Contacts of the helix formed by residues 42 - 71 (chain F) in PDB entry 3A68
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 VAL 42 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ARG* 3.5 1.9 + - - +
40F LYS* 5.0 4.3 - - - -
41F TYR* 1.3 81.0 - - - +
43F ASP* 1.3 66.4 + - - +
44F GLU* 3.7 10.8 - - + +
45F SER* 3.0 24.5 + - - +
46F GLU* 3.1 10.4 + - - +
157F ASN* 3.6 42.4 - - + +
159F ASP* 4.9 0.2 + - - -
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Residues in contact with ASP 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ARG* 3.0 26.0 + - - +
42F VAL* 1.3 74.2 - - - +
44F GLU* 1.3 58.4 + - - +
46F GLU* 3.3 12.5 + - - +
47F SER* 2.9 35.3 + - - +
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Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F VAL* 3.1 5.6 - - + +
43F ASP* 1.3 78.3 - - - +
45F SER* 1.3 57.9 + - - +
47F SER* 3.5 6.2 + - - -
48F ALA* 3.0 27.4 + - - +
153F VAL* 3.7 19.2 - - + +
156F LYS* 5.0 9.0 - - - +
157F ASN* 2.8 34.0 + - - +
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Residues in contact with SER 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F TYR* 4.0 16.6 - - - -
42F VAL* 3.0 22.9 + - - +
44F GLU* 1.3 76.1 - - - +
46F GLU* 1.3 66.2 + - - +
48F ALA* 3.2 3.0 + - - +
49F VAL* 3.0 27.7 + - - +
153F VAL* 4.1 11.5 + - - -
157F ASN* 3.9 15.4 + - - +
159F ASP* 4.2 10.6 + - - +
162F LEU* 3.9 21.2 - - - +
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ARG* 3.7 24.3 + - - +
41F TYR* 3.8 21.6 - - + -
42F VAL 3.1 10.6 + - - +
43F ASP* 3.5 17.0 - - - +
45F SER* 1.3 76.8 - - - +
47F SER* 1.3 62.9 + - - +
49F VAL 3.3 0.9 + - - -
50F ASN* 3.1 16.1 + - - +
102F GLN* 3.0 37.3 + - - +
107F GLY* 3.4 7.3 - - - -
108F LYS* 2.7 35.2 + - - +
110F LYS* 5.5 2.2 + - - -
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Residues in contact with SER 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F ASP* 2.9 20.4 + - - +
44F GLU* 3.8 6.7 - - - -
46F GLU* 1.3 79.1 + - - +
48F ALA* 1.3 57.7 + - - +
50F ASN* 3.2 11.2 + - - +
51F GLU* 2.9 27.3 + - - +
112F GLN* 5.2 0.5 - - - +
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLU 3.0 17.9 + - - +
45F SER 3.2 4.7 + - - +
47F SER* 1.3 73.2 - - - +
49F VAL* 1.3 65.1 + - - +
51F GLU* 3.3 8.9 + - - +
52F GLN* 3.0 23.2 + - - +
150F LEU* 3.7 22.5 - - + +
153F VAL* 3.8 26.0 - - + -
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Residues in contact with VAL 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F TYR* 3.3 20.9 - - - +
45F SER 3.0 14.0 + - - +
46F GLU 3.7 7.6 - - - +
47F SER 3.3 0.2 - - - -
48F ALA* 1.3 77.5 - - - +
50F ASN* 1.3 57.5 + - - +
52F GLN* 3.2 5.1 + - - +
53F ILE* 2.9 30.5 + - + +
98F LEU* 3.8 34.7 - - + +
101F TYR* 4.7 3.1 - - + -
102F GLN* 3.7 20.9 - - + +
150F LEU* 4.1 10.8 - - + -
162F LEU* 4.0 27.1 - - + -
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Residues in contact with ASN 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F GLU* 3.1 17.1 + - - +
47F SER* 3.2 11.8 + - - +
49F VAL* 1.3 75.6 - - - +
51F GLU* 1.3 63.1 + - - +
53F ILE* 3.3 15.5 + - - +
54F ASN* 3.1 21.1 + - - +
102F GLN* 3.0 19.4 + - - +
108F LYS 3.1 20.6 + - - -
109F VAL* 3.4 4.7 - - - -
