Contacts of the helix formed by residues 4 - 35 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O GLY* 1.3 69.5 - - - -
5O LYS* 1.3 68.0 + - - +
6O LYS* 3.2 5.6 + - - +
7O VAL* 3.0 31.3 + - + +
8O ILE* 3.1 26.4 + - - +
65O LEU* 5.6 0.2 - - - +
107O HIS* 2.8 30.4 + - - -
111O VAL* 4.1 20.4 - - + +
113O ASP* 5.8 2.3 + - + -
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Residues in contact with LYS 5 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O GLY 3.5 4.1 + - - +
4O ASP* 1.3 76.0 + - - +
6O LYS* 1.3 59.6 + - + +
8O ILE* 3.5 10.2 + - + +
9O GLN* 3.1 36.0 + - + +
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Residues in contact with LYS 6 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4O ASP* 3.2 5.2 + - - +
5O LYS* 1.3 78.3 - - + +
7O VAL* 1.3 57.6 + - - +
9O GLN* 3.3 18.2 + - - +
10O HIS* 2.9 38.9 + - + +
107O HIS* 3.3 29.2 - - + +
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Residues in contact with VAL 7 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4O ASP* 3.0 37.9 + - + +
6O LYS* 1.3 75.5 - - - +
8O ILE* 1.3 58.5 + - - +
10O HIS* 3.1 8.2 + - - +
11O LEU* 2.9 45.1 + - + +
65O LEU* 4.2 6.1 - - + -
107O HIS* 3.8 11.4 - - + -
108O CYS* 4.1 17.9 - - - -
111O VAL* 3.7 18.8 - - + -
113O ASP* 3.3 27.4 - - + +
116O SER* 4.0 2.9 - - - +
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Residues in contact with ILE 8 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O GLY 4.2 10.3 - - - +
4O ASP 3.1 17.8 + - - +
5O LYS* 3.8 9.2 - - + +
7O VAL* 1.3 76.4 - - - +
9O GLN* 1.3 63.7 + - + +
11O LEU* 3.3 8.7 + - + +
12O ASN* 3.0 37.1 + - - +
62O ILE* 4.2 9.4 - - + +
65O LEU* 3.9 43.3 - - + +
66O GLU 4.7 0.9 - - - +
67O GLY* 4.0 28.3 - - - -
68O LEU 4.7 1.3 - - - +
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Residues in contact with GLN 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O LYS* 3.1 23.5 + - + +
6O LYS* 3.6 25.1 - - - +
7O VAL 3.2 0.2 - - - -
8O ILE* 1.3 78.3 - - + +
10O HIS* 1.3 63.3 + - + +
12O ASN* 3.4 7.4 + - - +
13O LYS* 3.0 22.3 + - - +
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Residues in contact with HIS 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6O LYS* 2.9 26.1 + - + +
7O VAL* 3.3 9.4 - - - +
9O GLN* 1.3 76.7 - - + +
11O LEU* 1.3 58.6 + - + +
13O LYS* 3.0 15.8 + - + +
14O ILE* 2.8 34.8 + - - +
100O ASP 4.8 1.8 + - - -
103O GLU* 4.0 18.2 - - + -
104O ALA* 3.5 40.5 + - + +
107O HIS* 3.7 34.2 + + + +
108O CYS* 5.9 1.8 - - - -
120O LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7O VAL* 2.9 36.3 + - + +
8O ILE* 3.3 5.8 + - - +
10O HIS* 1.3 76.1 - - + +
12O ASN* 1.3 53.3 + - - +
14O ILE* 3.3 4.9 + - - +
15O LEU* 2.8 34.7 + - - +
58O LEU* 3.8 17.0 - - + +
61O ARG* 3.9 27.6 - - + -
62O ILE* 3.7 27.8 - - + +
65O LEU* 4.0 9.9 - - + -
108O CYS* 5.7 0.2 - - - -
116O SER* 4.1 7.9 - - - +
119O LEU* 5.2 2.2 - - + -
120O LEU* 3.8 35.2 - - + -
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Residues in contact with ASN 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O ILE* 3.0 30.0 + - - +
9O GLN* 3.8 6.2 - - - +
11O LEU* 1.3 74.0 - - - +
13O LYS* 1.3 60.8 + - - +
15O LEU* 3.4 6.9 - - - +
16O GLY* 2.7 27.0 + - - -
62O ILE* 3.5 15.3 - - - +
68O LEU 3.0 21.2 + - - -
69O PRO* 3.6 0.2 - - - +
70O ASN* 2.9 40.2 + - + +
