - + +
67B GLU* 3.4 34.3 - - + +
70B ASP 3.0 9.8 + - - +
71B ALA 3.1 5.1 + - - +
73B ALA* 1.3 75.3 - - - +
75B ALA* 1.3 62.2 + - - +
77B VAL* 3.6 3.1 - - - +
78B GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY* 6.5 0.4 - - - -
67B GLU* 4.9 1.0 + - - -
71B ALA 2.9 14.8 + - - +
72B GLU* 3.8 9.0 - - + +
73B ALA 3.2 0.2 - - - -
74B ALA* 1.3 76.2 - - - +
76B MET* 1.3 56.5 + - - +
78B GLU* 3.3 8.7 + - - +
79B HIS* 2.8 30.2 + - - +
291B GLY 4.3 19.1 - - - +
292B VAL* 4.1 12.3 - - + +
293B PRO* 4.6 4.0 - - + -
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLU 3.0 18.3 + - - +
73B ALA* 2.8 14.3 + - - +
75B ALA* 1.3 68.5 - - - +
77B VAL* 1.3 66.5 + - - +
79B HIS* 3.2 4.6 + - - +
80B MET* 2.9 26.5 + - - +
226B TRP* 3.0 49.6 - - + +
229B GLN* 4.0 36.3 - - - +
230B MET* 4.3 14.6 - - + +
233B ARG* 4.5 8.1 - - + -
234B PHE* 4.4 14.2 - - + -
292B VAL* 4.7 0.9 - - - -
293B PRO* 4.1 20.0 - - + -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B MET* 3.4 44.4 - - + +
58B LEU* 4.0 11.0 - - + +
66B VAL* 4.4 11.2 - - + -
73B ALA* 2.9 23.1 + - + +
74B ALA* 3.6 11.4 - - - +
76B MET* 1.3 76.2 - - - +
78B GLU* 1.3 63.6 + - - +
80B MET* 3.3 6.9 + - - +
81B ARG* 3.1 33.7 + - - +
234B PHE* 3.7 23.3 - - + -
237B VAL* 5.2 1.6 - - + -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE 3.5 13.5 - - - +
101A ASP* 3.4 42.6 - - - +
102A GLY* 3.8 6.9 - - - +
180A ARG* 4.9 4.6 + - - -
74B ALA 3.0 17.5 + - - +
75B ALA* 3.5 8.8 - - - +
77B VAL* 1.3 72.8 - - - +
79B HIS* 1.3 82.8 + - - +
81B ARG* 3.0 18.5 + - - +
82B SER* 2.6 47.5 + - - -
287B ARG 4.5 6.0 - - - +
289B GLY 5.6 2.1 + - - -
292B VAL* 5.8 2.1 - - - +
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 2.8 19.7 + - - +
76B MET* 3.2 6.0 + - - +
78B GLU* 1.3 82.7 + - - +
80B MET* 1.3 54.8 + - - +
82B SER* 3.3 2.6 + - - -
83B TYR* 2.7 60.2 + + + +
226B TRP* 3.5 19.1 + + + -
282B MET* 3.7 31.0 - - + +
288B TRP* 4.1 5.2 - + - -
289B GLY 5.4 1.6 - - - -
292B VAL* 3.5 33.7 - - + -
301B PHE* 3.7 31.9 - + - -
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Residues in contact with MET 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 3.6 46.9 - - + +
21B VAL* 5.5 0.4 - - - -
24B ALA* 4.7 2.9 - - + -
54B TRP* 5.0 0.9 - - + -
57B MET* 5.1 0.9 - - + -
58B LEU* 3.8 30.3 - - + -
76B MET 2.9 12.4 + - - +
77B VAL* 3.8 5.2 - - - +
79B HIS* 1.3 77.1 + - - +
81B ARG* 1.3 66.8 + - - +
83B TYR* 4.4 4.9 - - + -
84B GLN* 2.9 47.7 + - + +
230B MET* 5.2 9.4 - - + +
234B PHE* 3.5 31.2 - - + -
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 3.1 42.9 + - - +
101A ASP* 4.6 3.2 + - - -
24B ALA* 4.2 21.7 - - - +
27B ALA* 4.5 4.5 - - + +
28B GLU* 3.7 31.4 - - + +
31B ARG* 4.6 7.9 - - - +
57B MET 5.0 0.6 + - - -
58B LEU* 3.3 40.8 + - + +
59B ASP 4.8 0.8 + - - -
60B PRO* 4.7 6.7 - - - +
63B VAL* 4.5 12.3 - - - +
77B VAL* 3.1 24.7 + - - +
78B GLU* 3.0 22.5 + - - +
80B MET* 1.3 77.7 - - - +
82B SER* 1.3 64.7 + - - +
84B GLN* 3.3 1.7 + - - +
85B ALA* 3.0 20.1 + - - +
287B ARG* 4.3 3.3 - - - +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 2.6 33.4 + - - -
79B HIS* 3.6 7.2 - - - -
81B ARG* 1.3 76.9 - - - +
83B TYR* 1.3 57.1 + - - +
85B ALA* 2.9 4.3 + - - +
86B VAL* 2.8 35.5 + - - +
282B MET* 4.0 5.4 - - - -
