Contacts of the helix formed by residues 4 - 36 (chain W) in PDB entry 3ISE
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 W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2W LYS 3.3 3.2 + - - -
3W GLY* 1.3 70.5 - - - -
5W LYS* 1.3 68.6 + - - +
6W LYS* 3.7 4.9 + - - +
7W VAL* 2.9 40.3 + - + +
8W ILE* 3.0 15.9 + - - +
65W LEU* 5.1 1.8 - - - +
107W HIS* 3.3 26.2 + - - -
111W VAL* 4.0 20.4 - - + +
113W ASP* 5.7 2.8 + - + +
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Residues in contact with LYS 5 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3W GLY 3.5 5.1 + - - -
4W ASP* 1.3 76.1 + - - +
6W LYS* 1.3 63.3 + - + +
8W ILE* 3.3 10.6 + - - +
9W GLN* 3.1 42.2 + - + +
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Residues in contact with LYS 6 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W ASP* 3.2 4.4 + - - +
5W LYS* 1.3 78.4 - - + +
7W VAL* 1.3 66.4 + - - +
9W GLN* 3.3 20.2 + - + +
10W HIS* 3.1 28.8 + - + -
107W HIS* 3.3 35.2 - - + +
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Residues in contact with VAL 7 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W ASP* 2.9 32.4 + - + +
6W LYS* 1.3 77.0 - - - +
8W ILE* 1.3 52.1 + - - +
10W HIS* 3.0 10.0 + - - +
11W LEU* 2.7 52.9 + - + +
65W LEU* 4.2 5.8 - - + -
107W HIS* 3.7 17.7 - - + -
108W CYS* 4.4 15.7 - - - -
111W VAL* 4.0 12.6 - - + -
113W ASP* 3.6 27.4 - - + +
116W SER* 4.1 3.1 - - - +
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Residues in contact with ILE 8 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3W GLY* 3.8 14.1 - - - +
4W ASP 3.0 15.0 + - - +
5W LYS* 3.5 10.5 - - - +
7W VAL* 1.3 75.2 - - - +
9W GLN* 1.3 57.4 + - + +
11W LEU* 3.7 8.5 - - + +
12W ASN* 2.9 43.3 + - - +
62W ILE* 4.2 9.6 - - + -
65W LEU* 3.6 42.8 - - + +
66W GLU 4.8 0.4 - - - -
67W GLY* 4.1 25.4 - - - +
68W LEU 4.8 1.6 - - - +
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Residues in contact with GLN 9 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5W LYS* 3.1 34.3 + - + +
6W LYS* 3.5 28.6 + - - +
8W ILE* 1.3 76.3 - - + +
10W HIS* 1.3 58.4 + - + +
12W ASN* 3.5 7.3 + - - +
13W LYS* 3.0 27.5 + - - +
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Residues in contact with HIS 10 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W LYS* 3.1 19.7 + - + -
7W VAL* 3.0 10.3 + - + +
9W GLN* 1.3 77.2 - - + +
11W LEU* 1.3 68.2 + - + +
13W LYS* 3.0 18.7 + - + +
14W ILE* 2.9 28.1 + - - +
100W ASP 4.6 3.0 + - - -
103W GLU* 4.0 27.3 + - + -
104W ALA* 3.7 26.8 + - + +
107W HIS* 3.9 33.7 + + + +
108W CYS* 6.3 1.1 - - - -
120W LEU* 6.0 0.2 - - + -
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Residues in contact with LEU 11 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W VAL* 2.7 29.2 + - + +
8W ILE* 3.3 6.7 + - - +
10W HIS* 1.3 73.9 - - + +
12W ASN* 1.3 51.0 + - - +
14W ILE* 3.1 4.9 + - - +
15W LEU* 2.7 34.8 + - - +
58W LEU* 3.9 23.7 - - + +
61W ARG* 3.9 20.4 - - + -
62W ILE* 3.6 26.9 - - + -
65W LEU* 3.8 28.9 - - + -
108W CYS* 5.6 0.2 - - - -
116W SER* 4.1 9.2 - - - +
119W LEU* 5.3 2.5 - - + -
120W LEU* 4.1 26.5 - - + -
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Residues in contact with ASN 12 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W ILE* 2.9 32.6 + - - +
9W GLN* 3.6 7.3 - - - +
11W LEU* 1.3 75.6 - - - +
13W LYS* 1.3 57.3 + - - +
15W LEU* 3.5 12.3 - - - +
16W GLY* 2.8 25.3 + - - -
62W ILE* 3.9 5.5 - - - +
68W LEU 3.1 20.2 + - - -
69W PRO* 3.5 5.0 - - - +
70W ASN* 2.8 41.9 + - + +
