Contacts of the helix formed by residues 4 - 35 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLY* 1.3 73.5 - - - -
5M LYS* 1.3 67.3 + - - +
6M LYS* 3.3 6.1 + - - +
7M VAL* 3.0 28.7 + - + +
8M ILE* 3.3 21.5 + - - +
65M LEU* 5.7 0.6 - - - +
107M HIS* 2.8 31.6 + - - -
111M VAL* 4.3 17.7 - - + +
113M ASP* 5.9 1.3 + - + +
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Residues in contact with LYS 5 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLY 3.5 4.3 + - - +
4M ASP* 1.3 77.3 + - - +
6M LYS* 1.3 59.5 + - + +
8M ILE* 3.3 11.4 + - - +
9M GLN* 3.1 43.5 + - + +
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Residues in contact with LYS 6 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M ASP* 3.3 4.3 + - - +
5M LYS* 1.3 77.8 - - + +
7M VAL* 1.3 65.1 + - - +
9M GLN* 3.3 20.2 + - - +
10M HIS* 2.9 35.3 + - + -
107M HIS* 3.4 32.6 - - + +
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Residues in contact with VAL 7 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M ASP* 3.0 33.8 + - + +
5M LYS 3.4 0.2 - - - -
6M LYS* 1.3 73.5 - - - +
8M ILE* 1.3 54.2 + - - +
10M HIS* 3.0 8.5 + - - +
11M LEU* 2.7 41.6 + - + +
65M LEU* 4.0 15.3 - - + -
107M HIS* 3.5 18.8 + - + -
108M CYS* 4.2 13.7 - - - -
111M VAL* 3.6 16.6 - - + -
113M ASP* 3.4 26.7 - - + +
116M SER* 4.1 9.9 - - - +
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Residues in contact with ILE 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M GLY 4.4 6.7 - - - +
4M ASP 3.3 14.4 + - - +
5M LYS* 3.4 12.3 - - + +
6M LYS 3.2 0.4 - - - -
7M VAL* 1.3 76.1 - - - +
9M GLN* 1.3 59.0 + - + +
11M LEU* 3.3 9.1 + - + +
12M ASN* 2.9 41.9 + - - +
62M ILE* 4.6 7.7 - - + +
65M LEU* 3.8 31.4 - - + +
66M GLU 4.3 1.1 - - - +
67M GLY* 3.5 37.9 - - - +
68M LEU 4.8 1.1 - - - +
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Residues in contact with GLN 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M LYS* 3.1 31.3 + - + +
6M LYS* 3.7 23.9 - - - +
7M VAL 3.2 0.2 - - - -
8M ILE* 1.3 75.7 - - + +
10M HIS* 1.3 63.2 + - + +
12M ASN* 3.3 7.7 + - - +
13M LYS* 2.8 27.7 + - - +
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Residues in contact with HIS 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M LYS* 2.9 27.8 + - + +
7M VAL* 3.3 10.5 - - - +
9M GLN* 1.3 77.6 - - + +
11M LEU* 1.3 63.8 - - + +
13M LYS* 3.0 17.3 + - + +
14M ILE* 3.0 28.8 + - - +
100M ASP 4.6 2.0 + - - -
103M GLU* 3.8 18.1 + - + -
104M ALA* 3.3 42.8 + - + +
107M HIS* 4.0 27.8 - + + +
108M CYS* 6.0 1.8 - - - -
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Residues in contact with LEU 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M VAL* 2.7 29.6 + - + +
8M ILE* 3.7 7.6 - - - +
10M HIS* 1.3 71.9 - - + +
12M ASN* 1.3 58.1 + - - +
14M ILE* 3.3 5.1 + - - +
15M LEU* 2.9 29.5 + - - +
58M LEU* 4.0 23.5 - - + +
61M ARG* 4.0 17.5 - - + -
62M ILE* 3.7 28.3 - - + +
65M LEU* 4.0 27.4 - - + -
108M CYS* 5.6 0.2 - - - -
116M SER* 4.4 10.1 - - - +
119M LEU* 5.5 2.0 - - + -
120M LEU* 4.1 27.4 - - + -
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Residues in contact with ASN 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M ILE* 2.9 30.4 + - - +
9M GLN* 3.6 6.9 - - - +
10M HIS 3.2 0.2 - - - -
11M LEU* 1.3 73.8 - - - +
13M LYS* 1.3 61.9 + - - +
15M LEU* 3.6 7.7 - - - +
16M GLY* 2.8 26.0 + - - -
62M ILE* 3.7 10.0 - - - +
