Contacts of the helix formed by residues 3 - 34 (chain O) in PDB entry 2X17
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 SER 3 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O MET 4.0 0.6 + - - -
2O LEU* 1.3 77.2 - - - +
4O GLU* 1.3 63.8 + - - +
5O ARG 3.9 1.9 + - - -
6O MET* 3.3 14.5 + - - +
7O LEU* 3.0 23.7 + - - +
111O GLU* 2.7 35.6 + - - -
113O ASP* 5.5 1.0 + - - -
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Residues in contact with GLU 4 (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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3O SER* 1.3 74.9 - - - +
5O ARG* 1.3 60.4 + - - +
7O LEU* 3.9 8.1 + - + +
8O LYS* 3.4 21.0 + - - +
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Residues in contact with ARG 5 (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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3O SER* 3.3 2.2 + - - +
4O GLU* 1.3 76.7 - - - +
6O MET* 1.3 54.4 - - - +
8O LYS* 3.3 8.9 + - + +
9O ALA* 2.8 34.7 + - + +
107O LEU* 3.8 30.9 - - + +
111O GLU* 3.9 18.8 + - - +
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Residues in contact with MET 6 (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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2O LEU* 3.8 14.8 - - + -
3O SER* 3.3 26.3 + - - +
5O ARG* 1.3 75.7 - - - +
7O LEU* 1.3 56.6 + - - +
9O ALA* 3.2 3.1 + - - +
10O LEU* 2.8 43.4 + - + +
104O LEU* 4.1 12.1 - - - -
107O LEU* 3.7 23.3 - - + +
108O ALA* 3.6 34.3 - - + +
111O GLU* 3.6 16.7 + - - +
113O ASP* 3.8 21.8 - - + +
116O THR* 3.8 18.4 - - - +
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Residues in contact with LEU 7 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O LEU* 4.1 18.3 - - + +
3O SER 3.0 17.0 + - - +
4O GLU* 4.0 9.0 - - + +
6O MET* 1.3 75.7 - - - +
8O LYS* 1.3 54.9 + - - +
10O LEU* 3.6 4.6 + - - +
11O ASN* 2.8 44.0 + - - +
61O ILE* 3.7 16.4 - - + -
66O GLY* 3.9 9.0 - - - -
67O ARG* 3.5 44.4 - - + +
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Residues in contact with LYS 8 (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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4O GLU 3.4 11.7 + - - +
5O ARG* 3.3 12.7 + - + +
6O MET 3.2 0.4 - - - -
7O LEU* 1.3 77.3 - - - +
9O ALA* 1.3 60.1 + - - +
11O ASN* 3.8 5.9 - - + +
12O ASP* 2.9 59.8 + - - +
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Residues in contact with ALA 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5O ARG* 2.8 22.2 + - + +
6O MET 3.2 4.2 + - - +
8O LYS* 1.3 73.3 - - - +
10O LEU* 1.3 60.3 + - - +
12O ASP* 3.7 7.9 + - - +
13O GLN* 3.3 21.3 + - - +
16O ARG* 4.6 2.1 + - - -
104O LEU* 3.7 27.0 - - + +
107O LEU* 3.7 17.7 - - + -
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Residues in contact with LEU 10 (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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2O LEU* 3.8 32.5 - - + -
6O MET* 2.8 26.2 + - + +
7O LEU* 3.9 2.2 - - - +
9O ALA* 1.3 75.3 - - - +
