Contacts of the helix formed by residues 4 - 36 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3S GLY* 1.3 68.8 - - - -
5S LYS* 1.3 66.4 + - - +
6S LYS* 2.8 28.1 + - - +
7S VAL* 2.9 27.6 + - + +
8S ILE* 3.1 25.2 + - - +
65S LEU* 5.5 2.0 - - - +
107S HIS* 3.3 13.5 + - - -
111S VAL* 3.2 29.5 - - + +
113S ASP* 5.9 1.5 + - + +
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Residues in contact with LYS 5 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S GLY 3.6 4.1 + - - +
4S ASP* 1.3 75.5 + - - +
6S LYS* 1.3 59.8 + - + +
8S ILE* 3.5 10.7 + - + +
9S GLN* 3.1 37.4 + - + +
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Residues in contact with LYS 6 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S ASP* 2.8 10.0 + - - +
5S LYS* 1.3 74.3 - - + +
7S VAL* 1.3 58.9 + - - +
9S GLN* 3.4 22.2 + - + +
10S HIS* 2.9 36.0 + - + -
107S HIS* 3.4 32.3 - - + +
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Residues in contact with VAL 7 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S ASP* 2.9 21.2 + - + +
6S LYS* 1.3 73.0 - - - +
8S ILE* 1.3 60.4 + - - +
10S HIS* 3.0 7.9 + - - +
11S LEU* 2.7 50.4 + - + +
65S LEU* 4.2 6.3 - - + -
107S HIS* 3.6 13.5 - - + -
108S CYS* 4.2 15.7 - - - -
111S VAL* 3.6 32.3 - - + -
113S ASP* 3.4 24.2 - - - +
116S SER* 3.9 7.9 - - - +
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Residues in contact with ILE 8 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S GLY 4.4 9.2 - - - +
4S ASP 3.1 15.9 + - - +
5S LYS* 3.6 11.0 - - - +
6S LYS 3.3 0.2 - - - -
7S VAL* 1.3 75.1 - - - +
9S GLN* 1.3 57.2 + - + +
11S LEU* 3.1 9.6 + - + +
12S ASN* 2.8 43.3 + - - +
62S ILE* 4.3 7.2 - - + +
65S LEU* 3.9 32.5 - - + +
66S GLU 4.4 1.3 - - - +
67S GLY* 3.6 38.1 - - - +
68S LEU 4.6 1.1 - - - +
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Residues in contact with GLN 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S LYS* 3.1 24.6 + - + +
6S LYS* 3.5 28.7 - - - +
7S VAL 3.3 0.2 - - - -
8S ILE* 1.3 75.5 - - + +
10S HIS* 1.3 60.1 + - + +
12S ASN* 3.4 7.6 + - - +
13S LYS* 2.9 27.4 + - - +
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Residues in contact with HIS 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S LYS* 2.9 25.7 + - + +
7S VAL* 3.4 9.6 - - - +
9S GLN* 1.3 77.9 - - + +
11S LEU* 1.3 63.2 + - + +
13S LYS* 3.0 25.4 + - + +
14S ILE* 3.1 20.5 + - - +
100S ASP 4.8 1.4 + - - -
103S GLU* 4.0 20.6 + - + -
104S ALA* 3.6 34.7 - - + +
107S HIS* 3.9 31.9 - + + +
108S CYS* 6.0 2.0 - - - -
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Residues in contact with LEU 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S VAL* 2.7 42.0 + - + +
8S ILE* 3.6 7.6 - - - +
10S HIS* 1.3 72.6 - - + +
12S ASN* 1.3 58.7 + - - +
14S ILE* 3.4 4.8 + - - +
15S LEU* 2.9 29.3 + - - +
58S LEU* 4.1 25.5 - - + +
61S ARG* 4.0 13.9 - - + -
62S ILE* 3.7 26.0 - - + +
65S LEU* 3.9 18.2 - - + -
108S CYS* 5.5 0.2 - - - -
116S SER* 4.0 10.3 - - - +
119S LEU* 5.5 1.1 - - + -
120S LEU* 4.1 28.0 - - + -
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Residues in contact with ASN 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ILE* 2.8 32.9 + - - +
9S GLN* 3.8 7.6 - - - +
11S LEU* 1.3 70.3 - - - +
13S LYS* 1.3 61.7 + - - +
15S LEU* 3.6 7.7 - - - +
16S GLY* 2.9 24.4 + - - -
62S ILE* 3.6 9.4 - - - +
68S LEU 3.0 24.0 + - - -
69S PRO* 3.6 4.3 - - - +
70S ASN* 2.7 41.1 + - + +
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Residues in contact with LYS 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S GLN 2.9 15.4 + - - +
