Contacts of the helix formed by residues 4 - 35 (chain F) in PDB entry 3E1J
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 4 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLY* 1.3 72.7 - - - -
5F THR* 1.3 66.6 + - - +
6F LYS* 3.0 6.2 + - - +
7F VAL* 2.9 43.3 + - + +
8F ILE* 3.1 20.2 + - - +
65F LEU* 5.4 0.8 - - - +
107F TYR* 2.9 27.2 + - - -
111F VAL* 3.7 19.6 - - + +
113F ASP* 5.5 3.4 + - + +
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Residues in contact with THR 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LYS* 4.7 12.0 + - - -
3F GLY 3.5 3.3 + - - -
4F ASP* 1.3 74.2 - - - +
6F LYS* 1.3 57.9 + - + +
8F ILE* 3.1 13.2 + - + +
9F ASN* 2.9 40.4 + - - +
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Residues in contact with LYS 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ASP* 3.0 10.5 + - - +
5F THR* 1.3 76.5 - - - +
7F VAL* 1.3 63.3 + - - +
9F ASN* 3.2 19.1 + - + +
10F TYR* 2.9 50.2 + - + -
103F GLU* 5.2 1.0 + - - -
107F TYR* 3.4 33.3 - - + +
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Residues in contact with VAL 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ASP* 2.9 30.7 + - + +
6F LYS* 1.3 76.7 - - - +
8F ILE* 1.3 57.3 + - - +
10F TYR* 3.2 9.0 + - + +
11F LEU* 2.8 48.0 + - + +
65F LEU* 4.2 4.5 - - + -
107F TYR* 3.7 11.0 - - + -
108F ALA* 4.4 8.7 - - + -
111F VAL* 3.7 24.9 - - + -
113F ASP* 3.4 28.7 - - + +
116F SER* 4.1 7.2 - - - +
120F MET* 5.8 1.1 - - + -
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Residues in contact with ILE 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F GLY 4.4 8.5 - - - +
4F ASP 3.1 13.9 + - - +
5F THR* 3.1 12.6 + - + +
7F VAL* 1.3 77.4 - - - +
9F ASN* 1.4 58.9 + - - +
11F LEU* 3.2 7.9 + - - +
12F ASN* 2.9 37.6 + - - +
62F ILE* 4.0 25.4 - - + -
65F LEU* 3.7 43.1 - - + +
66F GLU 4.6 0.7 - - - -
67F GLY* 4.1 20.2 - - - +
68F LEU 4.8 0.9 - - - +
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Residues in contact with ASN 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F THR* 2.9 34.3 + - - +
6F LYS* 3.2 21.9 + - + +
8F ILE* 1.4 75.5 - - - +
10F TYR* 1.3 57.6 + - + +
12F ASN* 3.2 8.8 + - - +
13F LYS* 2.9 28.8 + - - +
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Residues in contact with TYR 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LYS* 2.9 47.6 + - + -
7F VAL* 3.2 9.2 + - + +
9F ASN* 1.3 76.4 - - + +
11F LEU* 1.3 59.0 + - + +
13F LYS* 3.0 20.7 + - + +
14F LEU* 2.8 37.1 + - + +
100F ASN* 4.8 4.0 - - + -
103F GLU* 2.6 49.6 + - + +
104F ALA* 3.7 31.9 - - + -
107F TYR* 3.8 37.8 - + + +
120F MET* 5.7 0.4 - - + -
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 2.8 33.8 + - + +
8F ILE* 3.5 6.3 - - - +
10F TYR* 1.3 72.3 - - + +
12F ASN* 1.3 58.7 + - - +
14F LEU* 3.4 4.6 + - + +
15F LEU* 2.8 29.8 + - - +
58F TYR* 4.1 24.6 - - + +
61F ARG* 3.8 27.6 - - + -
62F ILE* 3.6 25.4 - - + -
65F LEU* 3.9 19.3 - - + -
116F SER* 4.2 5.6 - - - +
119F MET* 5.5 1.6 - - - -
120F MET* 3.9 30.1 - - + -
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Residues in contact with ASN 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ILE* 2.9 29.4 + - - +
9F ASN* 3.7 7.8 + - - +
11F LEU* 1.3 72.8 - - - +
13F LYS* 1.3 61.4 + - - +
15F LEU* 3.3 7.2 + - - +
