Contacts of the helix formed by residues 3 - 34 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU* 1.3 74.1 - - - +
4F LYS* 1.3 59.6 + - - +
5F ASP* 4.1 5.7 + - - +
6F ILE* 3.8 23.0 + - - +
7F ILE* 2.9 29.0 + - - +
111F SER* 4.8 9.6 + - - -
113F ASP* 5.0 4.1 + - - +
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Residues in contact with LYS 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU 4.0 0.4 + - - -
3F SER* 1.3 73.5 - - - +
5F ASP* 1.3 66.6 + - - +
7F ILE* 3.5 14.8 + - + +
8F LYS* 3.0 24.3 + - - +
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Residues in contact with ASP 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F SER* 3.3 5.8 + - - +
4F LYS* 1.3 78.3 - - - +
6F ILE* 1.3 61.8 + - - +
8F LYS* 3.3 6.6 + - - +
9F LEU* 3.1 29.8 + - + +
107F HIS* 3.1 38.6 + - + +
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Residues in contact with ILE 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU* 4.1 7.2 - - + -
3F SER* 3.3 21.0 + - - +
5F ASP* 1.3 72.5 - - - +
7F ILE* 1.3 67.7 + - - +
9F LEU* 3.3 6.1 + - + +
10F LEU* 2.8 46.9 + - + +
104F ILE* 4.3 11.4 - - + +
107F HIS* 3.6 27.8 - - + -
108F ALA* 4.0 24.7 - - + +
111F SER* 4.2 6.5 - - - +
113F ASP* 3.7 24.5 - - + +
116F THR* 4.0 10.3 - - + +
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Residues in contact with ILE 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0F PRO* 3.8 24.7 - - + -
2F LEU* 3.4 25.6 - - + +
3F SER 2.9 20.1 + - - +
4F LYS* 3.6 13.7 - - + +
6F ILE* 1.3 76.7 - - - +
8F LYS* 1.3 65.5 + - - +
10F LEU* 3.2 4.5 + - - +
11F ASN* 2.9 32.7 + - - +
61F LEU* 5.0 1.7 - - - +
66F VAL* 3.6 36.3 - - + -
67F PRO* 4.9 4.5 - - + +
69F GLN* 5.2 8.3 - - - +
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Residues in contact with LYS 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LYS 3.0 16.9 + - - +
5F ASP* 3.6 7.0 - - - +
6F ILE 3.3 0.2 - - - -
7F ILE* 1.3 78.9 - - - +
9F LEU* 1.3 59.0 + - + +
11F ASN* 3.4 5.4 + - - +
12F GLU* 2.7 66.2 + - + +
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Residues in contact with LEU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ASP* 3.1 22.7 + - + +
6F ILE* 3.8 7.0 - - + +
8F LYS* 1.3 77.0 - - + +
10F LEU* 1.3 59.2 + - - +
12F GLU* 3.4 19.1 + - + +
13F GLN* 3.0 27.9 + - - +
103F ASN* 3.8 21.5 - - - +
104F ILE* 3.9 29.6 - - + +
107F HIS* 3.9 39.0 - - + +
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Residues in contact with LEU 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU* 3.8 18.8 - - + -
6F ILE* 2.8 39.6 + - + +
7F ILE 3.8 2.5 - - - +
9F LEU* 1.3 73.3 - - - +
11F ASN* 1.3 60.7 + - - +
13F GLN* 3.2 4.8 + - + +
14F VAL* 3.0 32.8 + - - +
57F LEU* 4.5 16.2 - - + +
60F PHE* 4.0 20.0 - - + -
61F LEU* 3.9 19.3 - - + -
104F ILE* 4.2 23.8 - - + -
116F THR* 4.3 4.0 - - + -
120F LEU* 4.3 18.6 - - + -
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Residues in contact with ASN 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ILE* 2.9 31.1 + - - +
8F LYS* 3.8 5.6 - - - +
10F LEU* 1.3 73.9 - - - +
12F GLU* 1.3 64.3 + - + +
14F VAL* 3.2 6.8 + - - +
15F ASN* 2.8 30.4 + - - +
61F LEU* 3.7 13.2 - - - +
66F VAL* 4.3 2.3 - - - +
67F PRO 3.2 16.1 - - - +
68F VAL* 3.4 14.8 - - - +
69F GLN* 2.9 46.1 + - + +