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Residues in contact with LYS 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O GLN 3.0 13.4 + - - +
10O HIS* 3.2 19.3 - - + +
12O ASN* 1.3 78.6 - - - +
14O ILE* 1.3 63.5 + - + +
16O GLY* 3.2 2.6 + - - -
17O ASN* 3.0 24.2 + - - +
96O LYS* 4.2 9.8 - - - +
100O ASP* 3.1 42.8 + - + +
103O GLU* 4.9 8.5 + - - -
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Residues in contact with ILE 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O HIS* 2.8 27.0 + - - +
11O LEU* 3.6 6.3 - - - +
13O LYS* 1.3 73.6 - - + +
15O LEU* 1.3 63.7 + - - +
17O ASN* 3.0 18.8 + - + +
18O GLU* 3.1 21.5 + - + +
58O LEU* 3.7 23.8 - - + -
97O ALA 4.9 0.9 - - - +
100O ASP* 3.8 35.7 - - + +
101O LEU* 3.4 39.3 - - + +
104O ALA* 4.3 5.4 - - + -
120O LEU* 4.3 11.4 - - + -
123O ILE* 4.8 1.8 - - + -
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Residues in contact with LEU 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O LEU 2.8 21.2 + - - +
12O ASN* 3.4 23.1 - - - +
14O ILE* 1.3 73.1 - - - +
16O GLY* 1.3 63.0 + - - +
18O GLU* 3.0 2.6 + - - +
19O LEU* 3.0 42.8 + - + +
55O ALA* 3.7 40.4 - - + +
58O LEU* 3.8 12.7 - - + +
59O ILE* 4.0 23.1 - - + +
62O ILE* 4.1 9.0 - - + -
69O PRO* 4.3 0.7 - - + -
70O ASN 3.8 20.4 - - - +
71O LEU* 4.3 5.8 - - + -
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Residues in contact with GLY 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O ASN 2.7 19.8 + - - -
13O LYS* 3.7 2.7 - - - -
14O ILE 3.2 0.2 - - - -
15O LEU* 1.3 73.0 - - - +
17O ASN* 1.3 63.9 + - - +
19O LEU* 3.4 13.5 + - - +
20O ILE* 3.3 27.8 + - - +
70O ASN 5.4 2.0 + - - -
73O ASP 4.9 9.2 - - - +
75O GLY 5.4 0.3 + - - -
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Residues in contact with ASN 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O LYS* 3.0 17.6 + - - +
14O ILE* 3.0 15.1 + - + +
16O GLY* 1.3 79.0 - - - +
18O GLU* 1.3 57.4 + - + +
20O ILE* 3.3 15.7 + - - +
21O ALA* 3.0 27.4 + - - +
93O LEU* 4.8 7.3 - - + +
96O LYS* 3.6 21.6 + - - +
97O ALA* 3.7 28.8 + - + +
100O ASP* 2.9 35.9 + - - +
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Residues in contact with GLU 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O ILE* 3.1 20.5 + - + +
15O LEU* 3.0 7.9 + - - +
17O ASN* 1.3 76.3 - - + +
19O LEU* 1.3 54.3 + - - +
21O ALA* 3.0 4.7 + - - +
22O ILE* 2.8 40.0 + - - +
51O GLU* 2.6 50.4 - - - +
54O HIS* 3.6 12.6 - - + +
55O ALA* 4.2 10.8 - - + +
58O LEU* 3.8 17.7 - - + -
101O LEU* 5.4 0.9 - - - +
123O ILE* 3.4 18.2 - - - +
127O GLU* 3.0 19.1 - - - +
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Residues in contact with LEU 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O LEU* 3.0 33.0 + - + +
16O GLY* 3.7 10.3 - - - +
18O GLU* 1.3 73.3 - - - +
20O ILE* 1.3 64.9 + - - +
22O ILE* 3.7 10.7 + - + +
23O ASN* 3.4 19.8 + - - +
55O ALA* 5.0 2.5 - - + -
59O ILE* 6.2 0.2 - - + -
70O ASN 4.0 20.4 - - - +
71O LEU* 4.2 20.4 - - + +
73O ASP 4.9 7.0 - - - +
74O LEU* 3.8 21.3 - - + +
23P ASN* 4.4 11.4 - - - +
159P HEM 3.9 28.9 - - + -
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Residues in contact with ILE 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O GLY 3.3 15.3 + - - +
17O ASN* 3.5 16.6 - - - +
18O GLU 3.3 0.2 - - - -
19O LEU* 1.3 76.4 - - - +
21O ALA* 1.3 58.5 + - - +
23O ASN* 3.3 4.5 + - - +
24O GLN* 2.9 28.3 + - - +
74O LEU* 4.1 8.1 - - + -