68M LEU 2.9 24.5 + - - -
69M PRO* 3.7 4.0 - - - +
70M ASN* 2.9 38.9 + - + +
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Residues in contact with LYS 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M GLN 2.8 14.8 + - - +
10M HIS* 3.0 21.3 + - + +
12M ASN* 1.3 78.5 - - - +
14M ILE* 1.3 62.9 + - + +
16M GLY* 3.2 3.7 + - - -
17M ASN* 3.1 23.6 + - - +
96M LYS* 4.7 9.6 - - - +
99M LYS* 5.4 1.4 - - - +
100M ASP* 3.8 38.1 + - + +
103M GLU* 4.8 8.3 + - - -
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Residues in contact with ILE 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M HIS* 3.0 22.9 + - - +
11M LEU* 3.7 5.8 - - - +
13M LYS* 1.3 73.2 - - + +
15M LEU* 1.3 67.5 + - - +
17M ASN* 2.9 21.0 + - + +
18M GLU* 2.9 25.5 + - + +
58M LEU* 3.7 20.2 - - + -
100M ASP* 3.6 40.2 - - + +
101M LEU* 3.5 36.8 - - + +
104M ALA* 4.3 4.0 - - + -
120M LEU* 3.9 20.0 - - + -
123M ILE* 4.9 2.5 - - + -
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Residues in contact with LEU 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M LEU 2.9 18.2 + - - +
12M ASN* 3.6 21.5 - - - +
14M ILE* 1.3 75.4 - - - +
16M GLY* 1.3 66.2 + - - +
18M GLU* 2.9 4.2 + - - +
19M LEU* 2.8 42.5 + - + +
55M ALA* 4.0 37.5 - - + +
58M LEU* 3.7 14.3 - - + +
59M ILE* 3.8 25.4 - - + +
62M ILE* 4.2 9.9 - - + -
69M PRO* 4.3 0.4 - - + -
70M ASN 4.0 18.4 - - - +
71M LEU* 4.2 4.9 - - + -
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Residues in contact with GLY 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M ASN 2.8 15.1 + - - -
13M LYS* 3.5 5.6 - - - -
14M ILE 3.1 0.4 - - - -
15M LEU* 1.3 78.2 - - - +
17M ASN* 1.3 61.7 + - - +
19M LEU* 3.3 13.0 + - - +
20M ILE* 3.3 28.2 + - - +
70M ASN 5.3 2.2 + - - -
73M ASP 4.9 8.8 - - - +
75M GLY 5.3 0.2 + - - -
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Residues in contact with ASN 17 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LYS* 3.1 19.2 + - - +
14M ILE* 2.9 16.3 + - + +
16M GLY* 1.3 74.0 - - - +
18M GLU* 1.3 67.1 + - + +
20M ILE* 3.3 18.1 + - - +
21M ALA* 3.1 22.8 + - - +
93M LEU* 4.9 3.7 - - + +
96M LYS* 4.0 12.8 + - - +
97M ALA* 4.0 28.6 - - + +
100M ASP* 2.9 39.5 + - - +
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Residues in contact with GLU 18 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ILE* 2.9 21.1 + - + +
15M LEU* 3.4 7.2 - - - +
17M ASN* 1.3 78.6 - - - +
19M LEU* 1.3 58.8 + - - +
21M ALA* 3.1 4.3 + - - +
22M ILE* 2.8 36.3 + - - +
51M GLU* 3.1 40.3 - - - +
54M HIS* 3.6 13.2 - - + +
55M ALA* 4.3 17.7 - - + +
58M LEU* 3.9 19.1 - - + -
97M ALA* 5.9 1.6 - - - +
101M LEU* 5.1 1.7 - - - +
123M ILE* 3.5 14.8 - - - +
127M GLU* 2.8 22.9 - - - +
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Residues in contact with LEU 19 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 2.8 37.8 + - + +
16M GLY* 3.7 9.6 - - - +
17M ASN 3.2 0.2 - - - -
18M GLU* 1.3 78.4 - - - +
20M ILE* 1.3 61.6 + - - +
22M ILE* 3.7 9.6 + - + +
23M ASN* 3.5 20.8 + - - +
55M ALA* 4.9 0.4 - - + -
70M ASN 3.8 21.8 - - - +
71M LEU* 3.9 19.1 - - + +
73M ASP 4.5 9.0 - - - +
74M LEU* 3.7 20.7 - - + +
23N ASN* 4.6 9.2 - - - +
159N HEM 3.8 32.8 - - + -
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Residues in contact with ILE 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M GLY 3.3 16.9 + - - +
17M ASN* 3.6 19.3 - - - +
19M LEU* 1.3 76.9 - - - +
