Contacts of the helix formed by residues 3 - 33 (chain A) in PDB entry 3BVI
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 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 1.3 74.0 - - - +
4A LYS* 1.3 63.7 + - - +
5A ASP* 3.8 5.6 + - - +
6A ILE* 3.3 28.4 + - - +
7A ILE* 2.9 24.1 + - - +
107A HIS* 5.3 0.2 - - - -
111A SER* 4.8 8.7 + - - -
113A ASP* 5.1 3.5 + - - +
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Residues in contact with LYS 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU 3.9 0.4 + - - -
3A SER* 1.3 73.1 - - - +
5A ASP* 1.3 60.2 + - - +
7A ILE* 3.5 15.1 + - + +
8A LYS* 3.1 28.1 + - - +
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Residues in contact with ASP 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 3.2 5.2 + - - +
4A LYS* 1.3 77.4 - - - +
6A ILE* 1.3 63.9 + - - +
8A LYS* 3.4 11.8 + - - +
9A LEU* 3.1 29.9 + - + +
107A HIS* 3.3 33.1 + - + +
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Residues in contact with ILE 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.0 11.7 - - + -
3A SER* 3.2 21.8 + - - +
5A ASP* 1.3 73.1 - - - +
7A ILE* 1.3 56.4 + - - +
9A LEU* 3.1 7.1 + - + +
10A LEU* 2.8 58.6 + - + +
104A ILE* 4.5 8.3 - - + +
107A HIS* 3.8 23.3 - - + +
108A ALA* 3.9 29.8 - - + +
111A SER* 4.5 4.5 - - - +
113A ASP* 3.8 24.7 - - + +
116A THR* 4.1 8.7 - - + +
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Residues in contact with ILE 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A PRO* 4.0 22.9 - - + -
2A LEU* 3.3 28.0 - - + +
3A SER 2.9 18.4 + - - +
4A LYS* 3.5 15.0 - - + +
6A ILE* 1.3 77.7 - - - +
8A LYS* 1.3 64.6 + - - +
10A LEU* 3.9 5.4 - - - +
11A ASN* 2.9 42.9 + - - +
61A LEU* 5.1 0.4 - - - +
66A VAL* 3.7 28.5 - - + -
67A PRO* 5.0 3.4 - - + +
69A GLN* 4.9 8.1 - - - +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS 3.1 13.6 + - - +
5A ASP* 3.5 16.4 - - - +
6A ILE 3.2 0.2 - - - -
7A ILE* 1.3 78.5 - - - +
9A LEU* 1.3 65.1 + - + +
11A ASN* 3.9 4.1 - - - +
12A GLU* 2.8 68.9 + - + +
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP* 3.1 17.6 + - + +
6A ILE* 3.1 8.7 + - + +
8A LYS* 1.3 88.1 - - + +
10A LEU* 1.3 58.0 + - - +
12A GLU* 3.5 17.4 + - - +
13A GLN* 3.0 27.5 + - - +
103A ASN* 3.7 25.8 - - - +
104A ILE* 3.8 33.3 - - + +
107A HIS* 3.7 37.9 - - + +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.7 19.3 - - + -
6A ILE* 2.8 45.1 + - + +
7A ILE 4.0 0.4 - - - +
9A LEU* 1.3 69.4 - - - +
11A ASN* 1.3 66.3 + - - +
13A GLN* 3.2 5.4 + - + +
14A VAL* 3.0 27.8 + - - +
57A LEU* 4.5 15.9 - - + +
60A PHE* 4.1 17.3 - - + -
61A LEU* 3.9 23.3 - - + -
104A ILE* 4.1 24.5 - - + -
116A THR* 4.3 5.2 - - + -
120A LEU* 4.3 19.5 - - + -
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Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 2.9 37.2 + - - +
8A LYS* 3.9 4.2 - - - +
