Contacts of the helix formed by residues 4 - 35 (chain N) in PDB entry 3IS7
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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3N GLY* 1.3 69.5 - - - -
5N LYS* 1.3 65.4 + - - +
6N LYS* 3.1 9.3 + - - +
7N VAL* 2.9 32.4 + - + +
8N ILE* 3.2 21.4 + - - +
65N LEU* 5.8 0.6 - - - +
107N HIS* 2.9 31.0 + - - -
111N VAL* 4.0 21.2 - - + +
113N ASP* 5.9 0.8 + - + +
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Residues in contact with LYS 5 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3N GLY 3.4 4.8 + - - +
4N ASP* 1.3 75.0 + - - +
6N LYS* 1.3 58.8 + - + +
8N ILE* 3.4 11.1 + - - +
9N GLN* 3.1 36.1 + - + +
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Residues in contact with LYS 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N ASP* 3.1 5.1 + - - +
5N LYS* 1.3 77.5 - - + +
7N VAL* 1.4 60.9 + - - +
8N ILE 3.2 0.4 - - - -
9N GLN* 3.3 21.6 + - + +
10N HIS* 2.8 35.9 + - + +
107N HIS* 3.4 31.9 - - + +
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Residues in contact with VAL 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N ASP* 2.9 38.0 + - + +
6N LYS* 1.4 73.5 - - - +
8N ILE* 1.3 58.4 + - + +
10N HIS* 3.1 6.6 + - - +
11N LEU* 2.8 46.4 + - + +
65N LEU* 4.2 6.7 - - + -
107N HIS* 3.6 17.2 - - + -
108N CYS* 4.2 14.8 - - - -
111N VAL* 3.7 13.9 - - + -
113N ASP* 3.4 29.8 - - + +
116N SER* 4.0 2.0 - - - +
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Residues in contact with ILE 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3N GLY 4.1 10.5 - - - +
4N ASP 3.2 14.7 + - - +
5N LYS* 3.7 10.5 - - - +
6N LYS 3.2 0.4 - - - -
7N VAL* 1.3 76.8 - - - +
9N GLN* 1.3 57.6 + - + +
11N LEU* 3.2 7.5 + - - +
12N ASN* 2.8 43.2 + - - +
62N ILE* 4.4 10.0 - - + +
65N LEU* 3.7 45.8 - - + +
66N GLU 4.5 1.6 - - - +
67N GLY* 4.0 26.5 - - - -
68N LEU 4.8 0.9 - - - +
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Residues in contact with GLN 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5N LYS* 3.1 20.7 + - + +
6N LYS* 3.3 33.4 + - - +
8N ILE* 1.3 73.1 - - + +
10N HIS* 1.3 61.8 + - + +
12N ASN* 3.4 6.6 + - - +
13N LYS* 2.9 27.4 + - - +
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Residues in contact with HIS 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N LYS* 2.8 31.1 + - + +
7N VAL* 3.4 8.1 - - + +
9N GLN* 1.3 74.5 - - + +
11N LEU* 1.3 65.2 + - + +
13N LYS* 3.0 23.8 + - + +
14N ILE* 3.1 22.3 + - - +
100N ASP 4.7 2.0 + - - -
103N GLU* 3.8 27.6 + - + -
104N ALA* 3.5 27.5 + - + +
107N HIS* 3.8 31.1 - + + +
108N CYS* 6.1 1.6 - - - -
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Residues in contact with LEU 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N VAL* 2.8 39.9 + - + +
8N ILE* 3.2 3.3 + - - +
10N HIS* 1.3 74.9 - - + +
12N ASN* 1.3 56.8 + - - +
14N ILE* 3.4 3.9 + - - +
15N LEU* 2.9 28.4 + - - +
58N LEU* 3.9 15.3 - - + +
61N ARG* 3.9 29.6 - - + -
62N ILE* 3.6 27.1 - - + +
65N LEU* 4.0 9.6 - - + -
108N CYS* 5.5 0.4 - - - -
116N SER* 4.1 8.1 - - - +
119N LEU* 5.4 2.0 - - + -
120N LEU* 3.8 38.4 - - + -
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Residues in contact with ASN 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N ILE* 2.8 30.1 + - - +
9N GLN* 3.9 7.1 - - - +
11N LEU* 1.3 75.0 - - - +
13N LYS* 1.3 58.8 + - - +
15N LEU* 3.7 8.5 - - - +
16N GLY* 3.0 23.9 + - - -
62N ILE* 3.7 9.8 - - - +
