Contacts of the helix formed by residues 33 - 65 (chain B) in PDB entry 3OAX
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 GLU 33 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA* 1.3 75.7 - - - +
34B PRO* 1.3 69.9 - - + +
35B TRP* 3.1 34.7 - - + +
36B GLN* 3.0 36.7 + - + +
37B PHE* 3.5 4.2 - - - -
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Residues in contact with PRO 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508A HTG 3.8 29.8 - - - +
29B TYR* 3.6 48.2 - - + +
32B ALA 3.8 3.1 - - - +
33B GLU* 1.3 91.2 - - + +
35B TRP* 1.3 65.2 + - + +
37B PHE* 3.2 14.4 + - + +
38B SER* 3.3 12.0 + - - -
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Residues in contact with TRP 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 5.6 4.7 - - - +
1508A HTG 3.5 40.7 + - + +
33B GLU* 3.2 39.0 - - + +
34B PRO* 1.3 79.8 - - + +
36B GLN* 1.3 83.5 + - + +
38B SER* 3.1 12.2 - - - -
39B MET* 3.0 53.6 + - + +
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Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA* 2.9 32.4 - - - +
33B GLU* 3.0 24.8 + - + +
35B TRP* 1.3 118.8 - - + +
37B PHE* 1.3 58.8 + - - +
38B SER 3.1 0.4 - - - -
39B MET* 3.1 7.5 + - - +
40B LEU* 3.0 31.0 + - - +
183B MET* 4.5 13.9 - - + -
286B ILE* 4.7 10.4 - - - +
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLN 3.6 22.7 - - - -
29B TYR* 3.7 27.1 - + + -
31B LEU* 5.0 0.7 - - + -
32B ALA* 3.5 29.6 - - + -
33B GLU 3.5 11.0 - - - -
34B PRO* 3.2 6.5 + - + +
36B GLN* 1.3 76.0 - - + +
38B SER* 1.3 58.1 + - - +
40B LEU* 3.3 10.8 + - + +
41B ALA* 2.9 28.8 + - - +
98B SER* 3.5 16.8 - - - +
101B GLY* 3.7 18.8 - - - -
183B MET* 3.6 39.5 - - + -
185B CYS* 3.6 25.4 - - - -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 4.1 12.6 + - - +
309A MET* 5.3 0.3 - - - +
1508A HTG 3.7 52.4 + - - +
34B PRO 3.3 4.8 + - - -
35B TRP* 3.1 16.8 + - - -
37B PHE* 1.3 80.0 - - - +
39B MET* 1.3 55.2 + - - +
41B ALA* 3.3 7.7 + - - +
42B ALA* 2.8 30.5 + - - +
98B SER 5.5 0.2 - - - -
99B LEU* 6.1 1.4 - - - +
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Residues in contact with MET 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1410A 4E6 4.1 29.2 - - + -
1508A HTG 4.1 26.0 - - + -
35B TRP* 3.0 33.7 + - + +
36B GLN* 3.1 15.0 + - - +
38B SER* 1.3 74.9 - - - +
40B LEU* 1.3 61.3 + - + +
42B ALA* 3.4 3.2 + - + +
43B TYR* 3.0 27.9 + - - +
1407B 4E6 3.5 33.2 - - + +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN 3.0 17.6 + - - +
37B PHE* 3.6 10.5 - - + +
39B MET* 1.3 74.4 - - + +
41B ALA* 1.3 60.7 + - - +
43B TYR* 3.3 9.6 - - + +
44B MET* 3.0 32.1 + - - +
98B SER* 4.0 10.1 - - - +
183B MET* 3.9 34.1 - - + -
185B CYS* 4.4 11.0 - - + -
289B THR* 4.0 23.3 - - + -
290B ILE* 6.3 1.3 - - + -
293B PHE* 4.0 34.8 - - + -
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 2.9 26.5 - - + -
37B PHE 2.9 17.3 + - - +
38B SER* 3.5 4.5 - - - +
40B LEU* 1.3 74.9 - - - +
42B ALA* 1.3 63.1 + - - +
44B MET* 3.3 1.3 + - - -
45B PHE* 2.9 18.5 + - - +