10A LEU* 1.3 76.4 - - - +
12A GLU* 1.3 61.3 + - + +
14A VAL* 3.2 14.9 + - - +
15A ASN* 2.9 23.2 + - - +
61A LEU* 3.6 9.6 - - - +
66A VAL* 4.2 4.0 - - - +
67A PRO 3.2 19.0 + - - -
68A VAL* 3.4 10.6 - - - +
69A GLN* 2.8 46.8 + - + +
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 2.8 62.4 + - + +
9A LEU* 3.7 17.2 - - - +
11A ASN* 1.3 75.3 - - + +
13A GLN* 1.3 57.2 + - - +
15A ASN* 3.3 9.8 + - - +
16A LYS* 3.0 41.1 + - - +
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU 3.0 13.6 + - - +
10A LEU* 3.2 10.5 + - + +
12A GLU* 1.3 73.0 - - - +
14A VAL* 1.3 66.3 + - - +
16A LYS* 3.3 13.3 + - - +
17A GLU* 3.0 24.7 + - - +
57A LEU* 3.8 13.9 - - + -
97A ILE* 4.2 9.3 - - - +
100A SER* 3.0 31.9 + - - -
101A ILE* 3.5 13.1 - - - +
104A ILE* 3.4 24.9 - - + +
123A TYR* 2.8 35.0 + - + +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 3.0 16.0 + - - +
11A ASN* 3.2 10.0 + - - +
13A GLN* 1.3 77.4 - - - +
15A ASN* 1.3 61.9 + - - +
17A GLU* 3.3 5.8 + - - +
18A MET* 3.1 28.4 + - + +
54A ALA* 4.3 5.5 - - + +
57A LEU* 3.7 29.6 - - + -
58A ILE* 3.8 27.4 - - + -
61A LEU* 4.1 18.8 - - + -
68A VAL* 4.9 1.3 - - + -
70A LEU* 3.8 23.1 - - + -
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Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN 2.9 23.8 + - - -
12A GLU* 3.6 9.4 - - - +
13A GLN 3.3 0.2 - - - -
14A VAL* 1.3 77.4 - - - +
16A LYS* 1.3 55.7 + - - +
18A MET* 3.5 4.3 + - - +
19A ASN* 3.0 28.2 + - - +
69A GLN 3.0 21.6 + - - -
70A LEU* 3.5 12.7 - - - +
71A THR* 3.0 43.3 + - - +
73A ILE* 3.5 20.3 - - + +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.0 25.5 + - - +
13A GLN* 3.5 18.8 - - - +
14A VAL 3.3 0.2 - - - -
15A ASN* 1.3 76.6 - - - +
17A GLU* 1.3 56.3 + - - +
19A ASN* 3.4 8.5 + - - +
20A SER* 2.9 32.0 + - - -
93A HIS* 5.3 0.2 - - - -
96A HIS* 4.0 22.6 + - + -
97A ILE* 4.1 20.7 - - + +
100A SER* 3.9 32.1 - - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.0 16.5 + - + +
14A VAL 3.7 7.0 - - - +
16A LYS* 1.3 72.6 - - - +
18A MET* 1.3 61.0 + - - +
20A SER* 3.3 6.6 + - - -
21A SER* 2.9 29.3 + - - -
50A GLU* 3.5 44.5 - - - +
53A HIS* 3.9 14.1 - - + -
54A ALA* 3.8 12.3 - - + +
57A LEU* 4.2 5.2 - - + -
97A ILE* 4.1 8.3 - - - +
123A TYR* 2.3 35.1 + - - +
1006A FE 2.7 23.9 - - - -
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Residues in contact with MET 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 3.1 20.0 + - + +
15A ASN* 3.6 10.3 - - - +
17A GLU* 1.3 74.8 - - - +
19A ASN* 1.3 61.7 + - - +
21A SER* 3.3 7.4 + - - -
22A ASN* 3.2 27.2 + - - +
51A TYR* 3.8 30.7 - - + -
54A ALA* 3.7 26.7 - - + -
55A LYS* 5.5 0.4 - - + +
58A ILE* 4.0 22.7 - - + -
70A LEU* 4.6 10.8 - - + -
73A ILE* 4.0 22.7 - - + -
22F ASN* 4.4 17.7 - - - +
25F MET* 5.1 5.2 - - + -
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Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN 3.0 17.7 + - - +