11O ASN* 1.3 59.5 + - - +
13O GLN* 3.5 3.1 + - - +
14O LEU* 3.2 26.3 + - - +
57O PHE* 3.7 33.6 - - + -
60O TYR* 3.8 21.1 - - + -
61O ILE* 3.9 20.9 - - + +
104O LEU* 4.1 10.8 - - + -
116O THR* 4.1 17.9 - - + -
119O PHE* 4.2 8.3 - - + -
120O LEU* 5.1 0.9 - - + -
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Residues in contact with ASN 11 (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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7O LEU* 2.8 36.0 + - - +
8O LYS* 3.4 8.4 + - + +
10O LEU* 1.3 75.3 - - - +
12O ASP* 1.3 66.5 + - - +
14O LEU* 3.6 8.3 - - - +
15O ASN* 3.2 21.1 + - - +
61O ILE* 4.0 7.1 - - - +
67O ARG 3.2 21.6 + - - -
68O VAL* 3.3 14.0 - - - +
69O GLU* 2.9 43.8 + - + +
71O ASP* 5.0 3.5 - - - +
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Residues in contact with ASP 12 (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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8O LYS* 2.9 49.7 + - - +
9O ALA* 3.9 6.4 - - - +
10O LEU 3.3 0.2 - - - -
11O ASN* 1.3 77.6 - - - +
13O GLN* 1.3 59.0 + - - +
15O ASN* 3.3 8.3 + - - +
16O ARG* 2.9 53.1 + - - +
71O ASP* 3.9 15.6 - - - +
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Residues in contact with GLN 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 ALA 3.3 6.4 + - - +
10O LEU 3.9 4.7 - - - +
11O ASN 3.3 0.6 - - - -
12O ASP* 1.3 76.9 - - - +
14O LEU* 1.3 54.9 + - - +
16O ARG* 3.1 26.7 + - - +
17O GLU* 2.8 62.1 + - - +
57O PHE* 3.3 31.4 - - + -
97O ILE* 4.1 8.3 - - - +
100O SER* 3.1 32.8 + - - +
101O ILE* 3.8 14.6 - - + +
104O LEU* 3.7 20.5 - - + +
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Residues in contact with LEU 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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256 PHE* 4.2 6.3 - - + -
10O LEU 3.2 12.5 + - - +
11O ASN* 3.6 11.9 - - - +
13O GLN* 1.3 75.4 - - - +
15O ASN* 1.3 57.8 + - - +
17O GLU* 3.4 7.3 + - - +
18O LEU* 3.1 45.8 + - + +
54O ALA* 3.4 21.0 - - + +
57O PHE* 4.0 12.9 - - + -
58O TYR* 3.6 33.4 - - + +
61O ILE* 4.3 5.2 - - + -
68O VAL* 3.9 23.3 - - + -
70O LEU* 3.8 17.9 - - + -
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Residues in contact with ASN 15 (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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226 TYR* 3.4 10.5 + - - -
11O ASN 3.2 11.1 + - - +
12O ASP* 3.4 12.1 - - - +
13O GLN 3.2 0.6 - - - -
14O LEU* 1.3 78.1 - - - +
16O ARG* 1.3 59.0 + - - +
18O LEU* 3.5 8.2 + - - +
19O TYR* 3.1 25.5 + - - +
69O GLU 6.1 0.2 - - - +
70O LEU* 5.1 1.0 - - - +
71O ASP* 2.9 52.3 + - + +
72O GLU 3.7 14.7 + - - +
73O ILE* 4.4 6.4 - - - +
74O PRO* 4.9 5.5 - - - +
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Residues in contact with ARG 16 (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 ALA* 4.6 3.0 + - - +
12O ASP* 2.9 33.4 + - - +
13O GLN* 3.2 54.2 + - - +
15O ASN* 1.3 75.3 - - - +
17O GLU* 1.3 59.6 + - - +
19O TYR* 3.5 8.2 + - - +
20O SER* 3.1 30.2 + - - -