10S HIS* 3.0 23.3 + - + +
12S ASN* 1.3 76.8 - - - +
14S ILE* 1.3 63.3 + - + +
16S GLY* 3.1 4.7 + - - -
17S ASN* 3.1 22.6 + - - +
96S LYS* 4.4 10.3 - - - +
100S ASP* 3.3 41.8 + - + +
103S GLU* 5.8 1.6 + - - -
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Residues in contact with ILE 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S HIS* 3.1 16.8 + - - +
11S LEU* 3.7 6.5 - - - +
13S LYS* 1.3 72.6 - - + +
15S LEU* 1.3 62.0 + - - +
17S ASN* 2.9 11.8 + - + +
18S GLU* 2.9 37.2 + - - +
58S LEU* 3.9 18.4 - - + -
97S ALA 4.7 0.7 - - - +
100S ASP* 3.8 18.8 - - + +
101S LEU* 3.5 56.3 - - + +
104S ALA* 4.2 5.4 - - + -
120S LEU* 4.2 15.3 - - + -
123S ILE* 4.9 2.0 - - + -
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Residues in contact with LEU 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S LEU 2.9 18.4 + - - +
12S ASN* 3.6 18.2 - - - +
14S ILE* 1.3 76.6 - - - +
16S GLY* 1.3 61.4 + - - +
18S GLU* 3.1 2.4 + - - +
19S LEU* 2.9 41.2 + - + +
55S ALA* 3.8 40.4 - - + +
58S LEU* 3.8 13.6 - - + +
59S ILE* 3.8 24.7 - - + -
62S ILE* 4.0 10.5 - - + -
69S PRO* 4.3 0.2 - - + -
70S ASN 3.7 18.6 - - - +
71S LEU* 3.9 8.3 - - + -
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Residues in contact with GLY 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S ASN 2.9 15.8 + - - -
13S LYS* 3.1 5.3 + - - -
15S LEU* 1.3 75.7 - - - +
17S ASN* 1.3 62.5 + - - +
19S LEU* 3.3 12.6 + - - +
20S ILE* 3.3 27.3 + - - +
70S ASN 5.3 2.4 + - - -
73S ASP 5.0 8.4 - - - +
75S GLY 5.1 1.7 + - - -
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Residues in contact with ASN 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13S LYS* 3.1 17.0 + - - +
14S ILE* 2.9 15.9 + - + +
16S GLY* 1.3 73.4 - - - +
18S GLU* 1.3 67.7 + - + +
20S ILE* 3.1 18.0 + - - +
21S ALA* 2.9 23.0 + - - +
93S LEU* 5.0 7.3 - - + +
96S LYS* 4.4 10.3 + - - +
97S ALA* 4.1 26.3 + - + +
100S ASP* 2.8 40.6 + - - +
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Residues in contact with GLU 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S ILE* 2.9 22.1 + - + +
15S LEU* 3.5 7.0 - - - +
17S ASN* 1.3 76.3 - - + +
19S LEU* 1.3 59.7 + - - +
21S ALA* 3.2 4.6 + - - +
22S ILE* 2.9 35.3 + - - +
51S GLU* 2.8 41.0 - - - +
54S HIS* 3.9 12.3 - - + +
55S ALA* 4.3 17.7 - - + +
58S LEU* 4.0 18.2 - - + -
97S ALA* 6.0 2.0 - - - +
101S LEU* 5.5 0.7 - - - +
123S ILE* 3.3 19.2 - - - +
127S GLU* 2.9 19.3 - - - +
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Residues in contact with LEU 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S LEU* 2.9 38.9 + - + +
16S GLY* 3.3 9.2 + - - +
17S ASN 3.1 0.4 - - - -
18S GLU* 1.3 78.3 - - - +
20S ILE* 1.3 61.7 + - - +
22S ILE* 3.6 11.8 + - + +
23S ASN* 3.5 17.8 + - - +
55S ALA* 4.9 2.7 - - + -
59S ILE* 5.9 0.2 - - + -
70S ASN 3.8 21.8 - - - +
71S LEU* 4.0 23.6 - - + +
73S ASP 4.6 7.2 - - - +
74S LEU* 3.8 22.0 - - + +
159S HEM 3.8 29.4 - - + -
23T ASN* 4.4 9.4 - - - +
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Residues in contact with ILE 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S GLY 3.3 15.5 + - - +
17S ASN* 3.1 18.1 + - - +
19S LEU* 1.3 78.3 - - - +
21S ALA* 1.3 57.4 + - - +
23S ASN* 3.3 3.6 + - - +
24S GLN* 2.8 28.9 + - - +
74S LEU* 4.1 8.0 - - + +
75S GLY* 3.7 39.7 - - - +
76S LYS 3.6 20.6 - - - +
77S LEU* 4.1 15.4 - - + +
93S LEU* 3.8 27.4 - - + -