16A LYS* 3.5 7.7 + - - +
18A MET* 1.3 73.4 - - - +
20A SER* 1.3 65.1 + - - +
22A ASN* 3.3 5.6 + - - +
23A LEU* 3.0 23.4 + - - +
73A ILE* 4.0 16.0 - - + +
74A SER* 3.8 22.7 + - - +
76A PRO* 5.4 5.5 - - - +
93A HIS* 4.4 16.4 - - - -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS 2.9 21.4 + - - -
17A GLU* 3.3 10.3 + - - -
19A ASN* 1.3 71.8 - - - +
21A SER* 1.3 64.0 + - - +
23A LEU* 3.2 4.4 + - - +
24A TYR* 3.0 32.6 + - - -
50A GLU* 3.9 21.4 + - - -
93A HIS* 2.5 35.5 + - - -
97A ILE* 3.8 11.8 - - - +
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU 2.9 13.6 + - - -
18A MET* 3.4 12.3 - - - -
19A ASN 3.3 0.2 - - - -
20A SER* 1.3 77.7 - - - +
22A ASN* 1.3 59.6 + - - +
25A MET* 3.0 28.3 + - - +
47A ALA* 3.2 29.4 + - - +
50A GLU* 4.0 5.6 - - - +
51A TYR* 4.1 9.4 - - - +
51F TYR* 3.0 31.4 + - - -
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Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 3.2 10.3 + - - +
19A ASN* 3.7 7.2 - - - +
20A SER 3.3 0.2 - - - -
21A SER* 1.3 77.4 + - - +
23A LEU* 1.3 66.2 + - - +
25A MET* 3.4 1.0 + - - +
26A SER* 3.0 23.7 + - - -
73A ILE* 3.4 30.3 - - + +
74A SER 5.0 2.5 + - - +
76A PRO* 3.5 20.6 - - + +
18F MET* 4.6 16.3 - - - +
51F TYR* 5.8 0.5 - - - -
70F LEU* 3.5 25.0 - - + +
71F THR 5.2 0.8 + - - -
73F ILE* 3.9 21.3 - - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 3.0 18.1 + - - +
20A SER* 3.2 9.1 + - - +
22A ASN* 1.3 76.3 - - - +
24A TYR* 1.3 62.1 + - + +
26A SER* 3.2 5.2 + - - -
27A MET* 2.9 56.5 + - + +
76A PRO* 3.7 16.1 - - + +
77A GLU* 3.8 34.5 - - + +
80A PHE* 4.6 0.4 - - + -
89A LYS 6.0 0.2 - - - -
93A HIS* 3.9 39.3 - - + +
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER 3.0 25.6 + - - +
23A LEU* 1.3 77.0 - - + +
25A MET* 1.3 58.9 + - - +
27A MET* 3.7 12.6 - - + +
28A SER* 2.7 30.8 + - - -
43A LEU* 3.7 27.8 - - + +
46A HIS* 3.3 23.6 - + - -
47A ALA* 3.5 22.0 - - + -
50A GLU* 3.9 11.2 - - + -
90A ALA* 3.5 27.9 + - + +
93A HIS* 3.6 22.9 - + - -
94A GLU* 2.5 40.7 + - - +
134A PHE* 3.9 11.1 - + - -
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Residues in contact with MET 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 3.0 24.2 + - - +
22A ASN* 4.8 0.7 - - - +
23A LEU 3.4 0.2 - - - -
24A TYR* 1.3 75.9 - - - +
26A SER* 1.3 56.8 + - - +
28A SER* 3.4 4.3 + - - -
29A SER* 3.0 29.6 + - - -
44A PHE* 3.5 46.7 - - + +
47A ALA* 3.7 15.7 - - + -
48A ALA 4.5 0.7 - - - +
18F MET* 5.3 3.4 - - + -
51F TYR* 3.5 25.1 - - + +
55F LYS* 4.0 16.6 - - + -
58F ILE* 4.2 26.0 - - + +
62F ASN* 5.5 0.2 - - - +
68F VAL* 5.1 5.2 - - + +
70F LEU* 3.8 20.9 - - + -
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN 3.0 13.7 + - - -
23A LEU 3.3 9.4 - - - -
25A MET* 1.3 74.0 - - - +
27A MET* 1.3 64.7 + - - +
29A SER* 3.4 6.2 + - - -
30A TRP* 3.1 21.7 + - - +
76A PRO* 3.9 11.9 - - - +
77A GLU 2.7 28.2 + - - -