287B ARG* 2.7 53.3 + - - +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B HIS* 2.7 41.0 + + + +
80B MET* 4.0 4.5 - - + +
82B SER* 1.3 73.0 - - - +
84B GLN* 1.3 80.6 + - + +
86B VAL* 3.1 3.1 + - + +
87B ARG* 2.9 36.1 + - - +
217B GLU* 2.7 30.4 + - - -
278B ALA* 3.7 24.0 - - + -
282B MET* 3.8 26.8 - - + +
301B PHE* 5.8 3.8 - + - -
302B ALA* 3.2 21.1 - - + +
304B PHE* 3.6 18.9 - + - -
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 6.0 0.4 - - - +
21B VAL* 3.5 34.8 - - + +
24B ALA* 3.9 25.4 - - + -
25B ARG* 5.0 6.1 + - + +
80B MET* 2.9 37.1 + - + +
81B ARG 3.9 0.7 - - - +
83B TYR* 1.3 90.0 - - - +
85B ALA* 1.3 57.6 + - - +
87B ARG* 3.2 45.3 + - - +
88B THR* 2.8 38.0 + - - +
186B GLU* 4.9 0.2 - - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 6.2 0.2 - - - -
25B ARG* 6.1 0.9 - - - +
28B GLU* 3.9 31.2 - - + +
35B LEU* 3.5 18.8 - - + +
36B ILE* 3.6 14.0 - - + +
81B ARG 3.0 12.6 + - - +
82B SER* 2.9 11.8 + - - +
84B GLN* 1.3 76.5 - - - +
86B VAL* 1.3 58.6 + - - +
89B ASN* 2.8 32.6 + - - +
287B ARG* 4.5 2.0 - - - +
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.8 9.6 - - + -
82B SER 2.8 21.4 + - - +
83B TYR* 3.6 4.0 - - + +
85B ALA* 1.3 75.9 - - - +
87B ARG* 1.3 52.2 + - - +
89B ASN* 3.2 5.9 + - - +
90B PHE* 2.7 32.2 + - - +
281B GLU* 3.5 34.2 - - + +
282B MET* 3.7 31.0 - - + -
285B VAL* 3.8 27.6 - - + -
287B ARG* 4.1 9.0 - - + -
304B PHE* 4.2 8.1 - - + -
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 4.0 17.8 - - - +
83B TYR* 2.9 19.1 + - + +
84B GLN* 3.2 44.5 + - - +
86B VAL* 1.3 75.3 - - - +
88B THR* 1.3 69.4 + - - +
90B PHE* 3.1 1.9 + - - -
91B PHE* 2.9 39.2 + - + -
186B GLU* 2.6 36.9 + - - +
187B GLY* 4.3 8.9 - - - -
190B MET* 6.3 0.4 - - - +
217B GLU* 2.9 41.5 + - - -
304B PHE* 3.3 29.2 - - + -
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.4 26.5 + - - +
36B ILE* 3.9 26.7 - - + -
84B GLN* 2.8 25.9 + - - +
85B ALA 3.8 2.5 - - - -
87B ARG* 1.3 79.6 - - - +
89B ASN* 1.3 64.1 + - - +
92B ASP* 3.0 28.2 + - - +
116B ARG* 3.3 11.5 + - - +
119B ARG* 3.6 26.5 - - - +
186B GLU* 4.6 7.0 + - - -
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.1 30.8 + - + +
36B ILE* 3.6 14.8 - - + +
85B ALA 2.8 18.5 + - - +
86B VAL* 3.2 6.2 - - - +
88B THR* 1.3 78.6 - - - +
90B PHE* 1.3 63.4 + - - +
92B ASP* 3.4 6.1 + - - +
93B THR* 3.0 34.2 + - - -
281B GLU* 4.7 4.7 - - - +
284B ARG* 4.9 3.6 + - - -
285B VAL* 4.6 11.8 - - - +
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL 2.7 19.2 + - - +
87B ARG* 3.1 5.6 + - - +
89B ASN* 1.3 73.5 + - - +
91B PHE* 1.3 88.7 + + - +
93B THR* 3.0 17.0 + - - -
94B TYR* 3.1 13.7 + - + +
215B ALA* 5.0 2.5 - - + -
276B GLN* 4.2 20.9 - - + -
281B GLU* 4.0 20.9 - - - +
304B PHE* 3.6 48.9 - + + -
305B VAL 5.0 0.2 - - - -
306B THR* 4.0 24.2 - - - -
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 2.9 51.2 + - + -
90B PHE* 1.3 87.7 - + - +
92B ASP* 1.3 67.6 + - - +
94B TYR* 3.0 15.5 + - + +
95B PHE* 3.0 15.9 + - - +
116B ARG* 3.5 17.3 - - - +
184B LEU* 3.4 31.9 - - + -
186B GLU* 3.8 29.2 - - + -
215B ALA* 3.9 18.8 - - + -
216B VAL 4.2 8.7 - - - -
217B GLU* 3.7 26.5 - - + -
304B PHE* 4.2 10.5 - + - -
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 5.1 4.7 - - - +
88B THR* 3.0 24.3 + - - +