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Residues in contact with ALA 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S ASN 2.9 13.2 + - - +
18S GLU* 3.2 8.5 + - - +
20S ILE* 1.3 74.8 - - - +
22S ILE* 1.3 55.9 + - - +
24S GLN* 4.3 0.9 - - - -
25S TYR* 2.7 51.0 + - + +
51S GLU* 3.0 29.8 - - - +
93S LEU* 3.7 20.6 - - + +
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Residues in contact with ILE 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S GLU 2.9 24.9 + - - +
19S LEU* 3.7 17.5 - - + +
20S ILE 3.3 0.2 - - - -
21S ALA* 1.3 74.2 - - - +
23S ASN* 1.3 67.7 - - - +
26S PHE* 2.9 27.5 + - - +
48S SER* 2.9 14.5 + - - +
51S GLU* 3.7 20.9 - - + +
52S MET* 3.8 39.9 - - + +
55S ALA* 4.3 4.9 - - + -
159S HEM 3.7 46.9 - - + -
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Residues in contact with ASN 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S LEU 3.5 10.2 + - - +
20S ILE 3.3 6.4 + - - +
21S ALA 3.3 0.4 - - - -
22S ILE* 1.3 82.2 - - - +
24S GLN* 1.3 63.3 + - - +
26S PHE* 3.3 1.2 + - - -
27S LEU* 3.1 25.8 + - - +
74S LEU* 3.8 14.7 - - - +
77S LEU* 4.1 16.6 - - + -
159S HEM 3.1 31.5 - - - +
19T LEU* 4.7 7.3 - - - +
71T LEU* 3.0 42.3 + - + +
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Residues in contact with GLN 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S ILE* 2.8 19.7 + - - +
21S ALA* 3.8 3.1 - - - +
23S ASN* 1.3 74.6 - - - +
25S TYR* 1.3 67.3 + - + +
27S LEU* 4.0 1.2 - - - +
28S HIS* 3.1 32.2 + - + -
77S LEU* 3.9 6.5 - - + +
78S LEU* 2.8 46.7 + - - +
79S ILE* 4.1 14.1 - - + -
89S CYS 3.4 12.3 + - - -
90S ASP* 2.9 43.6 + - - +
93S LEU* 3.6 20.6 - - - +
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Residues in contact with TYR 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S ALA* 2.7 30.2 + - + +
24S GLN* 1.3 81.1 - - - +
26S PHE* 1.3 61.9 + - - +
29S SER* 2.9 21.7 + - - -
44S GLU* 3.2 27.3 - - - +
47S GLU* 4.0 14.1 - - + -
48S SER* 3.8 18.6 - - - +
51S GLU* 3.4 34.5 + - + -
90S ASP* 3.4 37.5 + - + -
93S LEU* 4.1 10.5 - - + +
94S GLU* 2.5 33.1 + - - +
130S HIS* 3.6 16.3 - + - -
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Residues in contact with PHE 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S ILE 2.9 20.5 + - - +
23S ASN* 3.8 5.6 - - - +
24S GLN 3.2 0.4 - - - -
25S TYR* 1.3 77.1 - - - +
27S LEU* 1.3 63.8 + - - +
29S SER* 3.3 6.1 - - - -
30S ARG* 3.1 51.3 + - + -
45S TYR* 3.9 23.1 - + - -
48S SER* 3.6 19.0 + - - -
52S MET* 4.1 8.7 - - + -
159S HEM 3.6 46.4 - + + -
56T ASP* 3.5 31.0 - - + -
59T ILE* 4.1 13.0 - - + -
71T LEU* 4.8 3.1 - - + -
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Residues in contact with LEU 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23S ASN 3.1 15.1 + - - +
24S GLN 4.0 2.7 - - - +
26S PHE* 1.3 81.3 - - - +
28S HIS* 1.3 56.6 + - - +
30S ARG* 3.2 3.3 + - - +
31S MET* 2.9 51.5 + - + +
77S LEU* 5.4 1.6 - - + -
79S ILE* 3.9 37.0 - - + -
59T ILE* 4.4 8.1 - - + -
63T LEU* 4.5 0.9 - - + -
69T PRO* 3.8 52.3 - - + +
71T LEU* 4.2 19.0 - - + +
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Residues in contact with HIS 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S GLN* 3.1 20.4 + - + +
25S TYR 3.7 0.4 - - - +
27S LEU* 1.3 74.1 - - - +
29S SER* 1.3 65.4 + - - +
31S MET* 3.3 12.0 + - - -
32S TRP* 2.8 34.1 + - + -
44S GLU* 3.3 19.6 + - + +
78S LEU 3.6 17.0 - - - -
79S ILE* 3.7 11.0 - - + +
80S GLY 3.2 22.3 + - - -
86S MET* 3.5 47.7 + - + +
89S CYS* 4.2 0.7 - - + -
90S ASP* 2.8 30.3 + - - -
