Contacts of the helix formed by residues 11 - 42 (chain N) in PDB entry 2DYS
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 ASN 11 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N SER* 3.1 8.0 + - - +
10N THR* 1.3 78.5 - - - +
12N HIS* 1.3 64.2 + - - +
13N LYS* 3.3 16.9 + - - +
14N ASP* 3.0 30.5 + - + +
15N ILE* 3.0 25.8 + - - +
91N ASP* 3.4 11.0 + - - -
502N TYR* 2.9 70.7 + - + +
503N HIS* 5.0 4.0 - - - -
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Residues in contact with HIS 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ASN* 1.3 72.2 - - - +
13N LYS* 1.3 100.0 + - + +
15N ILE* 3.9 0.6 - - - -
16N GLY* 2.9 22.5 + - - -
80N ASN* 2.7 36.8 + - - +
81N TRP 3.5 18.1 + - - -
84N PRO* 3.5 17.8 - - + +
85N LEU* 3.9 12.4 - - + +
89N ALA 5.0 1.0 + - - -
90N PRO 4.2 4.9 + - - -
91N ASP* 2.8 53.4 + - - +
92N MET* 3.8 17.3 - - + -
98N ASN* 4.5 10.8 - - - +
504N THR* 4.4 1.8 + - - -
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Residues in contact with LYS 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ASN* 3.3 8.4 + - - +
12N HIS* 1.3 99.9 + - + +
14N ASP* 1.3 64.5 + - - +
16N GLY 3.1 1.9 + - - -
17N THR* 2.9 32.1 + - - -
81N TRP* 3.3 33.6 + - + -
85N LEU* 4.0 4.5 - - - -
90N PRO 5.4 1.4 + - - -
500N PRO* 3.6 29.8 - - + +
501N PRO 3.0 20.4 + - - +
502N TYR* 2.8 27.5 + - - +
504N THR* 2.8 31.2 + - - +
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Residues in contact with ASP 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5N ARG* 2.7 53.0 + - - +
6N TRP* 3.3 27.8 - - + -
9N SER* 3.8 16.6 - - - +
11N ASN* 3.0 17.2 + - - +
13N LYS* 1.3 77.6 - - - +
15N ILE* 1.3 56.8 + - - +
17N THR* 3.2 6.0 + - - -
18N LEU* 3.0 32.9 + - - +
502N TYR* 3.3 11.4 + - - -
10Y ASN* 4.0 4.9 - - - +
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Residues in contact with ILE 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N SER* 3.6 17.9 - - - +
11N ASN 3.0 24.5 + - - +
12N HIS 4.0 2.9 - - - +
14N ASP* 1.3 71.7 - - - +
16N GLY* 1.3 66.4 + - - +
18N LEU* 3.2 11.4 + - + +
19N TYR* 3.0 52.2 + - + -
80N ASN* 3.9 1.8 - - - +
95N PRO* 3.9 8.7 - - + +
98N ASN* 3.7 31.9 - - - +
99N ASN* 3.6 43.3 - - + +
102N PHE* 4.5 5.8 - - + -
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Residues in contact with GLY 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N HIS 2.9 17.1 + - - -
13N LYS 3.5 4.3 - - - -
15N ILE* 1.3 75.7 - - - +
17N THR* 1.3 56.8 + - - +
19N TYR* 3.2 4.3 + - - +
20N LEU* 3.0 31.5 + - - +
76N GLY 3.6 20.2 - - - -
77N GLY* 3.5 3.8 - - - -
80N ASN* 3.9 2.0 - - - -
81N TRP* 3.7 15.9 - - - -
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Residues in contact with THR 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N TRP* 4.3 5.4 - - + -
13N LYS 2.9 16.4 + - - -
14N ASP* 3.3 13.4 + - - -
16N GLY* 1.3 73.7 - - - +
18N LEU* 1.3 65.8 + - - +
20N LEU* 3.1 9.5 + - - +
21N LEU* 3.0 29.1 + - + +
81N TRP* 3.2 16.8 + - - +
606N TGL 3.4 30.0 - - + +
10Y ASN 4.4 7.2 + - - +
11Y ILE* 4.7 0.2 - - + -
12Y PRO* 4.2 24.5 - - + -
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Residues in contact with LEU 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N TRP* 3.5 47.6 - - + +
9N SER* 5.1 2.9 - - - -
14N ASP 3.0 18.9 + - - +