75O GLY* 3.4 46.9 - - - +
76O LYS 3.7 19.5 - - - +
77O LEU* 4.2 13.0 - - + +
93O LEU* 3.8 26.2 - - + -
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Residues in contact with ALA 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O ASN 3.0 13.8 + - - +
18O GLU* 3.0 7.6 + - - +
20O ILE* 1.3 72.4 - - - +
22O ILE* 1.3 61.5 + - - +
24O GLN* 4.4 0.4 - - - -
25O TYR* 2.8 51.9 + - + +
51O GLU* 3.3 27.4 - - + +
93O LEU* 3.6 20.4 - - + -
94O GLU* 5.1 0.2 - - - +
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Residues in contact with ILE 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O GLU 2.8 22.2 + - - +
19O LEU* 3.8 8.5 - - - +
21O ALA* 1.3 77.1 - - - +
23O ASN* 1.3 68.6 + - - +
26O PHE* 3.0 23.6 + - - +
48O SER* 3.1 11.6 + - - +
51O GLU* 3.6 22.4 - - + +
52O MET* 3.5 52.9 - - + +
55O ALA* 4.2 11.2 - - + -
159P HEM 3.9 33.4 - - + -
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Residues in contact with ASN 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O LEU 3.4 9.5 + - - +
20O ILE 3.3 6.9 + - - +
22O ILE* 1.3 77.7 - - - +
24O GLN* 1.3 67.8 + - - +
26O PHE* 3.3 2.0 + - - -
27O LEU* 2.9 27.0 + - - +
74O LEU* 3.8 15.0 - - - +
77O LEU* 4.2 9.9 - - + -
19P LEU* 4.7 8.5 - - - +
71P LEU* 3.0 46.7 + - + +
159P HEM 3.2 29.1 - - - +
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Residues in contact with GLN 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O ILE* 2.9 17.8 + - - +
21O ALA* 3.9 3.1 - - - +
23O ASN* 1.3 79.0 - - - +
25O TYR* 1.3 61.1 + - + +
27O LEU* 3.9 1.2 - - - +
28O HIS* 2.9 37.2 + - + -
77O LEU* 3.9 8.4 - - + +
78O LEU* 2.9 48.9 + - - +
79O ILE* 4.1 14.6 - - + -
89O CYS* 3.4 22.6 + - - +
90O ASP* 3.1 25.1 + - - +
93O LEU* 3.7 21.3 - - - +
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Residues in contact with TYR 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O ALA* 2.8 37.7 + - + +
24O GLN* 1.3 85.2 - - + +
26O PHE* 1.3 60.3 + - - +
29O SER* 2.9 26.0 + - - -
44O GLU* 3.0 36.2 - - - +
47O GLU* 4.0 14.6 - - + -
48O SER* 3.8 16.2 - - - -
51O GLU* 3.7 20.9 - - + -
90O ASP* 3.5 29.0 + - + -
93O LEU* 4.0 10.2 - - + +
94O GLU* 2.4 38.9 + - - +
130O HIS* 3.5 18.0 - + - -
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Residues in contact with PHE 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22O ILE 3.0 20.3 + - - +
23O ASN* 3.8 5.2 - - - +
25O TYR* 1.3 76.1 - - - +
27O LEU* 1.3 61.8 + - - +
29O SER* 3.2 6.1 + - - -
30O ARG* 3.0 46.6 + - + +
45O TYR* 4.0 18.2 - + - -
48O SER* 3.6 19.7 - - - +
52O MET* 4.0 6.3 - - + -
56P ASP* 3.5 37.7 - - + -
59P ILE* 4.2 13.5 - - + -
71P LEU* 4.8 0.4 - - + -
159P HEM 3.6 53.4 - + + -
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Residues in contact with LEU 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O ASN 2.9 16.7 + - - +
24O GLN 3.9 3.4 - - - +
26O PHE* 1.3 74.8 - - - +
28O HIS* 1.3 66.8 + - - +
30O ARG* 3.2 2.0 + - - -
31O MET* 2.9 47.2 + - + +
77O LEU* 5.7 2.2 - - + -
79O ILE* 4.1 33.7 - - + -
59P ILE* 4.2 11.2 - - + -
63P LEU* 4.5 1.6 - - + -
69P PRO* 3.6 49.4 - - + +
71P LEU* 4.3 19.2 - - + +
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Residues in contact with HIS 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O GLN* 2.9 21.1 + - + +
25O TYR 3.2 0.4 + - - +
27O LEU* 1.3 76.8 - - - +
29O SER* 1.3 61.3 + - - +
31O MET* 3.5 10.5 + - - -