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Residues in contact with SER 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S TYR 2.9 13.6 + - - -
26S PHE* 3.3 13.2 - - - -
28S HIS* 1.3 76.1 - - - +
30S ARG* 1.3 80.1 + - - -
32S TRP* 3.2 3.3 + - - +
33S ASN* 2.9 28.5 + - - -
41S GLY* 2.7 29.0 + - - -
44S GLU* 3.4 7.7 - - - +
45S TYR* 3.3 17.3 - - - +
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Residues in contact with ARG 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S PHE* 3.1 34.5 + - + +
27S LEU 3.2 1.5 + - - +
29S SER* 1.3 94.8 + - - +
31S MET* 1.3 61.2 + - - +
33S ASN* 3.4 23.1 + - + +
34S ASP* 2.9 29.1 + - - +
41S GLY 4.7 0.2 + - - -
42S ALA* 6.1 0.2 - - - +
45S TYR* 3.6 27.2 - - - +
159S HEM 5.4 0.2 - - - +
56T ASP* 2.8 42.0 + - - +
59T ILE* 3.8 15.3 - - + -
60T GLU* 3.8 25.0 + - + +
63T LEU* 3.7 19.9 - - + +
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Residues in contact with MET 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S LEU* 2.9 47.7 + - + +
28S HIS* 3.5 19.7 - - - +
30S ARG* 1.3 74.9 - - - +
32S TRP* 1.3 64.6 + - - +
34S ASP* 3.1 7.2 + - - +
35S TRP* 2.9 57.7 + - + -
79S ILE* 4.1 9.4 - - + -
80S GLY 3.5 21.5 - - - +
81S GLU* 4.8 2.5 - - - -
86S MET* 3.9 9.4 - - + -
63T LEU* 4.1 16.4 - - + -
68T LEU* 6.5 1.3 - - + -
69T PRO* 5.9 0.4 - - + -
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Residues in contact with TRP 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28S HIS* 2.8 28.3 + - + +
29S SER 3.5 4.0 - - - +
31S MET* 1.3 77.6 - - - +
33S ASN* 1.3 61.7 + - - +
35S TRP* 3.2 14.1 + + - +
36S GLY 3.1 4.3 + - - -
37S LEU* 3.0 53.8 + - + +
40S LEU* 3.7 30.8 - - + +
41S GLY 3.8 4.0 - - - +
44S GLU* 3.7 42.6 - - + -
83S THR* 2.9 42.2 + - + -
86S MET* 3.3 39.7 - - + +
87S LEU* 4.1 20.6 - - + -
90S ASP* 4.8 0.7 - - - -
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Residues in contact with ASN 33 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136K THR* 5.2 0.7 + - - +
29S SER* 2.9 18.2 + - - +
30S ARG* 3.4 38.2 + - + +
31S MET 3.3 0.2 - - - -
32S TRP* 1.3 71.7 - - - +
34S ASP* 1.3 62.9 + - - +
36S GLY* 3.0 15.1 + - - +
37S LEU 4.8 2.0 - - - +
38S LYS* 3.8 26.3 + - + +
41S GLY* 3.4 22.8 - - - -
42S ALA 4.3 0.4 - - - +
60T GLU* 5.2 4.2 - - + +
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Residues in contact with ASP 34 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132K ASP* 4.5 10.6 - - - +
136K THR* 3.1 24.1 + - - +
30S ARG 2.9 18.2 + - - +
31S MET* 3.1 9.4 + - - +
33S ASN* 1.3 75.1 - - - +
35S TRP* 1.3 75.9 + - - +
36S GLY 3.4 0.2 + - - -
63T LEU* 3.9 39.6 - - + +
64T PHE* 4.2 6.8 + - - +
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Residues in contact with TRP 35 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136K THR* 3.5 10.4 - - - +
140K LEU* 3.3 21.1 + - - +
143K LYS* 3.6 36.4 + - - +
31S MET* 2.9 41.7 + - + +
32S TRP* 3.2 24.2 + + - +
34S ASP* 1.3 94.5 + - - +
36S GLY* 1.3 60.8 + - - +
37S LEU* 3.3 15.5 - - + -
81S GLU 3.6 24.7 - - - -
82S ASN* 4.0 7.0 - - - -
83S THR* 4.5 2.9 - - - -
86S MET* 3.6 27.1 - - + -
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Residues in contact with GLY 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K THR* 3.6 15.7 - - - -
140K LEU* 3.9 7.0 - - - +
33S ASN 3.0 15.2 + - - -
34S ASP 3.3 0.8 + - - -
35S TRP* 1.3 80.1 - - - +
37S LEU* 1.3 60.4 + - - +
38S LYS* 3.4 12.2 - - - +
154S MET* 3.5 28.6 - - - +
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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