21M ALA* 1.3 59.4 + - - +
23M ASN* 3.3 3.3 + - - +
24M GLN* 2.9 27.3 + - - +
74M LEU* 3.8 7.4 - - + -
75M GLY* 3.6 40.2 - - - +
76M LYS 3.5 21.5 - - - +
77M LEU* 4.0 12.4 - - + +
93M LEU* 3.9 25.8 - - + -
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Residues in contact with ALA 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ASN 3.1 14.4 + - - +
18M GLU 3.1 5.2 + - - +
20M ILE* 1.3 75.3 - - - +
22M ILE* 1.3 68.3 + - - +
24M GLN* 4.4 1.3 - - - -
25M TYR* 2.8 45.1 + - + +
51M GLU* 3.4 27.1 - - + +
93M LEU* 3.8 19.3 - - + -
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Residues in contact with ILE 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M GLU 2.8 22.1 + - - +
19M LEU* 3.7 9.4 - - + +
21M ALA* 1.3 74.4 - - - +
23M ASN* 1.3 68.4 + - - +
26M PHE* 2.8 27.7 + - - +
48M SER* 2.9 19.1 + - - +
51M GLU* 3.7 22.8 - - + +
52M MET* 3.6 35.9 - - + +
55M ALA* 4.1 10.3 - - + -
159N HEM 3.7 47.1 - - + -
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Residues in contact with ASN 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M LEU 3.5 10.2 + - - +
20M ILE 3.3 6.1 + - - +
21M ALA 3.1 0.6 - - - -
22M ILE* 1.3 87.4 - - - +
24M GLN* 1.3 67.4 + - - +
26M PHE* 4.4 1.1 - - - +
27M LEU* 2.9 26.7 + - - +
74M LEU* 3.8 11.9 - - - +
77M LEU* 4.1 15.3 - - + -
19N LEU* 4.5 12.3 - - - +
71N LEU* 3.0 49.1 + - + +
159N HEM 3.6 13.3 - - - +
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Residues in contact with GLN 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M ILE* 2.9 16.8 + - - +
21M ALA* 3.9 4.0 - - - +
23M ASN* 1.3 78.9 - - - +
25M TYR* 1.3 60.9 + - + +
27M LEU* 3.7 1.6 - - - +
28M HIS* 2.8 39.0 + - + +
77M LEU* 3.9 6.8 - - + +
78M LEU* 2.9 45.9 + - - +
79M ILE* 4.1 13.9 - - + +
89M CYS* 3.2 24.0 + - - +
90M ASP* 3.1 23.9 + - - +
93M LEU* 3.6 22.7 - - - +
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Residues in contact with TYR 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ALA* 2.8 30.5 + - + +
24M GLN* 1.3 80.9 - - + +
26M PHE* 1.3 65.7 + - - +
29M SER* 2.9 21.7 + - - -
44M GLU* 3.0 33.4 - - - +
47M GLU* 3.9 16.8 - - + -
48M SER* 3.9 17.3 - - - +
51M GLU* 3.8 24.5 - - + -
90M ASP* 3.4 28.5 + - + -
93M LEU* 3.9 13.1 - - + +
94M GLU* 2.7 36.7 + - - +
130M HIS* 3.5 17.7 - + - -
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Residues in contact with PHE 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M ILE 2.8 20.4 + - - +
23M ASN* 4.0 4.7 - - - +
25M TYR* 1.3 78.3 - - - +
27M LEU* 1.3 63.6 + - - +
29M SER* 3.3 5.8 + - - -
30M ARG* 3.1 36.3 + - + +
45M TYR* 3.8 26.0 - + - -
48M SER* 3.5 19.9 + - - +
52M MET* 4.0 8.1 - - + -
56N ASP* 3.4 39.5 - - + -
59N ILE* 4.0 19.3 - - + -
71N LEU* 4.8 2.0 - - + -
159N HEM 3.6 45.5 - + + -
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Residues in contact with LEU 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M ASN 2.9 18.0 + - - +
24M GLN 3.9 2.0 - - - +
26M PHE* 1.3 79.7 - - - +
28M HIS* 1.3 63.8 + - - +
30M ARG* 3.3 2.1 + - - +
31M MET* 3.1 39.3 + - + +
77M LEU* 5.6 1.8 - - + -
79M ILE* 3.9 36.3 - - + -
59N ILE* 4.3 9.4 - - + -
63N LEU* 4.5 1.8 - - + -
69N PRO* 3.9 48.2 - - + +
71N LEU* 4.3 20.3 - - + +
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Residues in contact with HIS 28 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M GLN* 2.8 26.5 + - + +
26M PHE 3.3 0.2 - - - -