95B LEU* 3.1 15.7 - - + +
98B SER* 3.8 18.1 - - - -
99B LEU* 3.9 16.2 - - + +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A VAL* 4.0 10.9 - - + +
308A MET* 3.7 12.3 - - + +
1410A 4E6 5.2 1.1 - - + -
1508A HTG 3.5 26.2 - - + -
38B SER 2.8 17.1 + - - +
39B MET* 3.6 13.9 - - + +
41B ALA* 1.3 74.7 - - - +
43B TYR* 1.3 64.1 + - - +
45B PHE* 3.0 14.9 + - - +
46B LEU* 3.0 20.0 + - - +
1407B 4E6 4.5 5.6 - - + -
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Residues in contact with TYR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B MET 3.0 13.8 + - - +
40B LEU* 3.3 11.9 - - + +
42B ALA* 1.3 76.2 - - - +
44B MET* 1.3 59.7 + - - +
46B LEU* 3.3 5.2 + - - +
47B LEU* 3.0 45.9 + - + +
293B PHE* 2.6 60.1 + + + -
294B PHE* 3.5 9.6 - + - -
297B THR* 3.1 25.9 - - + +
1407B 4E6 3.7 44.8 - - + +
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Residues in contact with MET 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU 3.0 20.9 + - - +
41B ALA 3.8 4.3 - - - +
43B TYR* 1.3 72.8 - - - +
45B PHE* 1.3 67.4 + - - +
47B LEU* 3.6 14.3 - - + +
48B ILE* 2.9 31.9 + - - +
91B PHE* 3.5 42.2 - - + +
94B THR* 3.3 39.7 - - + +
95B LEU* 4.2 17.9 - - + -
293B PHE* 3.7 21.3 - - + -
296B LYS* 3.8 17.5 - - + -
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Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 4.1 26.7 - - + -
57A LEU* 5.8 1.8 - - + -
304A VAL* 3.9 28.9 - - + -
307A ILE* 3.4 38.1 - - + -
308A MET* 4.3 10.1 - - - -
317A MET* 4.4 16.8 - - + -
41B ALA 2.9 13.8 + - - +
42B ALA* 3.0 12.1 + - - +
44B MET* 1.3 78.3 - - - +
46B LEU* 1.3 59.9 + - + +
48B ILE* 3.3 4.8 + - + +
49B MET* 2.8 59.2 + - + +
95B LEU* 4.0 21.5 - - + +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.7 21.5 - - + +
54A ILE* 4.1 15.9 - - + -
300A VAL* 4.6 1.6 - - + -
304A VAL* 4.1 19.3 - - + -
1410A 4E6 3.6 33.0 - - + -
42B ALA 3.0 14.8 + - - +
43B TYR 3.7 5.4 - - - +
45B PHE* 1.3 74.4 - - + +
47B LEU* 1.3 61.2 + - - +
49B MET* 3.2 4.6 + - - +
50B LEU* 2.8 33.1 + - - +
1407B 4E6 3.4 52.9 - - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.0 45.8 + - + +
44B MET* 3.2 20.2 + - + +
46B LEU* 1.3 75.1 - - - +
48B ILE* 1.3 54.6 + - - +
50B LEU* 3.8 3.1 - - + +
51B GLY* 2.6 36.0 + - - -
87B VAL* 4.7 1.0 - - - +
91B PHE* 4.2 13.0 - - + -
296B LYS* 3.8 29.8 - - + +
297B THR* 4.0 27.6 - - + -
300B VAL* 4.1 21.0 - - + +
1407B 4E6 5.0 12.5 - - + +
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1322A PLM 4.5 26.5 - - + -
44B MET 2.9 20.6 + - - +
45B PHE* 3.5 5.6 - - + +
47B LEU* 1.3 76.3 - - - +
49B MET* 1.3 62.9 + - - +
52B PHE* 2.9 36.9 + - + +
87B VAL* 3.9 21.5 - - + +
88B PHE* 5.6 0.4 - - + -
91B PHE* 3.6 46.2 - - + +
92B THR* 4.1 11.2 - - + +
95B LEU* 3.9 24.9 - - + -
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Residues in contact with MET 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET 4.2 6.6 - - - +
50A LEU* 4.0 8.6 - - + +
53A PRO* 4.1 21.3 - - + +
54A ILE* 3.8 46.9 - - + +