93O HIS* 5.3 0.2 - - - -
96O PHE* 4.2 26.4 - - + -
97O ILE* 4.0 9.4 - - + +
100O SER* 4.0 23.4 + - - -
103O GLU* 5.9 1.4 + - - -
104O LEU* 5.2 1.6 - - - +
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Residues in contact with GLU 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 GLN* 2.8 40.6 + - - +
14O LEU 3.6 5.6 - - - +
15O ASN 3.3 0.2 - - - -
16O ARG* 1.3 77.9 - - - +
18O LEU* 1.3 61.1 + - - +
20O SER* 3.4 3.3 + - - -
21O ALA* 3.2 16.6 + - - +
50O GLU* 3.0 52.6 - - - +
53O HIS* 3.3 27.1 + - + +
54O ALA* 3.9 10.1 - - + +
57O PHE* 4.3 10.6 - - + -
97O ILE* 4.0 14.6 - - - +
101O ILE* 4.7 1.4 - - - +
123O PHE* 4.3 12.3 - - - -
127O GLN* 4.7 2.9 + - - -
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Residues in contact with LEU 18 (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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226 TYR* 3.6 38.1 - - + +
256 PHE* 4.4 10.1 - - + -
14O LEU* 3.1 39.0 + - + +
15O ASN* 3.8 6.7 - - - +
16O ARG 3.3 0.4 - - - -
17O GLU* 1.3 75.4 - - - +
19O TYR* 1.3 58.6 + - - +
21O ALA* 3.5 7.5 - - + +
22O TYR* 3.1 24.3 + - - +
51O ILE* 4.8 21.8 - - + -
54O ALA* 3.8 17.0 - - + -
70O LEU* 4.2 2.5 - - + -
73O ILE* 4.0 18.0 - - + +
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Residues in contact with TYR 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 ASN* 3.1 16.5 + - - +
16O ARG* 3.8 7.0 - - - +
17O GLU 3.3 0.2 - - - -
18O LEU* 1.3 73.4 - - - +
20O SER* 1.3 55.5 + - - +
22O TYR* 3.0 3.7 + - + -
23O LEU* 2.6 48.2 + - + +
73O ILE* 3.9 13.8 - - + +
74O PRO* 3.7 48.7 - - + -
75O LYS 4.6 2.3 + - - -
76O PRO* 4.1 15.1 - - + +
77O PRO* 3.7 23.0 - - - +
93O HIS* 3.6 32.8 - + - -
96O PHE* 6.1 0.9 - + - -
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Residues in contact with SER 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 ARG 3.1 13.6 + - - -
17O GLU* 3.4 11.5 + - - -
18O LEU 3.3 0.2 - - - -
19O TYR* 1.3 76.1 - - - +
21O ALA* 1.3 60.9 + - - +
23O LEU* 3.4 3.4 + - - +
24O TYR* 3.1 33.7 + - - -
50O GLU* 3.6 24.9 + - - -
93O HIS* 3.0 31.9 + - - -
94O GLU* 5.3 0.6 + - - -
97O ILE* 3.5 13.5 - - - +
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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 GLU 3.2 6.1 + - - +
18O LEU* 3.5 11.9 - - + +
19O TYR 3.2 0.2 - - - -
20O SER* 1.3 79.3 - - - +
22O TYR* 1.3 56.0 + - - +
25O PHE* 3.0 28.2 + - - +
47O ALA* 3.3 35.2 - - + +
50O GLU* 3.6 14.0 - - + +
51O ILE* 3.8 18.8 - - + -
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Residues in contact with TYR 22 (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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156 ASN* 3.4 13.2 + - - -
186 LEU* 3.6 27.6 - - + +
706 LEU* 3.5 30.1 - - + +
716 ASP 2.6 30.3 + - - -
736 ILE* 3.6 21.8 - - + +
18O LEU 3.1 14.5 + - - +
19O TYR* 3.0 9.2 + + + +
21O ALA* 1.3 74.1 - - - +
23O LEU* 1.3 59.1 + - - +
25O PHE* 3.8 6.9 - + + +
26O ALA* 3.1 25.1 + - - +
73O ILE* 3.8 24.2 - - + -
74O PRO 3.9 5.4 - - - -