68N LEU 3.0 23.2 + - - +
69N PRO* 3.5 4.7 - - - +
70N ASN* 2.7 40.8 + - + +
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Residues in contact with LYS 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N GLN 2.9 15.1 + - - +
10N HIS* 3.0 20.9 + - + +
12N ASN* 1.3 76.0 - - - +
14N ILE* 1.3 65.8 + - + +
16N GLY* 3.2 3.2 + - - -
17N ASN* 3.1 23.9 + - - +
96N LYS* 4.0 6.7 - - - +
100N ASP* 3.2 44.0 + - + +
103N GLU* 4.8 7.9 + - - -
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Residues in contact with ILE 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10N HIS* 3.1 19.0 + - - +
11N LEU* 3.6 6.1 - - - +
13N LYS* 1.3 75.7 - - + +
15N LEU* 1.4 57.8 + - - +
17N ASN* 3.2 10.7 + - + +
18N GLU* 2.9 35.0 + - - +
58N LEU* 3.9 18.6 - - + -
97N ALA 5.0 0.7 - - - +
100N ASP* 3.7 37.9 - - + +
101N LEU* 3.3 37.5 - - + +
104N ALA* 4.2 5.8 - - + -
120N LEU* 4.0 14.8 - - + -
123N ILE* 4.9 1.8 - - + -
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Residues in contact with LEU 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11N LEU 2.9 17.8 + - - +
12N ASN* 3.7 17.5 - - - +
13N LYS 3.2 0.2 - - - -
14N ILE* 1.4 76.3 - - - +
16N GLY* 1.3 57.7 + - - +
18N GLU* 3.1 2.9 + - - +
19N LEU* 2.9 47.9 + - + +
55N ALA* 3.7 40.4 - - + +
58N LEU* 3.9 13.6 - - + +
59N ILE* 3.9 24.0 - - + -
62N ILE* 4.2 7.9 - - + -
69N PRO* 4.3 0.7 - - + -
70N ASN 3.7 23.6 - - - +
71N LEU* 4.2 6.3 - - + -
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Residues in contact with GLY 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12N ASN 3.0 15.1 + - - -
13N LYS 3.2 4.4 + - - -
15N LEU* 1.3 75.9 - - - +
17N ASN* 1.3 62.8 + - - +
19N LEU* 3.4 13.4 + - - +
20N ILE* 3.2 30.3 + - - +
70N ASN 5.3 1.5 + - - -
73N ASP 4.8 8.7 - - - +
74N LEU* 5.0 0.2 - - - +
75N GLY 5.0 1.6 + - - -
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Residues in contact with ASN 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LYS* 3.1 18.6 + - - +
14N ILE* 3.2 14.8 + - + +
16N GLY* 1.3 75.6 - - - +
18N GLU* 1.3 65.9 + - + +
20N ILE* 3.4 17.1 + - - +
21N ALA* 3.1 22.2 + - - +
93N LEU* 4.8 7.7 - - + +
96N LYS* 3.6 18.0 + - - +
97N ALA* 3.9 27.4 + - + +
100N ASP* 2.8 37.8 + - - +
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Residues in contact with GLU 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N ILE* 2.9 23.0 + - - +
15N LEU 3.1 5.8 + - - +
17N ASN* 1.3 77.4 - - - +
19N LEU* 1.3 57.9 + - - +
21N ALA* 3.2 3.5 + - - +
22N ILE* 2.8 37.0 + - - +
51N GLU* 2.6 42.5 - - - +
54N HIS* 3.8 12.0 - - + +
55N ALA* 4.1 18.8 - - + +
58N LEU* 3.9 17.9 - - + -
97N ALA* 6.0 1.7 - - - +
101N LEU* 5.4 0.9 - - - +
123N ILE* 3.7 17.5 - - - +
127N GLU* 3.0 17.1 - - - +
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Residues in contact with LEU 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M ASN* 4.5 9.2 - - - +
15N LEU* 2.9 39.7 + - + +
16N GLY* 3.7 9.6 - - - +
18N GLU* 1.3 76.1 - - - +
20N ILE* 1.3 63.0 + - - +
22N ILE* 3.7 9.4 - - + +
23N ASN* 3.4 23.6 + - - +
55N ALA* 4.8 0.2 - - + -
70N ASN 3.8 22.4 - - - +
71N LEU* 3.9 19.7 - - + +
73N ASP 4.5 6.7 - - - +
74N LEU* 3.8 15.6 - - + +
159N HEM 3.3 38.1 - - + -
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Residues in contact with ILE 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N GLY 3.2 17.1 + - - +
17N ASN* 3.5 19.1 - - - +
18N GLU 3.2 0.2 - - - -