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Residues in contact with GLU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F LYS* 2.7 59.0 + - + +
9F LEU* 3.7 23.8 - - + +
11F ASN* 1.3 76.2 - - + +
13F GLN* 1.3 58.0 + - - +
15F ASN* 3.3 9.0 + - - +
16F LYS* 2.9 40.6 + - - +
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Residues in contact with GLN 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F LEU 3.0 13.7 + - - +
10F LEU* 3.4 11.0 - - + +
11F ASN 3.2 0.4 - - - -
12F GLU* 1.3 75.1 - - - +
14F VAL* 1.3 65.6 + - - +
16F LYS* 3.3 16.1 + - - +
17F GLU* 3.0 25.2 + - - +
57F LEU* 3.8 9.2 - - + -
97F ILE* 4.1 9.1 - - - +
100F SER* 3.3 31.8 + - - -
101F ILE* 3.7 11.4 - - - +
104F ILE* 3.5 23.7 - - + +
123F TYR* 3.0 38.3 + - + +
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Residues in contact with VAL 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU 3.0 19.5 + - - +
11F ASN* 3.5 11.2 - - - +
13F GLN* 1.3 76.8 - - - +
15F ASN* 1.3 62.9 + - - +
17F GLU* 3.3 4.3 + - - +
18F MET* 3.1 34.4 + - + +
54F ALA* 4.1 4.2 - - + +
57F LEU* 3.7 29.8 - - + +
58F ILE* 3.9 24.5 - - + -
61F LEU* 3.9 19.7 - - + -
68F VAL* 4.8 1.3 - - + -
70F LEU* 3.8 27.4 - - + -
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Residues in contact with ASN 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASN* 2.8 23.8 + - - +
12F GLU* 3.6 9.9 - - - +
14F VAL* 1.3 78.0 - - - +
16F LYS* 1.3 55.3 + - - +
18F MET* 3.4 6.9 + - - +
19F ASN* 2.9 29.0 + - - +
69F GLN 2.9 24.4 + - - -
70F LEU* 3.5 13.1 - - - +
71F THR* 2.9 45.8 + - + +
73F ILE* 4.3 11.2 - - + +
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Residues in contact with LYS 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F GLU* 2.9 24.5 + - - +
13F GLN* 3.6 28.0 - - - +
14F VAL 3.3 0.2 - - - -
15F ASN* 1.3 76.4 - - - +
17F GLU* 1.3 57.6 + - - +
19F ASN* 3.2 8.3 + - - +
20F SER* 2.9 32.5 + - - -
93F HIS* 5.3 0.7 - - - -
96F HIS* 3.0 38.0 + - + -
97F ILE* 4.4 14.0 - - + +
100F SER* 3.8 25.3 - - - +
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Residues in contact with GLU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLN* 3.0 18.3 + - - +
14F VAL 3.3 4.5 + - - +
16F LYS* 1.3 72.7 - - - +
18F MET* 1.3 59.1 + - - +
20F SER* 3.4 6.5 + - - -
21F SER* 2.9 28.2 + - - -
50F GLU* 3.3 49.5 - - - +
51F TYR* 5.7 0.2 - - - -
53F HIS* 4.0 15.5 - - + -
54F ALA* 3.9 11.2 - - + +
57F LEU* 4.5 3.8 - - + -
97F ILE* 3.8 11.2 - - - +
123F TYR* 2.4 33.9 + - + +
1006F FE 2.6 21.7 - - - -
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Residues in contact with MET 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN* 4.6 15.7 - - - +
25A MET* 5.3 4.9 - - + -
14F VAL* 3.1 26.0 + - + +
15F ASN* 3.6 9.2 - - - +
17F GLU* 1.3 74.3 - - - +
19F ASN* 1.3 62.6 + - - +
21F SER* 3.3 8.0 + - - -
22F ASN* 3.2 25.6 + - - +
51F TYR* 3.8 36.6 - - + +
54F ALA* 3.8 21.1 - - + -
55F LYS 5.3 0.2 - - - +
58F ILE* 3.9 23.1 - - + -
70F LEU* 4.7 9.9 - - + -
73F ILE* 4.0 25.7 - - + +
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Residues in contact with ASN 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ASN 2.9 15.2 + - - +
16F LYS* 3.2 12.7 + - - +
18F MET* 1.3 76.3 - - - +
20F SER* 1.3 56.6 + - - +
22F ASN* 3.2 5.6 + - - +
23F LEU* 3.0 28.6 + - - +