16F GLY* 2.8 25.5 + - - -
62F ILE* 3.2 17.7 - - - +
68F LEU 3.0 22.4 + - - -
69F PRO* 3.3 0.2 - - - +
70F ASN* 2.7 41.6 + - + +
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Residues in contact with LYS 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ASN 2.9 14.2 + - - +
10F TYR* 3.0 23.5 + - + +
12F ASN* 1.3 77.4 - - - +
14F LEU* 1.3 63.3 + - + +
16F GLY* 3.0 4.8 + - - -
17F ASN* 3.0 23.6 + - - +
100F ASN* 3.5 42.7 + - + +
103F GLU* 6.4 1.3 - - - -
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Residues in contact with LEU 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F TYR* 2.8 25.7 + - + +
11F LEU* 3.7 2.7 - - + +
13F LYS* 1.3 73.6 - - + +
15F LEU* 1.3 62.3 + - - +
17F ASN* 2.9 22.9 + - - +
18F GLU* 3.0 15.6 + - - +
58F TYR* 3.5 34.5 - - + +
97F GLY 4.6 0.7 - - - +
100F ASN* 3.7 33.2 - - + +
101F LEU* 3.8 24.0 - - + +
104F ALA* 3.9 10.3 - - + -
120F MET* 3.6 29.8 - - - -
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU 2.8 21.8 + - - +
12F ASN* 3.4 23.8 - - - +
14F LEU* 1.3 70.1 - - - +
16F GLY* 1.3 57.2 + - - +
18F GLU* 3.1 2.9 + - - +
19F LEU* 2.9 47.0 + - + +
55F ALA* 3.6 39.5 - - + +
58F TYR* 3.8 16.2 - - + -
59F ILE* 3.9 22.4 - - + -
62F ILE* 4.3 4.5 - - + -
69F PRO* 4.2 3.4 - - + -
70F ASN 3.8 18.6 - - - +
71F LEU* 4.1 5.4 - - + -
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Residues in contact with GLY 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ASN 2.8 15.7 + - - -
13F LYS* 3.0 5.8 + - - -
15F LEU* 1.3 75.2 - - - +
17F ASN* 1.3 62.4 + - - +
19F LEU* 3.3 15.1 + - - +
20F VAL* 3.2 27.2 + - - +
70F ASN 5.3 1.3 + - - -
73F ASP 5.1 5.3 - - - +
74F LEU* 5.1 0.9 - - - +
75F GLY 5.1 1.6 + - - -
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Residues in contact with ASN 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LYS* 3.0 19.5 + - - +
14F LEU* 2.9 16.8 + - - +
16F GLY* 1.3 76.8 - - - +
18F GLU* 1.3 67.3 + - + +
20F VAL* 3.3 9.9 + - - +
21F ALA* 3.1 21.5 + - - +
93F LEU* 5.1 7.9 - - + +
96F ASP* 6.4 0.7 - - - -
97F GLY* 3.6 22.7 - - - -
100F ASN* 2.9 36.0 + - - +
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Residues in contact with GLU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU 3.0 16.7 + - - +
15F LEU 3.1 5.6 + - - +
17F ASN* 1.3 78.2 - - - +
19F LEU* 1.3 61.0 + - - +
21F ALA* 3.2 4.2 + - - +
22F ILE* 2.8 33.9 + - - +
51F GLU* 2.9 48.2 - - - +
54F HIS* 3.3 19.2 + - + +
55F ALA* 4.3 8.1 - - + -
58F TYR* 3.7 19.7 + - + -
101F LEU* 5.2 2.4 - - - +
123F ILE* 3.8 11.4 - - - +
127F GLU* 2.7 20.3 - - - +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ASN* 4.9 4.9 - - - +
15F LEU* 2.9 53.9 + - + +
16F GLY* 3.3 19.0 + - - +
17F ASN 3.2 0.2 - - - -
18F GLU* 1.3 79.6 - - - +
20F VAL* 1.3 61.3 + - - +
22F ILE* 3.7 5.6 + - + +
23F ASN* 3.5 18.2 + - - -
55F ALA* 4.7 3.4 - - + -
70F ASN 4.3 10.3 - - - +
71F LEU* 4.0 26.5 - - + +
73F ASP 4.5 11.9 - - - +
74F LEU* 3.8 19.0 - - + +
200F HEM 3.9 30.3 - - + -
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Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLY 3.2 19.0 + - - +
17F ASN* 3.3 8.3 + - - +
19F LEU* 1.3 75.9 - - - +
21F ALA* 1.3 64.0 + - - +
23F ASN* 3.2 4.5 + - - +
24F GLN* 2.9 21.6 + - - +