76O PRO* 3.6 30.7 - - + +
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Residues in contact with LEU 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 TYR* 2.6 33.1 + - + +
20O SER 3.7 4.0 - - - +
21O ALA 3.3 0.2 - - - -
22O TYR* 1.3 74.5 - - - +
24O TYR* 1.3 64.4 + - + +
26O ALA* 3.1 4.9 + - - +
27O MET* 2.9 46.6 + - + +
76O PRO* 4.1 7.4 - - + +
77O PRO* 3.8 29.4 - - + -
80O TRP* 4.1 17.9 - - + -
89O ALA 5.1 1.3 - - - +
93O HIS* 3.6 45.5 - - + +
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Residues in contact with TYR 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20O SER* 3.1 24.3 + - - +
21O ALA 4.1 3.1 - - - +
23O LEU* 1.3 80.5 - - + +
25O PHE* 1.3 61.3 + - - +
27O MET* 4.0 13.5 - - + -
28O ALA* 2.9 27.2 + - - +
42O TRP* 6.1 0.7 - + - -
43O MET* 3.4 46.8 - - + +
46O GLN* 3.7 21.1 - - + -
47O ALA* 4.1 2.9 - - + -
50O GLU* 3.6 29.4 - - + -
90O ALA* 3.8 30.4 + - + +
93O HIS* 4.4 9.1 - + - -
94O GLU* 2.6 34.3 + - - +
130O GLU* 4.6 0.2 + - - -
134O VAL* 4.8 5.2 - - + +
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Residues in contact with PHE 25 (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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146 LEU* 4.2 11.4 - - + -
186 LEU* 4.2 13.2 - - + -
546 ALA* 5.0 4.3 - - + -
556 LEU* 3.8 30.3 - - + -
586 TYR* 3.7 36.5 - + + -
706 LEU* 3.5 38.4 - - + +
21O ALA 3.0 18.2 + - - +
22O TYR* 3.8 16.8 - + + +
24O TYR* 1.3 76.2 - - - +
26O ALA* 1.3 57.6 + - - +
28O ALA* 3.6 8.1 + - + +
29O ALA* 3.2 24.4 + - - +
43O MET 5.7 0.2 - - - -
44O LYS* 4.7 9.2 - - + -
47O ALA* 4.2 8.9 - - + +
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Residues in contact with ALA 26 (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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676 ARG* 5.2 0.2 + - - -
706 LEU* 3.5 12.1 - - + +
22O TYR 3.1 14.6 + - - +
23O LEU 3.1 9.4 + - - +
25O PHE* 1.3 76.3 - - - +
27O MET* 1.3 58.9 + - - +
29O ALA* 3.5 6.5 + - - +
30O TYR* 3.2 23.7 + - - +
76O PRO* 3.7 19.1 - - + +
77O PRO 3.7 20.6 - - - +
78O LYS* 4.4 4.4 - - - +
80O TRP* 4.0 5.1 - - + -
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Residues in contact with MET 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 LEU* 2.9 36.3 + - + +
24O TYR* 3.4 12.3 + - + +
25O PHE 3.4 0.2 - - - -
26O ALA* 1.3 73.2 - - - +
28O ALA* 1.3 61.7 + - - +
30O TYR* 3.2 2.5 + - - +
31O PHE* 3.0 40.7 + - + -
43O MET* 3.7 32.1 - - + -
80O TRP* 3.5 38.1 - - + -
86O ALA* 3.4 31.2 - - + +
89O ALA* 4.2 5.6 - - + -
90O ALA* 3.8 22.4 - - + +
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Residues in contact with ALA 28 (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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586 TYR* 3.0 13.7 + - - +
24O TYR 2.9 17.0 + - - +
25O PHE* 3.6 11.0 - - + +
27O MET* 1.3 76.9 - - - +
29O ALA* 1.3 55.6 + - - +
31O PHE 3.4 0.3 + - - -
32O GLU* 2.9 24.9 + - - +
40O ALA* 3.4 30.7 - - - +
43O MET* 3.8 9.8 - - + +