73F ILE* 4.5 10.7 - - + +
74F SER* 3.3 39.2 + - - +
76F PRO* 5.6 1.9 - - - +
93F HIS* 4.8 11.1 - - - -
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Residues in contact with SER 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LYS 2.9 16.4 + - - -
17F GLU* 3.5 11.5 + - - -
19F ASN* 1.3 72.7 + - - +
21F SER* 1.3 67.1 + - - +
23F LEU* 3.2 3.9 + - - +
24F TYR* 3.0 34.1 + - - -
50F GLU* 4.1 20.6 + - - -
93F HIS* 2.6 33.5 + - - -
97F ILE* 3.6 11.6 - - - +
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Residues in contact with SER 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 2.8 31.5 + - - -
17F GLU 2.9 14.2 + - - -
18F MET* 3.5 11.4 - - - -
19F ASN 3.3 0.2 - - - -
20F SER* 1.3 76.0 - - - +
22F ASN* 1.3 67.0 + - - +
25F MET* 3.1 23.5 + - - +
47F ALA* 3.0 29.9 + - - +
50F GLU* 4.2 3.6 - - - +
51F TYR* 4.1 10.0 - - - +
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Residues in contact with ASN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 4.4 17.9 - - - +
51A TYR* 5.7 1.0 - - - -
70A LEU* 3.6 35.7 - - + +
71A THR 4.8 1.4 + - - -
73A ILE* 4.2 15.6 - - - +
18F MET 3.2 12.2 + - - +
19F ASN* 3.6 7.6 - - - +
20F SER 3.2 0.2 - - - -
21F SER* 1.3 80.8 + - - +
23F LEU* 1.3 61.8 + - - +
25F MET* 3.3 4.1 + - - +
26F SER* 3.0 20.8 + - - -
73F ILE* 3.4 26.9 - - + +
74F SER 4.7 1.1 + - - +
76F PRO* 3.8 15.6 - - + +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ASN* 3.0 18.0 + - - +
20F SER* 3.2 8.5 + - - +
22F ASN* 1.3 74.5 - - - +
24F TYR* 1.3 60.6 + - + +
26F SER* 3.2 4.5 + - - -
27F MET* 2.9 61.0 + - + +
76F PRO* 3.9 10.4 - - + +
77F GLU* 4.4 33.2 - - + +
80F PHE* 4.5 0.7 - - + -
89F LYS 5.8 0.2 - - - +
93F HIS* 3.9 39.7 - - + +
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Residues in contact with TYR 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F SER* 3.0 33.2 + - - +
23F LEU* 1.3 74.1 - - + +
25F MET* 1.3 60.9 + - - +
27F MET* 3.7 13.4 - - - +
28F SER* 2.8 31.0 + - - -
43F LEU* 3.7 35.4 - - + +
46F HIS* 3.4 24.9 - + - -
47F ALA* 3.7 11.7 - - + -
50F GLU* 4.2 5.8 - - + -
90F ALA* 3.3 33.0 + - + +
93F HIS* 3.5 23.1 - + - -
94F GLU* 2.5 41.9 + - - +
134F PHE* 3.9 6.6 - + - -
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Residues in contact with MET 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 5.1 4.5 - - + -
51A TYR* 3.8 18.6 - - + +
55A LYS* 4.1 15.3 - - + -
58A ILE* 4.1 28.1 - - + +
68A VAL* 5.1 5.4 - - + +
70A LEU* 3.9 15.7 - - + -
21F SER* 3.1 20.0 + - - +
22F ASN* 3.3 9.8 + - - +
24F TYR* 1.3 75.5 - - - +
26F SER* 1.3 57.3 + - - +
28F SER* 3.4 3.9 - - - -
29F SER* 3.0 28.2 + - - -
44F PHE* 3.5 47.3 - - + +
47F ALA* 3.6 20.6 - - + +
48F ALA 4.5 0.4 - - - +
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Residues in contact with SER 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 5.3 7.3 + - - -
70A LEU* 4.8 4.4 - - - +
22F ASN 3.0 13.2 + - - -
23F LEU 3.2 8.0 + - - -
25F MET* 1.3 74.9 - - - +
27F MET* 1.3 63.9 + - - +
29F SER* 3.4 7.7 + - - -
30F TRP* 3.1 22.0 + - - +
76F PRO* 3.9 14.8 - - - -
77F GLU 2.6 28.4 + - - -
78F HIS* 3.4 16.8 - - - +
80F PHE* 3.9 1.5 - - - -
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Residues in contact with MET 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 2.9 42.5 + - + +