15N ILE* 3.2 15.5 + - + +
17N THR* 1.3 74.9 - - - +
19N TYR* 1.3 56.5 + - - +
21N LEU* 3.2 13.0 + - + +
22N PHE* 2.9 29.3 + - - +
99N ASN* 4.8 6.3 - - - +
102N PHE* 3.6 37.0 - - + -
103N TRP* 4.3 3.8 - - + +
606N TGL 3.9 33.7 - - + +
12Y PRO* 5.2 0.4 - - + -
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Residues in contact with TYR 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N ILE* 3.0 35.0 + - + -
16N GLY 3.3 7.9 - - - +
17N THR 3.2 0.2 - - - -
18N LEU* 1.3 76.7 - - - +
20N LEU* 1.3 56.9 + - - +
22N PHE* 3.6 1.4 - - - +
23N GLY* 2.9 27.2 + - - -
72N PRO* 3.6 29.0 - - + +
76N GLY* 3.4 28.0 - - - -
77N GLY 3.4 14.1 - - - +
80N ASN* 3.4 18.6 + - - -
98N ASN* 4.6 2.4 + - - -
101N SER* 3.0 35.5 + - - -
102N PHE* 3.7 25.6 - + + -
105N LEU* 3.8 22.4 - - + -
156N SER* 4.1 2.9 + - - -
160N GLY* 5.8 0.3 - - - -
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Residues in contact with LEU 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N GLY 3.0 18.6 + - - +
17N THR* 3.1 7.6 + - - +
19N TYR* 1.3 76.1 - - - +
21N LEU* 1.3 57.4 + - - +
23N GLY* 3.5 0.7 + - - -
24N ALA* 2.9 31.5 + - - +
73N ILE* 4.0 27.2 - - + +
77N GLY* 3.8 18.8 - - - -
78N PHE* 4.4 11.7 - - + +
81N TRP* 4.0 15.7 - - + +
393N PHE* 5.5 4.0 - - + -
400N PHE* 4.0 28.7 - - + -
604N HEA 4.4 11.7 - - + +
606N TGL 3.5 28.0 - - + -
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Residues in contact with LEU 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N THR* 3.0 21.6 + - + +
18N LEU* 3.5 9.9 - - + +
20N LEU* 1.3 76.3 - - - +
22N PHE* 1.3 63.7 + - - +
24N ALA* 3.4 3.2 + - - +
25N TRP 3.1 18.2 + - - -
606N TGL 3.5 81.4 - - + -
12Y PRO* 3.4 36.3 - - + -
13Y PHE* 4.2 5.6 - - + -
28Y PHE* 3.3 21.4 - - + -
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Residues in contact with PHE 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N LEU 2.9 16.4 + - - +
19N TYR* 3.6 3.6 - - - +
21N LEU* 1.3 76.5 - - - +
23N GLY* 1.3 54.4 + - - +
25N TRP* 3.2 5.6 + + - +
26N ALA* 2.8 35.2 + - - +
68N PHE* 3.6 34.3 - + + -
72N PRO* 4.1 9.0 - - + -
102N PHE* 3.8 15.5 - + + -
105N LEU* 3.6 33.0 - - + -
106N PRO* 3.8 31.2 - - + -
109N PHE* 3.6 27.1 - + - -
606N TGL 3.7 32.7 - - + +
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Residues in contact with GLY 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N TYR 2.9 12.5 + - - -
22N PHE* 1.3 77.4 - - - +
24N ALA* 1.3 52.2 + - - +
26N ALA* 3.4 1.6 + - - +
27N GLY* 2.8 31.2 + - - -
68N PHE 3.4 18.8 - - - -
69N MET* 3.7 8.0 - - - +
72N PRO* 4.5 1.3 - - - -
73N ILE* 3.6 27.0 - - - +
604N HEA 4.6 0.2 - - - +
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Residues in contact with ALA 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N LEU 2.9 19.4 + - - +
21N LEU* 3.5 7.9 - - - +
23N GLY* 1.3 73.9 - - - +
25N TRP* 1.3 65.2 + - - +
27N GLY* 3.3 1.6 + - - -
28N MET* 3.3 31.3 + - - +
73N ILE* 4.2 0.8 - - - +
604N HEA 3.8 31.6 - - + -
606N TGL 5.0 5.2 - - + -
28Y PHE* 4.6 1.1 - - + -
29Y PHE* 4.0 21.8 - - + -
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Residues in contact with TRP 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N LEU 3.1 13.8 + - - +
22N PHE* 3.5 7.6 - + - +
24N ALA* 1.3 76.1 - - - +
26N ALA* 1.3 62.5 + - - +