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Residues in contact with LYS 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W GLN 3.0 13.6 + - - +
10W HIS* 3.0 23.1 + - + +
12W ASN* 1.3 77.3 - - - +
14W ILE* 1.3 59.4 + - + +
16W GLY* 2.9 4.4 + - - -
17W ASN* 2.9 30.8 + - - +
96W LYS* 4.5 8.7 - - - +
100W ASP* 4.1 34.2 + - + +
103W GLU* 5.3 5.7 + - - -
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Residues in contact with ILE 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W HIS* 2.9 22.4 + - - +
11W LEU* 3.4 6.1 - - - +
13W LYS* 1.3 75.7 - - + +
15W LEU* 1.3 64.4 + - - +
17W ASN* 3.0 11.0 + - + +
18W GLU* 2.9 28.4 + - + +
58W LEU* 3.9 17.3 - - + -
97W ALA 5.0 0.7 - - - +
100W ASP* 3.7 34.8 - - + +
101W LEU* 3.4 42.4 - - + +
104W ALA* 4.5 6.1 - - + -
120W LEU* 4.1 15.3 - - + -
123W ILE* 5.0 4.3 - - + -
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Residues in contact with LEU 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W LEU 2.7 19.4 + - - +
12W ASN* 3.5 23.3 - - - +
14W ILE* 1.3 73.3 - - - +
16W GLY* 1.3 56.6 + - - +
18W GLU* 3.1 2.2 + - - +
19W LEU* 2.9 39.1 + - + +
55W ALA* 3.9 36.1 - - + +
58W LEU* 3.8 14.9 - - + +
59W ILE* 3.8 24.7 - - + +
62W ILE* 4.5 5.8 - - + -
69W PRO* 4.4 3.4 - - + -
70W ASN 3.9 22.4 - - - +
71W LEU* 4.2 5.4 - - + -
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Residues in contact with GLY 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W ASN 2.8 18.3 + - - -
13W LYS* 2.9 6.0 + - - -
15W LEU* 1.3 72.0 - - - +
17W ASN* 1.3 63.4 + - - +
19W LEU* 3.2 21.3 + - - +
20W ILE* 3.2 21.5 + - - +
70W ASN 5.5 1.8 - - - -
73W ASP 5.0 8.8 - - - +
75W GLY 5.4 0.3 + - - -
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Residues in contact with ASN 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13W LYS* 2.9 18.6 + - - +
14W ILE* 3.0 13.4 + - + +
16W GLY* 1.3 78.1 - - - +
18W GLU* 1.3 62.9 + - + +
20W ILE* 3.5 16.9 + - - +
21W ALA* 3.2 22.3 + - - +
93W LEU* 5.0 6.5 - - + +
96W LYS* 4.3 10.3 + - - +
97W ALA* 3.8 28.7 + - + +
100W ASP* 2.6 39.6 + - - +
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Residues in contact with GLU 18 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14W ILE* 2.9 21.9 + - + +
15W LEU* 3.7 8.5 - - - +
17W ASN* 1.3 77.2 - - + +
19W LEU* 1.3 62.9 + - - +
20W ILE 3.3 0.2 + - - -
21W ALA* 3.3 4.3 + - - +
22W ILE* 3.0 30.0 + - - +
51W GLU* 2.1 53.9 - - - +
54W HIS* 3.3 18.8 - - + +
55W ALA* 4.4 8.7 - - + -
58W LEU* 4.1 17.7 - - + -
101W LEU* 5.4 1.0 - - - +
123W ILE* 3.6 9.5 - - + +
127W GLU* 2.5 17.4 - - - +
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Residues in contact with LEU 19 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15W LEU* 2.9 32.6 + - + +
16W GLY* 3.5 9.6 - - - +
18W GLU* 1.3 77.2 - - - +
20W ILE* 1.3 62.2 + - - +
22W ILE* 3.6 11.0 + - + +
23W ASN* 3.5 23.2 + - - +
55W ALA* 4.7 1.8 - - + -
59W ILE* 5.9 0.4 - - + -
70W ASN 3.9 8.1 - - - +
71W LEU* 3.7 39.7 - - + +
73W ASP 4.5 10.1 - - - +
74W LEU* 3.9 15.9 - - + +
159W HEM 3.8 35.0 - - + -
23X ASN* 4.7 5.2 - - - +
74X LEU* 6.1 0.4 - - + -
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Residues in contact with ILE 20 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16W GLY 3.2 15.7 + - - +
17W ASN* 3.6 19.3 - - - +
19W LEU* 1.3 77.2 - - - +
21W ALA* 1.3 59.5 + - - +
23W ASN* 3.1 5.5 + - - +
24W GLN* 2.8 28.1 + - - +
74W LEU* 4.1 8.3 - - + -
75W GLY* 3.8 38.6 - - - +
76W LYS 3.6 21.1 - - - +
77W LEU* 4.1 14.7 - - + +
93W LEU* 3.8 24.7 - - + -