74F LEU* 3.9 6.4 - - + +
75F GLY* 3.9 29.6 - - - +
76F LYS 3.8 15.0 - - - +
77F LEU* 3.7 25.9 - - + +
93F LEU* 3.7 26.9 - - + -
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Residues in contact with ALA 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ASN 3.1 14.9 + - - +
18F GLU* 3.6 9.0 - - - +
20F VAL* 1.3 77.5 - - - +
22F ILE* 1.3 53.9 + - - +
24F GLN* 4.0 1.1 - - - +
25F TYR* 2.8 48.5 + - + +
51F GLU* 3.8 25.4 - - + +
93F LEU* 3.8 21.3 - - + +
94F GLU* 5.6 1.8 - - - +
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Residues in contact with ILE 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F GLU 2.8 24.7 + - - +
19F LEU* 3.8 6.1 - - - +
20F VAL 3.3 0.2 - - - -
21F ALA* 1.3 70.8 - - - +
23F ASN* 1.3 72.1 + - - +
26F PHE* 3.0 17.3 + - - +
48F SER* 2.8 31.4 + - - +
51F GLU* 3.6 12.3 - - + +
52F MET* 3.6 44.4 - - + +
55F ALA* 4.1 11.9 - - + -
200F HEM 3.6 49.8 - - + -
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Residues in contact with ASN 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU* 4.9 5.9 - - - +
71E LEU* 3.5 43.8 - - + +
19F LEU 3.5 9.7 + - - +
20F VAL 3.2 7.8 + - - +
22F ILE* 1.3 79.8 - - - +
24F GLN* 1.3 68.9 + - - +
26F PHE* 3.3 2.4 + - - +
27F LEU* 3.0 26.5 + - - +
74F LEU* 3.8 12.7 - - - +
77F LEU* 4.4 11.7 - - + -
200F HEM 3.2 34.4 - - - +
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Residues in contact with GLN 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F VAL* 2.9 19.3 + - - +
21F ALA* 4.0 2.2 - - - +
23F ASN* 1.3 76.6 - - - +
25F TYR* 1.3 58.1 + - - +
27F LEU* 3.9 0.9 - - - +
28F HIS* 3.0 45.5 + - + +
76F LYS 4.8 0.5 - - - +
77F LEU* 3.8 15.6 - - + +
78F ASN 3.0 34.3 + - - +
79F ILE* 4.5 9.0 - - + -
89F SER* 3.1 25.1 + - - -
90F ASP* 2.9 34.4 + - - +
93F LEU* 4.0 18.8 - - + +
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Residues in contact with TYR 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ALA* 2.8 30.0 + - + +
24F GLN* 1.3 78.1 - - - +
26F PHE* 1.3 56.6 + - - +
28F HIS* 3.3 1.9 + - - +
29F ALA* 2.8 30.1 + - - +
44F GLU* 3.4 38.6 - - - +
47F GLU* 3.7 33.7 + - + -
48F SER* 3.8 8.7 - - - +
51F GLU* 3.9 26.2 - - + -
90F ASP* 3.5 28.9 - - + +
93F LEU* 6.1 1.8 - - + -
94F GLU* 2.4 39.5 + - + +
130F HIS* 4.0 3.5 - - - +
134F LEU* 3.6 12.8 - - + +
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Residues in contact with PHE 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ASP* 3.3 41.7 - - + -
59E ILE* 3.9 13.0 - - + -
71E LEU* 5.2 1.8 - - + -
22F ILE 3.0 18.5 + - - +
23F ASN* 3.3 5.1 + - - +
25F TYR* 1.3 73.8 - - - +
27F LEU* 1.3 66.3 + - - +
29F ALA* 3.3 5.0 + - - +
30F ARG* 3.0 38.7 + - + +
45F TYR* 3.6 26.0 - + - -
48F SER* 3.6 19.2 + - - +
52F MET* 4.6 0.4 - - + -
200F HEM 3.4 57.4 - - + -
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ILE* 4.4 4.9 - - + -
63E LEU* 4.4 6.3 - - + -
69E PRO* 3.9 42.4 - - + +
71E LEU* 4.0 24.5 - - + +
23F ASN 3.0 16.8 + - - +
24F GLN 3.9 2.7 - - - +
26F PHE* 1.3 76.0 - - - +
28F HIS* 1.3 64.4 + - + +
30F ARG* 3.2 3.1 + - - -
31F MET* 2.9 39.0 + - + +
77F LEU* 5.6 0.2 - - + -
79F ILE* 3.5 43.5 - - + -
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Residues in contact with HIS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLN* 3.0 32.9 + - + +