110F LYS* 3.0 47.0 + - + +
112F GLN* 3.9 11.5 - - - +
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Residues in contact with GLU 51 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F SER 2.9 13.5 + - - +
48F ALA* 3.5 12.6 - - - +
49F VAL 3.2 0.2 - - - -
50F ASN* 1.3 76.6 - - - +
52F GLN* 1.3 58.5 + - - +
54F ASN* 3.2 5.6 + - - +
55F VAL* 3.0 32.3 + - + +
112F GLN* 3.4 18.0 + - - +
146F LYS* 5.7 5.6 + - + +
14O ILE* 3.1 33.4 - - - +
15O PHE* 3.7 18.9 - - - +
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Residues in contact with GLN 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ALA 3.0 15.5 + - - +
49F VAL* 3.2 4.2 + - - +
51F GLU* 1.3 73.5 - - - +
53F ILE* 1.3 66.5 + - - +
55F VAL* 3.1 18.7 + - - +
56F GLU* 2.9 49.9 + - - +
98F LEU* 3.6 21.1 - - + -
143F THR* 4.1 4.6 + - - +
146F LYS* 3.4 28.1 - - - +
147F LEU* 3.3 26.7 - - + +
150F LEU* 3.9 23.9 - - + +
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Residues in contact with ILE 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F VAL* 2.9 25.7 + - + +
50F ASN* 3.5 26.7 - - - +
51F GLU 3.3 0.2 - - - -
52F GLN* 1.3 78.1 - - - +
54F ASN* 1.3 57.1 + - - +
56F GLU* 3.3 2.4 + - - +
57F TYR* 2.9 32.9 + - + +
95F ALA* 3.9 8.0 - - + +
98F LEU* 3.5 28.2 - - + +
99F MET* 3.8 38.1 - - + +
102F GLN* 4.8 0.2 - - + -
109F VAL* 4.4 8.3 - - + -
110F LYS 5.9 0.9 - - - +
111F LEU* 3.7 28.9 - - + -
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Residues in contact with ASN 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 4.1 5.3 + - - -
50F ASN 3.1 6.8 + - - +
51F GLU* 3.2 9.6 + - - +
53F ILE* 1.3 79.2 - - - +
55F VAL* 1.3 59.5 + - - +
57F TYR* 3.9 4.0 - - - +
58F ASN* 2.9 53.2 + - - +
111F LEU* 6.4 0.2 - - - -
112F GLN* 3.4 46.2 - - + +
113F SER 3.1 22.4 + - - +
114F ILE* 4.3 2.6 - - - +
14O ILE 4.6 5.5 - - - +
15O PHE* 4.1 20.0 + - - +
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Residues in contact with VAL 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F GLU* 3.0 34.9 + - + +
52F GLN* 3.1 33.4 + - - +
54F ASN* 1.3 76.2 - - - +
56F GLU* 1.3 58.3 + - - +
58F ASN* 3.3 3.3 + - - +
59F VAL* 3.0 32.8 + - + +
143F THR* 4.3 19.1 - - + +
146F LYS* 4.2 27.8 - - + -
15O PHE* 4.0 28.4 - - + -
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Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLN* 2.9 44.3 + - - +
55F VAL* 1.3 72.1 - - - +
57F TYR* 1.3 66.7 + - - +
59F VAL* 3.2 3.8 + - - +
60F SER* 2.9 23.4 + - - -
91F GLU* 3.1 18.0 - - - +
94F HIS* 3.6 13.9 - - + +
95F ALA* 3.8 21.8 - - + +
98F LEU* 4.0 15.3 - - + -
143F THR* 3.7 11.3 - - - +
147F LEU* 3.9 10.9 - - - +
170F TYR* 4.4 5.1 - - - -
214F CA 2.5 29.7 - - - -
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Residues in contact with TYR 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 5.3 14.1 - + - -
60B SER* 4.9 2.9 + - - -
61B TYR* 3.6 40.3 - + - +
64B HIS* 2.6 41.8 + + - +
88B SER* 4.6 1.7 + - - -
53F ILE* 2.9 24.1 + - + +
54F ASN* 3.9 7.2 - - - +
56F GLU* 1.3 77.1 - - - +
58F ASN* 1.3 63.0 + - - +
60F SER* 3.3 12.3 + - - -
61F TYR* 3.0 22.2 + + + +
92F ARG* 3.8 22.4 + - + -
95F ALA* 3.8 21.9 - - + +
99F MET* 4.5 2.0 - - - -
111F LEU* 4.5 7.0 - - + -