57A LEU* 4.3 15.7 - - + -
1322A PLM 4.0 31.4 - - + -
45B PHE* 2.8 49.5 + - + +
46B LEU* 3.4 4.0 - - - +
48B ILE* 1.3 78.8 - - + +
50B LEU* 1.3 57.4 + - - +
52B PHE* 5.1 1.3 - - - -
53B PRO* 3.1 21.6 - - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.0 32.1 - - + +
49A MET* 4.4 11.2 - - + -
50A LEU* 4.0 26.5 - - + -
1410A 4E6 5.1 0.7 - - + -
46B LEU* 2.8 15.9 + - + +
47B LEU* 3.8 4.0 - - + +
49B MET* 1.3 77.5 - - - +
51B GLY* 1.3 67.0 + - - +
52B PHE 3.2 1.1 - - - -
53B PRO* 3.1 4.8 - - - +
54B ILE* 3.0 43.7 + - + +
300B VAL* 4.6 11.7 - - + -
304B VAL* 6.1 0.7 - - + -
1407B 4E6 3.8 35.4 - - + -
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU 2.6 19.3 + - - -
50B LEU* 1.3 73.6 - - - +
52B PHE* 1.3 60.1 + - - +
54B ILE* 3.9 1.6 - - - -
55B ASN* 2.6 37.5 + - - +
84B LEU* 4.3 1.0 - - - +
87B VAL* 4.0 10.7 - - - +
299B ALA 4.0 0.9 - - - -
300B VAL* 3.3 24.1 - - - +
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1322A PLM 3.8 37.9 - - + -
1323A PLM 6.2 3.1 - - + -
48B ILE* 2.9 20.0 + - + +
49B MET* 5.1 2.0 - - - -
51B GLY* 1.3 78.0 - - - +
53B PRO* 1.3 80.4 - - + +
56B PHE* 2.9 43.3 + + + +
84B LEU* 3.8 10.7 - - + +
87B VAL* 4.2 7.3 - - + +
88B PHE* 3.3 36.8 - + + -
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Residues in contact with PRO 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 3.8 30.9 - - + +
53A PRO* 5.4 4.9 - - + -
49B MET* 3.1 27.8 - - - +
50B LEU 3.1 12.6 - - - +
52B PHE* 1.3 105.8 - - + +
54B ILE* 1.3 55.2 + - - +
56B PHE* 3.9 3.4 - - + +
57B LEU* 2.9 33.6 + - - +
1322B PLM 4.3 17.9 - - + +
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 4.8 1.8 - - + -
46A LEU* 4.1 19.3 - - + -
49A MET* 3.6 20.2 - - + -
50B LEU* 3.0 27.6 + - + +
51B GLY* 3.9 11.0 - - - -
53B PRO* 1.3 78.1 - - - +
55B ASN* 1.3 70.9 + - - +
57B LEU* 3.9 3.7 - - + +
58B THR* 2.8 26.9 + - - -
300B VAL* 4.3 8.3 - - + +
303B PRO* 3.8 21.7 - - + +
304B VAL* 3.7 31.4 - - + +
307B ILE* 4.6 15.7 - - + -
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLY* 2.6 30.3 + - - +
54B ILE* 1.3 83.4 - - - +
56B PHE* 1.3 65.5 + - - +
58B THR* 3.1 6.9 + - - -
59B LEU* 3.0 18.5 + - - +
80B ALA* 3.5 25.5 - - - +
83B ASP* 2.7 36.7 - - - +
84B LEU* 3.7 10.1 - - + -
87B VAL* 4.8 0.2 - - - +
299B ALA 2.6 27.3 + - - -
303B PRO* 3.4 13.6 - - - +
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Residues in contact with PHE 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 2.9 39.4 + + + +
53B PRO* 3.9 4.5 - - + +
55B ASN* 1.3 76.6 - - - +
57B LEU* 1.3 54.2 + - - +
59B LEU* 2.8 29.3 + - + +
60B TYR* 2.7 67.3 + + + +
84B LEU* 4.0 10.0 - - + +
1322B PLM 5.3 10.3 - - + -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 4.4 15.9 - - + -
53B PRO 2.9 21.2 + - - +
54B ILE* 3.9 7.4 - - + +
56B PHE* 1.3 79.9 - - - +
58B THR* 1.3 65.3 + - - +
60B TYR* 4.5 7.9 - - + -
61B VAL* 3.0 42.1 + - + +
307B ILE* 5.0 4.9 - - + -
313B PHE* 5.1 1.8 - - + -
317B MET* 3.4 37.5 - - + -
320B THR* 5.3 3.4 - - + -
321B LEU* 3.6 30.5 - - + -