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Residues in contact with ALA 21 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W ASN 3.2 13.7 + - - +
18W GLU* 3.6 4.5 - - - +
20W ILE* 1.3 80.3 - - - +
22W ILE* 1.3 63.1 + - - +
24W GLN* 4.5 0.9 - - - -
25W TYR* 3.0 49.9 + - + +
51W GLU* 4.1 16.8 - - + +
93W LEU* 3.5 24.9 - - + -
94W GLU* 4.9 0.9 - - - +
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Residues in contact with ILE 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W GLU 3.0 20.6 + - - +
19W LEU* 3.7 11.2 - - - +
20W ILE 3.2 0.2 - - - -
21W ALA* 1.3 75.0 - - - +
23W ASN* 1.3 65.4 + - - +
26W PHE* 2.9 27.4 + - + +
48W SER* 3.1 20.1 + - - +
51W GLU* 3.9 9.6 - - + +
52W MET* 3.7 45.5 - - + +
55W ALA* 4.1 9.0 - - + -
159W HEM 3.7 53.4 - - + -
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Residues in contact with ASN 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W LEU 3.5 7.8 + - - +
20W ILE 3.1 7.3 + - - +
22W ILE* 1.3 84.5 - - - +
24W GLN* 1.3 57.2 + - - +
26W PHE* 4.4 2.2 - - - -
27W LEU* 2.9 32.6 + - - +
74W LEU* 3.6 20.2 - - - +
77W LEU* 4.2 9.9 - - + -
159W HEM 3.3 24.9 - - - +
19X LEU* 4.8 8.7 - - - +
71X LEU* 3.3 47.8 + - + +
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Residues in contact with GLN 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20W ILE* 2.8 22.3 + - - +
21W ALA* 4.2 2.7 - - - +
23W ASN* 1.3 74.3 - - - +
25W TYR* 1.3 59.7 + - + +
27W LEU* 3.4 2.4 + - - +
28W HIS* 2.9 40.8 + - + +
77W LEU* 3.9 15.9 - - + +
78W LEU* 2.9 49.1 + - - +
79W ILE* 4.5 6.1 - - + -
89W CYS 3.2 26.3 + - - -
90W ASP* 3.1 24.5 + - - +
93W LEU* 3.6 22.4 - - - +
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Residues in contact with TYR 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W ALA* 3.0 29.7 + - + +
24W GLN* 1.3 73.8 - - + +
26W PHE* 1.3 61.8 + - - +
29W SER* 2.8 27.5 + - - -
44W GLU* 3.2 36.7 - - - +
47W GLU* 4.0 23.6 - - + -
48W SER* 4.0 6.5 - - - +
51W GLU* 3.7 16.6 - - + -
90W ASP* 3.3 33.9 + - + -
93W LEU* 3.8 23.0 - - + +
94W GLU* 2.1 40.4 + - - +
130W HIS* 3.4 17.4 - + - -
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Residues in contact with PHE 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W ILE 2.9 21.4 + - - +
23W ASN* 3.8 5.4 - - - +
25W TYR* 1.3 77.3 - - - +
27W LEU* 1.3 64.5 + - - +
29W SER* 3.2 6.6 + - - -
30W ARG* 3.1 37.0 + - + -
45W TYR* 3.9 24.5 - + - -
48W SER* 3.5 19.7 + - - +
52W MET* 4.1 7.2 - - + -
159W HEM 3.0 51.4 - + + -
56X ASP* 3.0 35.4 - - - -
59X ILE* 3.9 18.6 - - + -
71X LEU* 5.0 1.1 - - + -
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Residues in contact with LEU 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23W ASN 2.9 17.4 + - - +
24W GLN 3.7 4.0 - - - +
26W PHE* 1.3 79.3 - - - +
28W HIS* 1.3 55.8 + - - +
30W ARG* 3.3 3.8 + - - +
31W MET* 2.9 46.5 + - + +
77W LEU* 5.3 4.7 - - + -
79W ILE* 3.5 39.5 - - + -
59X ILE* 4.5 9.6 - - + -
63X LEU* 4.6 0.7 - - + -
69X PRO* 4.0 46.2 - - + +
71X LEU* 4.4 15.1 - - + +
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Residues in contact with HIS 28 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24W GLN* 2.9 22.5 + - + +
25W TYR 3.7 0.2 - - - +
26W PHE 3.2 0.4 - - - -
27W LEU* 1.3 73.1 - - - +
29W SER* 1.3 70.2 + - - +
31W MET* 3.3 4.9 + - - +
32W TRP* 3.0 29.4 + - + +
44W GLU* 3.4 18.1 + - + +
78W LEU 3.5 17.0 - - - -
79W ILE* 3.5 21.1 - - + -
80W GLY 3.2 20.0 + - - -
86W MET* 3.6 47.7 - - + +
89W CYS* 4.3 0.2 - - + -
90W ASP* 3.1 28.7 + - - -
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Residues in contact with SER 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W TYR 2.8 17.2 + - - -