32O TRP* 3.1 37.0 + - + -
44O GLU* 3.3 19.8 + - + +
78O LEU 3.5 17.7 - - - -
79O ILE* 3.5 13.0 - - + +
80O GLY 3.2 21.0 + - - -
86O MET* 3.6 45.4 + - + +
89O CYS* 4.2 0.2 - - + -
90O ASP* 2.8 29.0 + - - -
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Residues in contact with SER 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O TYR 2.9 12.2 + - - -
26O PHE* 3.2 11.9 + - - -
28O HIS* 1.3 77.8 - - - +
30O ARG* 1.3 78.6 + - - +
32O TRP* 3.2 4.3 + - - +
33O ASN* 3.0 30.5 + - - -
41O GLY* 2.5 29.9 + - - -
44O GLU* 3.6 7.3 - - - +
45O TYR* 3.5 17.6 - - - +
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Residues in contact with ARG 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O PHE* 3.0 30.7 + - + +
27O LEU 3.2 2.2 + - - +
29O SER* 1.3 95.7 + - - +
31O MET* 1.3 57.3 + - - +
33O ASN* 3.4 20.2 + - - +
34O ASP* 2.8 29.8 + - - +
41O GLY 4.4 0.2 + - - -
45O TYR* 3.7 31.2 - - - +
56P ASP* 2.8 42.7 + - - +
59P ILE* 3.7 29.4 - - + -
60P GLU* 3.4 24.5 + - + +
63P LEU* 3.7 9.1 - - + +
159P HEM 5.3 0.2 - - - +
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Residues in contact with MET 31 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O LEU* 2.9 46.0 + - + +
28O HIS* 3.8 6.3 - - - +
30O ARG* 1.3 73.9 - - - +
32O TRP* 1.3 61.2 + - - +
34O ASP* 3.2 8.5 + - - +
35O TRP* 3.0 59.1 + - + -
79O ILE* 4.0 14.6 - - + -
80O GLY 3.7 21.1 - - - +
81O GLU* 4.8 2.7 - - - -
86O MET* 3.8 21.8 - - + -
63P LEU* 4.3 13.2 - - + -
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Residues in contact with TRP 32 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O HIS* 3.1 27.4 + - + -
29O SER 3.6 6.3 - - - +
31O MET* 1.3 75.8 - - - +
33O ASN* 1.3 64.7 + - - +
35O TRP* 3.3 17.7 + + - -
36O GLY 3.2 3.8 + - - -
37O LEU* 2.9 52.9 + - + +
40O LEU* 3.7 26.9 - - + +
41O GLY 3.7 4.5 - - - +
44O GLU* 3.7 40.8 - - + -
83O THR* 2.9 42.2 + - + -
86O MET* 3.7 38.7 - - + -
87O LEU* 4.2 21.5 - - + -
90O ASP* 4.6 0.9 - - - -
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Residues in contact with ASN 33 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I THR* 5.0 1.0 + - - +
29O SER* 3.0 15.1 + - - +
30O ARG* 3.5 34.6 + - + +
32O TRP* 1.3 75.6 - - - +
34O ASP* 1.3 64.3 + - - +
36O GLY* 3.0 14.7 + - - +
37O LEU 4.7 2.2 - - - +
38O LYS* 3.8 27.4 + - + +
41O GLY* 3.3 24.5 - - - +
42O ALA* 4.1 0.4 - - - +
60P GLU* 5.1 4.9 - - + +
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Residues in contact with ASP 34 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I ASP* 4.4 13.1 - - - +
136I THR* 3.3 22.2 + - - -
30O ARG 2.8 18.3 + - - +
31O MET* 3.2 6.4 + - - +
33O ASN* 1.3 78.7 - - - +
35O TRP* 1.3 72.2 + - - +
63P LEU* 3.8 43.2 - - + +
64P PHE* 4.4 4.0 - - - +
66P GLU* 6.1 0.3 - - - +
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Residues in contact with TRP 35 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I THR* 3.6 8.7 - - - +
139I GLY 5.6 0.2 - - - -
140I LEU* 3.4 22.7 + - - +
143I LYS* 3.7 40.4 + - - +
31O MET* 3.0 36.3 + - + +
32O TRP* 3.7 24.2 - + - +
33O ASN 3.2 0.4 - - - -
34O ASP* 1.3 88.8 + - - +
36O GLY* 1.3 61.4 + - - +
37O LEU* 3.4 12.0 + - + -
81O GLU 3.5 29.8 - - - -
82O ASN* 4.0 7.9 - - + -
83O THR* 4.2 4.7 - - - -
86O MET* 3.6 27.6 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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