78A HIS* 3.6 15.4 - - - +
80A PHE* 4.2 2.2 - - - -
68F VAL* 5.2 9.5 + - - -
70F LEU* 4.5 4.4 - - - +
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 2.9 45.0 + - + +
24A TYR* 3.4 30.9 + - - +
26A SER* 1.3 72.1 - - - +
28A SER* 1.3 61.3 + - - +
30A TRP* 3.3 5.2 + - - +
31A CYS* 3.2 26.9 + - - -
43A LEU* 4.0 8.3 - - + -
77A GLU* 6.1 0.2 - - - -
80A PHE* 3.6 29.2 - - + -
86A ILE* 3.6 44.5 - - + +
89A LYS* 3.9 18.8 - - + -
90A ALA* 3.9 8.1 - - - +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR 2.7 22.0 + - - -
25A MET* 3.5 9.2 - - - -
27A MET* 1.3 73.1 - - - +
29A SER* 1.3 57.0 + - - +
31A CYS* 3.2 4.9 + - - +
32A TYR* 3.1 36.3 + - - -
40A GLY* 2.7 23.3 + - - -
43A LEU* 3.7 9.4 - - - +
44A PHE* 3.4 29.2 - - - +
58F ILE* 6.4 0.2 - - - -
62F ASN* 4.2 3.7 + - - -
----------------------------------------------------------
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET 3.0 17.6 + - - -
26A SER* 3.8 4.9 - - - -
28A SER* 1.3 71.4 - - - +
30A TRP* 1.3 64.6 + - - +
32A TYR* 3.9 1.6 - - - +
33A THR* 2.8 30.5 + - - +
62F ASN* 3.8 12.5 + - - -
66F VAL 4.1 2.3 + - - -
67F PRO* 3.5 9.9 - - - +
68F VAL* 3.0 47.3 + - - +
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 3.1 13.3 + - - +
27A MET 3.3 8.5 + - - +
29A SER* 1.3 76.7 + - - +
31A CYS* 1.3 66.1 + - - +
33A THR* 3.2 4.6 + - - -
34A HIS* 2.7 71.2 + + + -
36A LEU* 4.0 24.5 - - + -
78A HIS 4.0 11.7 - - - +
80A PHE* 3.3 53.4 + + + +
81A GLU 4.1 4.3 - - - -
82A GLY* 3.5 29.2 - - - -
83A LEU 4.1 0.4 - - - -
86A ILE* 3.3 25.1 - - + -
1005F HIS* 6.4 1.3 - + - -
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Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET 3.2 15.9 + - - -
28A SER 3.6 4.7 - - - +
29A SER 3.2 0.4 - - - -
30A TRP* 1.3 85.7 - - - +
32A TYR* 1.3 61.0 + - - +
34A HIS 2.9 9.2 + - - -
35A SER 3.3 0.2 + - - -
36A LEU* 2.8 52.4 + - + +
39A ALA* 3.7 20.9 - - - -
40A GLY* 3.5 10.3 - - - +
43A LEU* 3.9 11.9 - - - -
83A LEU* 4.6 4.7 - - - -
86A ILE* 3.9 17.5 - - - -
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 3.1 25.7 + - - +
29A SER 3.5 4.2 + - - +
31A CYS* 1.3 76.4 - - - +
33A THR* 1.3 62.7 + - + +
34A HIS 3.2 1.3 + - - -
35A SER* 3.5 9.9 + - - -
36A LEU 4.0 3.7 + - - -
37A ASP* 3.8 31.9 - - + +
40A GLY* 3.3 19.3 - - - -
41A LEU* 3.3 34.6 - - - +
44A PHE* 4.7 5.1 - + + +
62F ASN* 3.3 61.2 - - + +
63F GLU* 5.7 2.2 - - + -
65F ASN* 3.7 15.7 + - - +
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 2.8 22.1 + - - +
30A TRP* 3.2 9.7 + - - -
32A TYR* 1.3 79.4 - - + +
34A HIS* 1.3 71.8 + - - +
35A SER 3.6 0.9 - - - -
62F ASN* 5.6 1.1 - - - +
65F ASN* 3.8 39.4 + - - +
66F VAL 3.8 4.3 - - - +
67F PRO* 3.8 28.1 - - + +
1002F GLN 5.0 1.6 - - - +
1003F SER* 3.4 18.5 - - - -
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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