26W PHE* 3.2 11.4 + - - -
28W HIS* 1.3 71.9 - - - +
30W ARG* 1.3 81.1 + - - +
32W TRP* 2.9 8.8 + - - +
33W ASN* 2.9 25.1 + - - -
41W GLY* 2.7 32.7 + - - -
44W GLU* 3.7 6.8 - - - +
45W TYR* 3.4 16.6 - - - +
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Residues in contact with ARG 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W PHE* 3.1 21.9 + - + +
27W LEU 3.7 7.2 - - - +
29W SER* 1.3 99.7 + - - +
31W MET* 1.3 60.8 + - - +
33W ASN* 3.5 20.1 + - + +
34W ASP* 3.0 27.7 + - - +
41W GLY 4.6 0.2 + - - -
42W ALA* 6.0 0.2 - - - +
45W TYR* 3.3 36.1 - - - +
56X ASP* 2.8 40.9 + - - +
59X ILE* 3.9 17.9 - - + -
60X GLU* 3.6 25.9 + - + +
63X LEU* 3.8 18.1 - - + +
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Residues in contact with MET 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W LEU* 2.9 47.2 + - + +
28W HIS* 3.6 10.8 - - - +
30W ARG* 1.3 75.6 - - - +
32W TRP* 1.3 63.2 + - - +
34W ASP* 3.5 5.4 + - - +
35W TRP* 3.2 51.8 + - + -
79W ILE* 3.9 12.6 - - + -
80W GLY 3.5 24.5 - - - +
81W GLU* 5.1 1.3 - - - -
86W MET* 3.8 16.6 - - + -
63X LEU* 4.2 18.8 - - + -
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Residues in contact with TRP 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W HIS* 3.0 24.6 + - + -
29W SER* 2.9 10.6 + - - +
31W MET* 1.3 73.6 - - - +
33W ASN* 1.3 63.7 + - - +
35W TRP* 3.2 21.6 + + - -
37W LEU* 3.0 45.1 + - + +
40W LEU* 3.8 39.5 - - + +
41W GLY 3.7 13.0 - - - +
44W GLU* 3.7 35.2 - - + -
83W THR* 2.8 40.3 + - + +
86W MET* 3.7 34.7 - - + -
87W LEU* 4.0 21.3 - - + -
90W ASP* 4.9 0.2 - - - -
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Residues in contact with ASN 33 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O THR* 4.8 0.9 + - - +
29W SER* 2.9 14.8 + - - +
30W ARG* 3.5 38.0 + - + +
31W MET 3.3 0.2 - - - -
32W TRP* 1.3 74.3 - - - +
34W ASP* 1.3 64.4 + - - +
36W GLY* 3.0 14.4 + - - -
37W LEU 4.7 0.7 - - - -
38W LYS* 3.8 31.7 + - + +
41W GLY* 3.4 22.1 - - - -
42W ALA* 4.2 0.6 - - - +
60X GLU* 5.2 5.4 - - + +
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Residues in contact with ASP 34 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132O ASP* 4.0 15.3 - - - +
136O THR* 3.2 23.7 + - - +
30W ARG 3.0 17.9 + - - +
31W MET* 3.6 8.7 - - - +
33W ASN* 1.3 77.0 - - - +
35W TRP* 1.3 68.8 + - - +
60X GLU 5.5 0.2 - - - +
63X LEU* 3.6 41.0 - - + +
64X PHE* 4.2 4.0 - - - -
66X GLU* 6.0 0.5 - - - +
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Residues in contact with TRP 35 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O THR* 3.1 16.9 - - - +
139O GLY 5.5 0.2 - - - -
140O LEU* 3.3 21.3 + - - +
143O LYS* 3.7 38.3 + - - +
31W MET* 3.2 36.9 + - + +
32W TRP* 3.2 25.3 + + - +
33W ASN 3.1 0.6 - - - -
34W ASP* 1.3 87.9 + - - +
36W GLY* 1.3 56.6 + - - +
37W LEU* 3.3 13.7 - - + -
81W GLU 3.6 24.0 - - - -
82W ASN* 4.1 2.0 - - - -
83W THR* 4.3 8.3 - - - -
86W MET* 3.5 32.8 - - + -
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Residues in contact with GLY 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O THR* 3.2 15.3 - - - +
140O LEU* 3.9 9.4 - - - +
33W ASN 3.0 14.9 + - - -
35W TRP* 1.3 79.2 - - - +
37W LEU* 1.3 60.6 + - - +
38W LYS* 3.3 13.2 - - - +
154W MET* 3.3 29.6 - - - +
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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) + - + + + + + -
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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