19N LEU* 1.3 78.4 - - - +
21N ALA* 1.3 58.7 + - - +
23N ASN* 3.3 3.8 + - - +
24N GLN* 2.9 31.9 + - - +
74N LEU* 3.9 8.1 - - + -
75N GLY* 3.6 41.1 - - - +
76N LYS 3.8 17.7 - - - +
77N LEU* 4.0 8.2 - - + +
93N LEU* 3.6 30.1 - - + -
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Residues in contact with ALA 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17N ASN 3.1 13.8 + - - +
18N GLU* 3.2 3.6 + - - +
20N ILE* 1.3 75.5 - - - +
22N ILE* 1.3 59.3 + - - +
24N GLN* 4.4 0.7 - - - -
25N TYR* 2.7 53.4 + - + +
51N GLU* 3.1 29.6 - - - +
93N LEU* 3.5 20.2 - - + -
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Residues in contact with ILE 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18N GLU 2.8 25.9 + - - +
19N LEU* 3.7 8.7 - - + +
21N ALA* 1.3 71.1 - - - +
23N ASN* 1.3 67.9 + - - +
26N PHE* 2.9 19.2 + - - +
48N SER* 2.9 31.0 + - - +
51N GLU* 3.8 11.8 - - + +
52N MET* 3.7 41.3 - - + +
55N ALA* 4.1 10.8 - - + -
159N HEM 3.8 48.9 - - + -
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Residues in contact with ASN 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M LEU* 4.6 11.1 - - - +
71M LEU* 3.1 48.4 + - + +
19N LEU 3.4 10.4 + - - +
20N ILE 3.3 7.1 + - - +
22N ILE* 1.3 79.5 - - - +
24N GLN* 1.3 65.5 + - - +
26N PHE* 3.3 1.5 + - - -
27N LEU* 3.0 26.5 + - - +
74N LEU* 3.6 14.1 - - - +
77N LEU* 4.2 11.4 - - + -
159N HEM 3.4 22.7 - - - +
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Residues in contact with GLN 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N ILE* 2.9 17.0 + - - +
21N ALA* 3.9 3.4 - - - +
23N ASN* 1.3 77.7 - - - +
25N TYR* 1.4 59.2 + - + +
27N LEU* 3.4 1.6 + - - +
28N HIS* 3.0 39.2 + - + +
77N LEU* 3.9 8.0 - - + +
78N LEU* 2.9 46.7 + - - +
79N ILE* 4.1 16.2 - - + -
89N CYS 3.3 23.6 + - - -
90N ASP* 3.3 22.5 + - - +
93N LEU* 3.5 22.7 - - - +
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Residues in contact with TYR 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N ALA* 2.7 29.1 + - + +
24N GLN* 1.4 78.8 - - - +
26N PHE* 1.3 56.4 + - - +
29N SER* 2.9 27.7 + - - -
44N GLU* 3.1 31.2 - - - +
47N GLU* 4.0 13.7 - - + -
48N SER* 3.7 15.7 - - - -
51N GLU* 3.6 28.3 - - + -
90N ASP* 3.3 41.7 + - + -
93N LEU* 4.1 11.5 - - + +
94N GLU* 2.5 42.5 + - - +
130N HIS* 3.5 13.9 - + - -
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Residues in contact with PHE 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M ASP* 3.2 47.3 - - + -
59M ILE* 4.1 10.3 - - + -
71M LEU* 5.0 0.7 - - + -
22N ILE 2.9 20.9 + - - +
23N ASN* 3.9 4.7 - - - +
25N TYR* 1.3 78.5 - - - +
27N LEU* 1.3 61.7 + - - +
29N SER* 3.2 7.3 - - - -
30N ARG* 3.1 36.9 + - + +
45N TYR* 3.8 26.7 - + - -
48N SER* 3.6 18.1 + - - +
52N MET* 4.0 6.7 - - + -
159N HEM 3.6 55.0 - + + -
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Residues in contact with LEU 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M ILE* 4.5 5.2 - - + -
63M LEU* 4.3 5.4 - - + -
69M PRO* 3.7 50.0 - - + +
71M LEU* 4.5 15.4 - - + +
23N ASN 3.0 17.1 + - - +
24N GLN 4.0 2.2 - - - +
26N PHE* 1.3 75.1 - - - +
28N HIS* 1.3 59.5 + - - +
30N ARG* 3.2 3.4 + - - -
31N MET* 2.8 52.5 + - + +
77N LEU* 5.4 4.0 - - + -
79N ILE* 3.8 36.8 - - + -
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Residues in contact with HIS 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N GLN* 3.0 24.5 + - + +
27N LEU* 1.3 75.7 - - - +