44O LYS* 3.8 17.5 - - + +
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Residues in contact with ALA 29 (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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586 TYR* 3.5 20.1 + - + -
626 TYR* 2.5 30.9 + - - +
676 ARG* 3.7 12.4 + - - +
686 VAL* 4.1 14.4 - - + +
706 LEU* 5.4 2.5 - - + -
25O PHE 3.2 11.5 + - - +
26O ALA* 3.7 11.4 - - - +
27O MET 3.3 0.4 - - - -
28O ALA* 1.3 76.9 - - - +
30O TYR* 1.3 61.5 + - - +
33O ASP* 3.2 14.6 + - - +
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Residues in contact with TYR 30 (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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676 ARG* 3.9 20.8 - - - +
26O ALA 3.2 14.5 + - - +
27O MET 3.2 9.6 + - - +
29O ALA* 1.3 77.4 - - - +
31O PHE* 1.3 76.6 - + - +
33O ASP* 3.3 14.6 + - + +
34O LEU* 3.4 43.9 + - + +
78O LYS 4.1 3.8 - - - +
79O GLU* 4.2 6.1 - - + -
80O TRP* 2.8 59.8 + + + -
81O GLU 3.8 2.3 + - - -
82O SER* 3.3 32.8 - - - -
83O PRO* 3.9 0.2 - - - +
86O ALA* 4.3 10.3 - - + -
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Residues in contact with PHE 31 (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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27O MET* 3.0 32.0 + - + +
28O ALA 4.0 2.0 - - - +
30O TYR* 1.3 82.7 - + - +
32O GLU* 1.3 63.3 + - - +
34O LEU* 3.4 3.9 + - + +
35O GLY 3.3 3.6 + - - -
36O LEU* 2.9 55.8 + - + +
39O PHE* 3.5 26.0 - + + -
40O ALA 3.8 8.7 - - - +
43O MET* 4.1 29.6 - - + -
83O PRO* 3.6 28.9 - - + -
86O ALA* 4.0 20.2 - - + -
87O PHE* 3.8 26.0 - + - -
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Residues in contact with GLU 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586 TYR* 2.9 27.3 + - - +
596 ASN* 6.0 0.2 - - - -
626 TYR* 3.7 35.5 - - + -
28O ALA 2.9 14.8 + - - +
29O ALA 3.7 5.6 - - - +
30O TYR 3.3 0.2 - - - -
31O PHE* 1.3 75.6 - - - +
33O ASP* 1.3 62.7 + - - +
35O GLY* 3.2 12.7 + - - +
36O LEU 4.6 1.8 - - - +
37O GLU* 3.4 31.5 - - - +
40O ALA* 3.4 14.6 - - - +
41O ASN* 5.0 0.3 - - - +
44O LYS* 3.1 20.8 + - - -
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Residues in contact with ASP 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626 TYR* 3.8 6.9 - - - -
666 GLY 4.3 8.1 - - - +
676 ARG* 3.5 41.9 + - - +
29O ALA 3.2 7.0 + - - +
30O TYR* 3.4 11.9 - - + +
32O GLU* 1.3 79.2 - - - +
34O LEU* 1.3 65.5 + - - +
35O GLY* 3.1 2.8 + - - -
79O GLU* 5.7 1.2 - - - +
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Residues in contact with LEU 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391 ASP* 6.0 1.6 - - - +
1431 PHE* 5.2 11.0 - - + -
30O TYR* 3.4 50.2 + - + +
31O PHE* 3.4 9.3 + - + +
32O GLU 3.3 0.4 - - - -
33O ASP* 1.3 84.6 - - - +
35O GLY* 1.3 60.4 + - - +
36O LEU* 3.5 18.1 + - + +
83O PRO* 4.0 21.1 - - + -
----------------------------------------------------------
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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