114F ILE* 3.5 26.0 - - + +
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Residues in contact with ASN 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F ASN* 2.9 48.1 + - - +
55F VAL 3.7 3.8 - - - +
57F TYR* 1.3 78.4 - - - +
59F VAL* 1.3 61.0 + - - +
61F TYR* 3.2 6.8 + - - +
62F VAL* 3.0 28.5 + - - +
113F SER 4.1 3.8 - - - +
114F ILE* 3.2 25.9 - - - +
115F VAL* 3.4 27.5 + - - +
15O PHE* 3.9 24.9 - - + +
17O PRO* 4.4 6.0 - - + +
18O PHE* 5.8 0.4 - - - -
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Residues in contact with VAL 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F VAL* 3.0 26.8 + - + +
56F GLU* 3.2 1.8 + - - +
58F ASN* 1.3 72.9 - - - +
60F SER* 1.3 65.8 + - - +
62F VAL* 3.2 2.4 + - - +
63F TYR* 2.9 46.2 + - + -
91F GLU* 3.4 24.5 - - - +
139F LEU* 3.8 29.2 - - + -
140F GLU* 4.3 5.2 - - - +
143F THR* 3.4 24.2 - - + +
15O PHE* 5.0 7.2 - - + -
17O PRO* 6.1 0.7 - - + -
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Residues in contact with SER 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 4.9 2.8 + - - -
92B ARG* 4.4 4.3 + - - -
56F GLU 2.9 9.5 + - - -
57F TYR* 3.4 15.5 - - - -
59F VAL* 1.3 77.8 - - - +
61F TYR* 1.3 56.6 + - - +
63F TYR 3.3 0.5 + - - -
64F HIS* 3.0 15.6 + - - +
88F SER* 2.8 52.1 + - - +
91F GLU* 3.5 19.2 - - - +
92F ARG* 3.7 18.2 - - - +
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Residues in contact with TYR 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 5.9 0.2 - - - +
54B ASN* 4.0 5.4 + - - -
57B TYR* 3.6 49.8 - + - +
111B LEU* 3.6 22.0 - - + +
112B GLN 2.6 37.7 + - - -
114B ILE* 3.8 17.7 - - + +
57F TYR* 3.0 13.1 + + + +
58F ASN* 3.2 9.2 + - - +
60F SER* 1.3 79.1 - - - +
62F VAL* 1.3 62.6 + - + +
64F HIS* 3.2 5.7 + - - +
65F ALA* 3.0 18.9 + - - +
114F ILE* 3.4 28.9 - - + -
115F VAL 3.8 4.9 - - - -
117F PRO* 3.7 33.1 - - + +
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ASN* 3.0 17.9 + - - +
59F VAL 3.2 6.5 + - - +
61F TYR* 1.3 76.4 - - + +
63F TYR* 1.3 56.3 + - - +
65F ALA* 3.1 4.7 + - - +
66F MET* 2.9 45.9 + - + +
117F PRO* 4.3 8.7 - - + -
121F PHE* 5.1 3.6 - - + -
139F LEU* 3.7 27.8 - - + -
17O PRO* 4.6 7.6 - - + -
18O PHE* 3.2 43.3 - - + -
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Residues in contact with TYR 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F VAL* 2.9 32.4 + - + +
60F SER 3.7 4.9 - - - +
62F VAL* 1.3 77.5 - - - +
64F HIS* 1.3 57.4 + - - +
66F MET* 3.3 11.8 + - + -
67F PHE* 2.9 26.2 + - - +
83F PHE* 5.6 1.6 - + - -
84F PHE* 3.6 45.2 - + - +
87F SER* 3.6 20.2 - - - -
88F SER 3.8 4.5 - - - +
91F GLU* 3.6 20.4 - - + -
136F ALA* 3.8 27.2 + - + -
139F LEU* 4.6 8.3 - - + +
140F GLU* 2.5 42.2 + - - +
181F ILE* 3.9 8.2 - - + +
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Residues in contact with HIS 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 2.6 35.4 + + - +
92B ARG* 3.6 19.3 + - + -
96B GLU* 2.7 41.0 + - + +
99B MET* 3.6 36.0 - - + +
111B LEU* 4.0 8.3 - - + -
60F SER 3.0 8.2 + - - +
61F TYR 3.5 9.0 - - - +
62F VAL 3.1 0.4 - - - -
63F TYR* 1.3 77.1 - - - +
65F ALA* 1.3 56.4 + - - +
67F PHE* 3.4 16.0 + + + +
68F ALA 3.0 21.5 + - - -
85F LYS* 5.0 2.5 - - + -