89B ASN* 3.6 9.7 - - - +
91B PHE* 1.3 75.1 - - - +
93B THR* 1.3 65.5 + - - +
94B TYR 3.1 0.3 + - - -
95B PHE* 3.2 4.3 + - - +
96B ASN* 2.9 34.1 + - - +
116B ARG* 2.6 37.3 + - - +
119B ARG* 2.9 36.2 + - - -
120B LEU* 4.0 11.4 - - + +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASN* 3.0 24.2 + - - -
90B PHE* 3.0 11.6 + - - -
92B ASP* 1.3 78.4 - - - +
94B TYR* 1.3 51.9 + - - +
96B ASN* 3.2 11.0 + - + +
97B ASN* 2.7 51.2 + - - +
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 3.1 15.6 + - + +
91B PHE* 3.0 14.3 + - + +
93B THR* 1.3 74.4 - - - +
95B PHE* 1.3 92.7 + + - +
97B ASN* 3.0 11.8 + - + +
98B ALA* 2.8 27.8 + - + +
182B ALA* 3.8 6.2 - - + -
183B TRP 2.7 31.6 + - - -
184B LEU* 4.7 5.4 - - + -
213B ARG* 3.0 49.6 + - + +
214B ILE 3.0 4.5 + - - -
215B ALA* 3.4 30.3 - - + -
306B THR* 4.3 14.4 - - + -
307B ALA 5.3 0.4 - - - -
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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 PHE 3.0 9.7 + - - +
92B ASP* 3.6 7.4 - - - +
94B TYR* 1.3 103.8 - + - +
96B ASN* 1.3 57.7 + - - +
98B ALA* 2.8 21.1 + - - +
99B VAL* 3.0 16.5 + - - +
106B PHE* 3.6 30.6 - + + -
107B VAL 4.7 0.2 - - - -
108B ILE* 4.2 20.2 - - + -
116B ARG* 3.7 28.9 - - - -
120B LEU* 4.1 10.5 - - + -
122B TRP* 3.6 27.1 - + + -
128B VAL* 5.7 0.2 - - + -
182B ALA* 3.9 12.3 - - + -
184B LEU* 3.7 26.2 - - + -
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASP* 2.9 41.9 + - - +
93B THR* 3.8 10.2 + - + +
95B PHE* 1.3 70.1 - - - +
97B ASN* 1.3 62.9 + - - +
99B VAL* 3.2 8.0 + - - +
100B ILE* 3.1 39.5 + - + +
120B LEU* 4.1 20.0 - - - +
121B ASP 5.1 7.6 + - - +
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Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 2.7 39.0 + - - +
94B TYR* 3.4 10.3 - - + +
96B ASN* 1.3 75.1 - - - +
98B ALA* 1.3 64.8 + - - +
100B ILE* 3.8 11.0 - - - +
101B ASP* 3.0 30.9 + - - +
213B ARG* 3.7 10.3 - - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 2.8 12.9 + - + +
95B PHE* 2.8 10.3 + - - +
97B ASN* 1.3 81.9 - - - +
99B VAL* 1.3 58.7 + - - +
101B ASP 3.5 1.0 + - - -
102B GLY 3.3 4.2 + - - -
103B ILE* 2.9 46.9 + - + +
106B PHE* 3.6 19.1 - - + -
182B ALA* 3.9 8.5 - - + -
213B ARG* 3.7 14.4 - - + +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE 3.0 12.6 + - - +
96B ASN* 3.7 11.0 - - - +
97B ASN 3.2 0.6 - - - -
98B ALA* 1.3 72.6 - - - +
100B ILE* 1.3 64.4 + - + +
102B GLY* 2.8 21.1 + - - -
103B ILE 3.9 2.7 - - - +
104B ARG* 2.8 23.4 + - - +
106B PHE* 3.6 21.8 - - + -
121B ASP 4.8 8.3 - - - +
122B TRP* 3.8 22.9 - - + -
123B PRO* 3.7 31.9 - - + -
126B THR* 5.6 0.2 - - + -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASN* 3.1 30.3 + - + +
97B ASN* 3.8 12.3 - - - +
99B VAL* 1.3 82.2 - - + +
101B ASP* 1.3 67.5 + - - +
102B GLY* 3.0 6.4 + - - -
104B ARG* 5.4 0.7 + - - -
----------------------------------------------------------
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASN* 3.0 20.9 + - - +
98B ALA 4.1 1.3 - - - +
99B VAL 3.3 0.4 - - - -
100B ILE* 1.3 84.9 - - - +
102B GLY* 1.3 55.4 + - - +
103B ILE 3.6 2.2 - - - -
180B ARG* 3.2 24.1 + - - +
213B ARG* 2.7 36.9 + - - +
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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