1322B PLM 4.6 14.3 - - + +
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 2.8 19.1 + - - +
55B ASN* 3.1 9.5 + - - -
57B LEU* 1.3 79.5 - - - +
59B LEU* 1.3 61.8 + - - +
62B THR* 3.1 28.4 + - - +
76B LEU* 4.1 10.3 - - + +
77B LEU* 4.6 0.8 - - - +
80B ALA* 4.0 17.0 - - + -
303B PRO* 3.4 21.4 - - + +
306B TYR* 4.0 19.3 - - + -
307B ILE* 5.3 1.4 - - - +
313B PHE* 3.9 28.6 - - + -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1323A PLM 5.0 10.1 - - + -
55B ASN 3.0 11.8 + - - +
56B PHE* 2.8 27.3 + - + +
58B THR* 1.3 76.7 - - - +
60B TYR* 1.3 63.3 + - - +
62B THR 3.5 1.2 + - - -
63B VAL* 3.3 38.2 + - + +
77B LEU* 3.1 40.8 - - + +
80B ALA* 4.2 6.3 - - + +
81B VAL* 4.2 15.7 - - + -
84B LEU* 3.8 24.5 - - + -
----------------------------------------------------------
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 2.7 47.8 + + + +
57B LEU* 3.9 9.4 - - + +
59B LEU* 1.3 73.5 - - - +
61B VAL* 1.3 66.8 + - + +
63B VAL* 3.7 4.4 + - - +
64B GLN* 3.0 56.3 + - + +
320B THR* 3.9 14.4 - - + -
339B LYS* 5.2 8.0 + - - -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.0 40.2 + - + +
60B TYR* 1.3 77.6 - - - +
62B THR* 1.3 63.5 + - - +
64B GLN* 4.5 0.7 - - - -
65B HIS* 3.1 24.8 + - - +
68B LEU* 4.0 9.4 - - + -
313B PHE* 3.8 23.8 - - + -
316B CYS* 3.9 7.9 - - + -
317B MET* 3.8 36.1 - - + +
320B THR* 3.8 23.1 - - + +
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Residues in contact with THR 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR* 3.1 19.3 + - - +
59B LEU 3.7 4.5 - - - -
60B TYR 3.3 0.4 - - - -
61B VAL* 1.3 75.4 - - - +
63B VAL* 1.3 68.8 + - - +
65B HIS 3.0 10.7 + - - +
68B LEU* 4.0 19.4 - - + +
69B ARG* 2.8 33.6 + - - +
73B ASN* 4.3 18.7 + - + +
77B LEU* 3.9 26.9 + - + +
306B TYR* 4.7 4.9 + - - -
313B PHE* 4.1 10.7 - - - -
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.3 30.2 + - + +
60B TYR* 4.1 4.3 - - - +
62B THR* 1.3 79.2 - - - +
64B GLN* 1.3 60.9 + - - +
66B LYS 4.7 0.2 + - - -
69B ARG* 2.9 23.2 + - - +
77B LEU* 4.5 12.8 - - + -
339B LYS* 5.7 0.5 - - - +
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 3.0 36.2 + - + +
61B VAL 3.9 0.2 - - - +
62B THR 3.1 0.2 - - - -
63B VAL* 1.3 78.3 - - - +
65B HIS* 1.3 89.2 + - + +
66B LYS 4.0 1.7 + - - -
319B THR* 6.0 0.6 - - - +
320B THR* 3.0 30.9 + - - +
338B SER* 4.3 2.2 - - - +
339B LYS* 3.1 71.0 + - + +
340B THR* 5.9 1.8 - - - +
----------------------------------------------------------
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Residues in contact with HIS 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.1 15.8 + - + +
62B THR 3.0 7.5 + - - +
64B GLN* 1.3 109.1 + - - +
66B LYS* 1.3 54.5 + - - +
67B LYS 3.3 1.1 - - - -
68B LEU* 3.0 18.9 + - + +
69B ARG* 2.8 24.3 + - - -
316B CYS* 3.0 38.9 - - + +
319B THR* 4.4 0.9 - - - -
320B THR* 2.7 16.2 + - - -
337B VAL* 2.7 43.6 + - + -
338B SER* 3.1 18.2 + - - -
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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