88F SER* 3.4 21.2 + - - +
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 6.1 0.2 - - - -
111B LEU* 3.6 11.8 - - + +
61F TYR 3.0 12.7 + - - +
62F VAL* 3.4 9.4 - - - +
64F HIS* 1.3 77.3 - - - +
66F MET* 1.3 61.4 + - - +
68F ALA* 3.2 6.7 + - - +
69F TYR* 3.0 21.3 + - - +
117F PRO* 3.9 15.9 - - + -
118F LEU 3.4 25.4 - - - +
119F SER* 4.5 4.7 - - - +
121F PHE* 3.8 6.1 - - + -
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Residues in contact with MET 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F VAL* 2.9 29.2 + - + +
63F TYR* 3.3 20.6 + - + +
65F ALA* 1.3 73.3 - - - +
67F PHE* 1.3 65.5 + - - +
69F TYR* 3.2 1.2 + - - +
70F PHE* 3.1 32.0 + - + -
84F PHE* 3.7 42.6 - - + -
121F PHE* 3.4 43.1 - - + -
132F ALA* 4.2 7.9 - - + +
135F LEU* 4.0 26.0 - - + -
136F ALA* 4.3 6.5 - - - +
139F LEU* 5.1 2.5 - - + -
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Residues in contact with PHE 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLU* 4.5 9.0 - - + -
99B MET* 4.1 17.0 - - + -
100B GLU* 4.0 21.1 - - + -
103B ASN* 5.5 0.2 - - - -
63F TYR 2.9 14.0 + - - +
64F HIS* 3.5 24.9 - + - +
66F MET* 1.3 75.5 - - - +
68F ALA* 1.3 70.8 + - - +
70F PHE* 3.2 0.7 + - - -
71F ASP* 2.9 48.7 + - + +
81F ALA* 3.3 28.6 - - + +
82F LYS* 5.8 0.2 - - - -
84F PHE* 3.6 7.5 - - - +
85F LYS* 3.5 54.1 - - + +
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Residues in contact with ALA 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B MET* 4.0 8.7 - - + -
103B ASN* 3.0 31.7 + - - +
109B VAL* 3.7 38.8 - - + +
64F HIS 3.0 14.5 + - - +
65F ALA* 3.6 10.1 - - - +
66F MET 3.2 0.2 - - - -
67F PHE* 1.3 82.9 - - + +
69F TYR* 1.3 62.7 + - - +
72F ARG* 3.6 5.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ALA 3.0 7.8 + - - +
66F MET 3.6 4.0 - - - +
67F PHE 3.2 0.4 - - - -
68F ALA* 1.3 77.7 - - - +
70F PHE* 1.3 77.9 + + - +
72F ARG* 3.1 57.0 + - - +
75F VAL* 3.6 33.2 - - + +
119F SER 3.6 8.9 + - - +
120F ASP* 3.2 21.5 + - - -
121F PHE* 3.5 37.5 - + + -
122F ASP* 3.3 32.5 + - - +
128F ASP* 4.0 19.5 + - + +
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Residues in contact with PHE 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F MET* 3.1 29.7 + - + +
69F TYR* 1.3 89.2 - + - +
71F ASP* 1.3 57.9 + - - +
72F ARG 3.2 1.8 + - - -
75F VAL* 3.6 16.2 - - + -
76F ALA* 3.8 5.5 + - - -
77F LEU* 3.5 49.5 + - + +
78F ARG* 5.2 0.3 - - - +
80F LEU* 3.7 19.1 - - + -
81F ALA* 3.8 25.6 - - - +
84F PHE* 3.7 20.0 - + - -
121F PHE* 4.6 5.4 - - + -
128F ASP* 3.7 24.9 - - + -
129F ALA 4.1 0.7 - - - -
132F ALA* 3.4 36.1 - - + -
----------------------------------------------------------
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Residues in contact with ASP 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLU* 4.1 12.5 - - - +
103B ASN* 3.0 33.2 + - - +
67F PHE* 2.9 45.2 + - + +
69F TYR 3.2 0.4 - - - -
70F PHE* 1.3 76.3 - - - +
72F ARG* 1.3 62.9 + - - +
76F ALA* 5.8 0.2 - - - -
81F ALA* 3.9 7.4 - - + +
179V LYS* 3.0 33.8 + - - -
183V GLU* 4.6 2.2 - - - +
----------------------------------------------------------
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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