24F TYR* 3.7 32.8 - - - +
26F SER* 1.3 74.6 - - - +
28F SER* 1.3 62.5 + - - +
30F TRP* 3.3 5.1 + - - +
31F CYS* 3.1 25.6 + - - -
43F LEU* 3.9 14.6 - - + -
80F PHE* 3.7 31.4 - - + -
86F ILE* 3.6 37.1 - - + +
89F LYS* 3.8 19.5 - - + -
90F ALA* 3.9 7.9 - - - +
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Residues in contact with SER 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 6.4 0.2 - - - -
62A ASN* 4.2 3.0 + - - -
24F TYR 2.8 22.4 + - - -
25F MET* 3.4 9.2 - - - -
27F MET* 1.3 69.6 - - - +
29F SER* 1.3 64.1 + - - +
31F CYS* 3.1 4.7 + - - +
32F TYR* 3.0 37.3 + - - -
40F GLY* 2.6 29.2 + - - -
43F LEU* 3.9 8.6 - - - +
44F PHE* 3.5 19.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 3.8 12.1 + - - -
66A VAL 4.0 2.3 + - - -
67A PRO* 3.5 9.7 - - - +
68A VAL* 2.8 48.6 + - - +
25F MET 3.0 16.5 + - - -
26F SER* 3.4 8.0 + - - -
28F SER* 1.3 76.1 - - - +
30F TRP* 1.3 63.1 + - - +
32F TYR* 3.3 1.6 + - - +
33F THR* 3.0 27.8 + - - +
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Residues in contact with TRP 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005A HIS* 6.5 0.4 - + - -
26F SER 3.1 12.8 + - - +
27F MET 3.5 9.2 - - - +
28F SER 3.2 0.2 - - - -
29F SER* 1.3 76.5 - - - +
31F CYS* 1.3 66.2 + - - +
33F THR* 3.2 5.0 + - - -
34F HIS* 2.8 75.6 + + + -
36F LEU* 4.2 15.9 - - + -
78F HIS 3.8 12.8 - - - +
79F LYS* 4.8 0.6 - - - +
80F PHE* 3.3 54.9 + + + +
81F GLU 4.1 4.5 - - - -
82F GLY* 3.6 29.2 - - - -
86F ILE* 3.4 22.0 - - + -
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Residues in contact with CYS 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F MET 3.1 17.1 + - - -
28F SER 3.1 6.5 + - - +
30F TRP* 1.3 84.0 - - - +
32F TYR* 1.3 60.1 + - - +
34F HIS 3.0 8.0 + - - -
36F LEU* 2.8 48.8 + - + +
39F ALA* 3.7 19.1 - - - -
40F GLY* 3.5 11.2 - - - +
43F LEU* 3.9 13.0 - - - -
83F LEU* 4.3 11.0 - - - -
86F ILE* 4.0 17.5 - - - -
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Residues in contact with TYR 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 3.3 60.1 - - + +
63A GLU* 6.0 1.8 - - + -
65A ASN* 3.5 18.2 + - - +
28F SER* 3.0 27.6 + - - +
29F SER 3.3 4.7 + - - +
31F CYS* 1.3 76.4 - - - +
33F THR* 1.3 60.8 + - + +
34F HIS 3.5 0.3 + - - -
35F SER* 3.8 8.1 + - - -
36F LEU 4.0 3.3 + - - -
37F ASP* 3.6 34.1 - - + +
40F GLY* 3.3 17.3 - - - -
41F LEU* 3.3 34.0 - - - +
44F PHE* 4.7 4.8 - - + +
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Residues in contact with THR 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 5.8 1.1 - - - +
65A ASN* 3.7 36.1 + - - +
66A VAL 3.9 3.4 - - - +
67A PRO* 3.8 32.3 - - + +
1002A GLN 5.2 0.9 - - - +
1003A SER* 3.4 17.6 - - - -
29F SER* 3.0 20.5 + - - +
30F TRP* 3.2 10.7 + - - -
32F TYR* 1.3 78.2 - - + +
34F HIS* 1.3 71.9 + - - +
35F SER 3.6 1.3 - - - -
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Residues in contact with HIS 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003A SER* 3.3 9.2 + - - +
1005A HIS* 2.8 29.6 + - + +
30F TRP* 2.8 81.3 + + + +
31F CYS 3.0 4.1 + - - +
33F THR* 1.3 93.8 + - - +
35F SER* 1.3 64.5 + - - +
36F LEU* 3.2 13.1 + - + +
----------------------------------------------------------
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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