27M LEU* 1.3 74.4 - - - +
29M SER* 1.3 56.5 + - - +
31M MET* 3.3 13.5 + - - +
32M TRP* 2.9 38.9 + - + -
44M GLU* 3.4 17.8 + - + +
78M LEU 3.3 19.7 - - - -
79M ILE* 3.6 9.4 - - + +
80M GLY 3.0 25.5 + - - -
86M MET* 3.5 43.8 + - + +
90M ASP* 2.9 29.3 + - - -
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Residues in contact with SER 29 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M TYR 2.9 17.7 + - - -
26M PHE* 3.3 7.9 - - - -
28M HIS* 1.3 75.0 - - - +
30M ARG* 1.3 79.9 + - - +
32M TRP* 3.2 5.6 + - - +
33M ASN* 2.9 28.9 + - - -
41M GLY* 2.7 27.8 + - - -
44M GLU* 3.5 10.4 - - - +
45M TYR* 3.5 17.1 + - - -
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Residues in contact with ARG 30 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M PHE* 3.1 32.0 + - + +
27M LEU 4.0 2.2 - - - +
28M HIS 3.3 0.2 - - - -
29M SER* 1.3 94.6 + - - +
31M MET* 1.3 60.8 + - - +
33M ASN* 3.4 20.7 + - + +
34M ASP* 2.9 28.4 + - - +
41M GLY 4.7 0.4 + - - -
45M TYR* 3.6 30.3 - - - +
56N ASP* 2.8 44.2 + - - +
59N ILE* 3.9 18.4 - - + -
60N GLU* 3.7 24.7 + - + +
63N LEU* 3.7 19.9 - - + +
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Residues in contact with MET 31 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M LEU* 3.1 44.5 + - + +
28M HIS* 3.5 16.2 - - + +
30M ARG* 1.3 75.1 - - - +
32M TRP* 1.3 66.1 + - - +
34M ASP* 3.3 6.7 + - - +
35M TRP* 2.9 52.5 + - + -
79M ILE* 4.2 8.7 - - + -
80M GLY 3.3 26.5 - - - +
81M GLU* 4.8 2.2 - - - -
86M MET* 3.9 16.4 - - + -
63N LEU* 4.2 17.7 - - + -
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Residues in contact with TRP 32 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M HIS* 2.9 28.6 + - + +
29M SER 3.2 4.7 + - - +
31M MET* 1.3 77.4 - - - +
33M ASN* 1.3 60.0 + - - +
35M TRP* 3.1 13.8 + + - -
36M GLY 3.1 4.2 + - - -
37M LEU* 2.9 54.1 + - + +
40M LEU* 3.6 32.9 - - + +
41M GLY 3.8 12.3 - - - +
44M GLU* 3.7 33.7 - - + -
83M THR* 2.9 41.6 + - + +
86M MET* 3.6 34.2 - - + +
87M LEU* 4.0 22.7 - - + -
90M ASP* 4.8 1.1 - - - -
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Residues in contact with ASN 33 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M SER* 2.9 13.2 + - - +
30M ARG* 3.5 37.4 + - + +
32M TRP* 1.3 74.4 - - - +
34M ASP* 1.3 59.6 + - - +
36M GLY* 2.9 19.6 + - - -
37M LEU 4.7 2.2 - - - +
38M LYS* 3.9 24.6 + - + +
41M GLY* 3.3 25.4 - - - -
42M ALA 4.2 0.4 - - - +
156M GLU* 5.7 2.0 + - - -
60N GLU* 5.0 6.2 - - + +
136X THR* 5.0 0.9 + - - +
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Residues in contact with ASP 34 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M ARG 2.9 17.9 + - - +
31M MET* 3.5 7.9 - - - +
33M ASN* 1.3 77.2 - - - +
35M TRP* 1.3 71.6 + - - +
63N LEU* 3.9 40.8 - - + +
64N PHE* 4.3 4.7 + - - -
132X ASP* 4.3 12.3 - - - +
136X THR* 3.3 23.2 + - - +
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Residues in contact with TRP 35 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M MET* 2.9 35.8 + - + +
32M TRP* 3.1 26.2 + + - +
34M ASP* 1.3 90.9 + - - +
36M GLY* 1.3 58.6 + - - +
37M LEU* 4.4 10.9 - - + +
81M GLU 3.4 25.6 - - - -
82M ASN* 4.1 6.7 - - + -
83M THR* 4.4 3.6 - - - -
86M MET* 3.6 31.9 - - + -
136X THR* 3.6 7.0 - - - +
140X LEU* 3.2 26.5 - - - +
143X LYS* 3.8 41.1 + - + +
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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