25F TYR 3.7 0.2 - - - +
27F LEU* 1.3 74.8 - - - +
29F ALA* 1.3 64.2 + - - +
31F MET* 3.0 4.7 + - - +
32F PHE* 2.9 31.4 + + + -
44F GLU* 3.1 17.3 - - - +
78F ASN 4.4 0.9 - - - -
79F ILE* 2.7 43.0 + - + -
86F MET* 3.2 49.3 + - + +
90F ASP* 2.7 37.0 + - - -
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Residues in contact with ALA 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F TYR 2.8 18.1 + - - +
26F PHE* 3.4 8.1 - - - +
28F HIS* 1.3 77.2 - - - +
30F ARG* 1.3 60.5 + - + +
32F PHE* 3.3 2.5 + - - +
33F LYS 2.9 21.7 + - - -
41F ASN* 3.0 28.0 - - - +
44F GLU* 3.9 9.3 - - + +
45F TYR* 3.6 33.0 - - + +
----------------------------------------------------------
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Residues in contact with ARG 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ASP* 2.6 46.8 + - - -
59E ILE* 4.1 9.2 - - + -
60E GLU* 3.0 32.5 + - + +
63E LEU* 3.7 20.4 - - + +
26F PHE* 3.0 35.7 + - + +
27F LEU 4.1 0.7 - - - +
29F ALA* 1.3 73.7 - - - +
31F MET* 1.3 60.3 + - - +
33F LYS* 3.6 13.1 - - + +
34F ASN* 2.9 28.1 + - - +
41F ASN* 3.4 29.5 + - - +
45F TYR* 3.4 34.3 - - - +
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Residues in contact with MET 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU* 4.3 16.8 - - + -
27F LEU* 2.9 33.0 + - + +
28F HIS* 3.3 9.4 - - - +
30F ARG* 1.3 73.8 - - - +
32F PHE* 1.3 65.3 + - - +
34F ASN* 3.1 6.4 + - - +
35F TRP* 2.9 49.6 + - + -
79F ILE* 3.7 23.3 - - + -
80F GLY 3.8 16.4 - - - +
81F GLU* 4.9 2.0 - - - +
86F MET* 3.7 33.0 - - + -
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Residues in contact with PHE 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F HIS* 2.9 24.1 + - + -
29F ALA 3.4 6.3 - - - +
31F MET* 1.3 74.5 - - - +
33F LYS* 1.3 60.5 + - - +
35F TRP* 3.2 14.0 + + - -
36F GLY 3.0 4.5 + - - -
37F LEU* 2.8 38.7 + - + +
40F LEU* 3.6 36.3 - - + -
41F ASN 3.9 12.6 - - - +
44F GLU* 3.9 27.8 - - + -
83F VAL* 4.0 20.9 - - + -
86F MET* 3.4 40.2 - - + -
87F LEU* 3.9 18.6 - - + -
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Residues in contact with LYS 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLU* 3.3 30.1 - - + -
29F ALA 2.9 8.9 + - - +
30F ARG* 3.6 17.3 - - + +
31F MET 3.2 0.2 - - - -
32F PHE* 1.3 72.7 - - - +
34F ASN* 1.3 66.6 + - - +
36F GLY* 2.9 15.0 + - - +
37F LEU 4.8 2.7 - - - +
38F LYS* 5.3 3.4 - - + +
41F ASN* 3.5 41.9 - - + +
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Residues in contact with ASN 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLU 5.1 1.2 + - - -
63E LEU* 4.2 24.1 - - + +
64E PHE* 4.0 30.7 - - - +
30F ARG 2.9 18.2 + - - +
31F MET* 3.5 5.4 - - - +
33F LYS* 1.3 79.2 - - - +
35F TRP* 1.3 72.6 + - + +
36F GLY* 3.2 1.6 + - - -
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Residues in contact with TRP 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F MET* 2.9 33.8 + - + -
32F PHE* 3.2 23.8 + + - +
34F ASN* 1.3 85.5 + - - +
36F GLY* 1.3 59.8 + - - +
37F LEU* 3.5 24.9 + - + +
81F GLU 3.4 27.1 - - - -
82F ASP* 4.3 2.0 - - - -
83F VAL* 4.4 11.0 - - + -
86F MET* 3.7 32.5 - - + -
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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