29N SER* 1.3 58.4 + - - +
31N MET* 4.1 10.8 - - - -
32N TRP* 2.9 38.0 + - + -
44N GLU* 3.5 17.9 + - + +
78N LEU 3.4 17.0 - - - -
79N ILE* 3.5 10.9 - - + -
80N GLY 3.2 23.9 + - - -
86N MET* 3.4 47.9 + - + +
89N CYS* 4.1 0.2 - - + -
90N ASP* 2.9 29.7 + - - -
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Residues in contact with SER 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N TYR 2.9 14.4 + - - -
26N PHE* 3.2 13.2 - - - -
28N HIS* 1.3 77.0 - - - +
30N ARG* 1.3 81.2 + - - +
32N TRP 3.3 1.7 + - - -
33N ASN* 2.9 28.1 + - - -
41N GLY* 2.8 28.5 + - - -
44N GLU* 3.5 10.4 - - - +
45N TYR* 3.6 15.4 - - - +
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Residues in contact with ARG 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M ASP* 2.9 41.1 + - - +
59M ILE* 3.8 29.6 - - + -
60M GLU* 3.7 24.1 + - + +
63M LEU* 4.2 7.8 - - + +
26N PHE* 3.1 30.9 + - + +
27N LEU 3.9 2.2 - - - +
29N SER* 1.3 96.6 + - - +
31N MET* 1.3 61.8 + - - +
33N ASN* 3.3 21.1 + - + +
34N ASP* 2.8 30.3 + - - +
41N GLY 4.8 0.4 + - - -
45N TYR* 3.5 28.1 - - - +
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Residues in contact with MET 31 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M LEU* 4.2 17.0 - - + +
27N LEU* 2.8 45.6 + - + +
28N HIS* 3.7 12.8 - - - +
30N ARG* 1.3 73.2 - - - +
32N TRP* 1.3 64.6 + - - +
34N ASP* 3.2 8.6 + - - +
35N TRP* 3.0 49.3 + - + -
79N ILE* 4.0 14.8 - - + -
80N GLY 3.4 23.3 - - - +
81N GLU* 4.8 2.0 - - - -
86N MET* 3.9 20.2 - - + -
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Residues in contact with TRP 32 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N HIS* 2.9 33.9 + - + +
29N SER 3.7 1.8 - - - +
31N MET* 1.3 72.7 - - - +
33N ASN* 1.3 60.5 + - - +
35N TRP* 3.2 12.2 + + - -
36N GLY 3.2 3.8 + - - -
37N LEU* 2.9 67.3 + - + +
40N LEU* 3.6 34.0 - - + +
41N GLY 3.7 6.3 - - - +
44N GLU* 3.6 36.1 - - + -
83N THR* 2.8 40.7 + - + +
86N MET* 3.4 34.2 - - + +
87N LEU* 4.1 21.1 - - + -
90N ASP* 4.8 1.3 - - - -
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Residues in contact with ASN 33 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M GLU* 5.1 4.6 - - + +
29N SER* 2.9 14.1 + - - +
30N ARG* 3.5 39.2 + - + +
32N TRP* 1.3 74.6 - - - +
34N ASP* 1.3 66.6 + - - +
36N GLY* 3.1 12.4 + - - -
37N LEU 4.9 1.1 - - - +
38N LYS* 3.9 26.4 + - + +
41N GLY* 3.4 23.3 - - - -
42N ALA 4.2 0.6 - - - +
136T THR* 5.1 1.2 + - - +
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Residues in contact with ASP 34 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M LEU* 3.7 42.5 - - + +
64M PHE* 4.1 6.9 + - - +
66M GLU* 6.1 0.7 - - - +
30N ARG 2.8 19.7 + - - +
31N MET* 3.2 6.7 + - - +
33N ASN* 1.3 74.0 - - - +
35N TRP* 1.3 73.6 + - - +
36N GLY 3.4 0.2 + - - -
132T ASP* 4.3 12.4 - - - +
136T THR* 3.2 23.7 + - - +
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Residues in contact with TRP 35 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N MET* 3.0 34.7 + - + +
32N TRP* 3.2 26.7 + + - +
33N ASN 3.1 0.6 - - - -
34N ASP* 1.3 92.6 + - - +
36N GLY* 1.3 57.5 + - - +
37N LEU* 4.1 15.3 - - + -
81N GLU 3.4 25.1 - - - -
82N ASN* 3.9 2.2 - - + -
83N THR* 4.2 9.9 - - - -
86N MET* 3.6 31.4 - - + -
136T THR* 3.6 7.3 - - - +
140T LEU* 3.0 27.7 + - - +
143T LYS* 3.8 35.8 + - - +
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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