28N MET* 2.9 24.0 + - - +
29N VAL* 3.2 19.3 + - + +
109N PHE* 3.5 34.1 - + - -
113N LEU* 4.7 3.4 - - + -
606N TGL 3.7 79.0 - - + +
28Y PHE* 2.8 60.4 + + + -
29Y PHE* 4.5 0.9 - - - -
31Y SER* 3.3 11.1 + - - -
32Y GLY* 3.2 25.7 - - - +
35Y ALA* 5.1 3.6 - - + -
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Residues in contact with ALA 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N PHE* 2.8 17.7 + - + +
23N GLY 3.5 1.8 - - - +
25N TRP* 1.3 72.8 - - - +
27N GLY* 1.3 57.3 + - - +
29N VAL* 3.0 4.0 + - - -
30N GLY 2.9 24.9 + - - -
64N VAL* 3.2 11.0 - - + +
68N PHE* 3.3 48.2 - - + +
69N MET* 4.0 1.8 - - - +
109N PHE* 4.0 18.2 - - + -
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Residues in contact with GLY 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N GLY 2.8 16.3 + - - -
24N ALA 3.3 3.1 + - - -
25N TRP 3.2 0.4 - - - -
26N ALA* 1.3 72.4 - - - +
28N MET* 1.3 58.4 + - - +
30N GLY* 3.8 1.0 - - - -
31N THR* 2.6 39.1 + - - -
65N MET* 4.6 4.2 - - - +
69N MET* 3.5 23.9 - - - +
604N HEA 3.8 12.0 - - - +
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Residues in contact with MET 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N ALA 3.3 16.7 + - - +
25N TRP* 2.9 10.6 + - - +
27N GLY* 1.3 74.4 - - - +
29N VAL* 1.3 65.8 + - - +
31N THR* 3.2 5.0 + - - -
32N ALA* 3.0 24.8 + - - +
465N VAL* 3.7 19.7 - - + -
468N MET* 4.2 11.4 - - + -
469N VAL* 4.3 1.3 - - - -
604N HEA 3.1 37.5 - - + -
29Y PHE* 3.5 35.7 - - + +
32Y GLY* 4.0 3.4 - - - -
33Y PHE* 3.6 24.2 - - - +
26Z PHE* 3.8 24.5 - - - -
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Residues in contact with VAL 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N TRP* 3.7 39.5 - - + +
26N ALA 3.3 6.1 - - - +
28N MET* 1.3 76.7 - - - +
30N GLY* 1.3 57.9 + - - +
32N ALA* 3.2 4.5 + - - +
33N LEU* 3.0 49.4 + - + +
64N VAL* 4.0 7.6 - - + -
109N PHE* 3.9 18.4 - - + -
113N LEU* 5.1 10.3 - - + -
32Y GLY* 3.3 22.2 - - - +
35Y ALA* 5.0 2.5 - - + -
36Y PRO* 3.8 13.9 - - + -
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Residues in contact with GLY 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N ALA 2.9 12.4 + - - -
29N VAL* 1.3 76.5 - - - +
31N THR* 1.3 55.8 + - - +
33N LEU* 3.5 8.0 + - - -
34N SER* 3.0 23.2 + - - -
61N HIS* 3.2 13.4 + - - -
64N VAL* 3.6 11.3 - - - +
65N MET* 3.6 27.7 - - - +
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Residues in contact with THR 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N GLY 2.6 23.0 + - - -
28N MET* 3.2 7.6 + - - -
30N GLY* 1.3 74.2 - - - +
32N ALA* 1.3 61.1 + - - +
34N SER* 2.7 27.3 + - - +
35N LEU* 2.9 23.7 + - + +
65N MET* 4.0 4.0 - - - +
462N LEU* 4.4 9.6 - - + -
465N VAL* 4.2 18.1 - - + +
604N HEA 3.6 34.4 - - + +
33Y PHE* 4.2 13.7 - - + -
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Residues in contact with ALA 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N MET 3.0 11.9 + - - +
29N VAL 3.4 9.0 - - - +
31N THR* 1.3 76.5 - - - +
33N LEU* 1.3 61.2 + - - +
35N LEU* 3.2 5.5 + - - +
36N LEU* 3.0 30.2 + - - +
33Y PHE* 3.0 42.7 - - + +
36Y PRO* 3.5 12.1 - - + -
37Y PHE* 3.7 11.5 - - + -
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Residues in contact with LEU 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N VAL* 3.0 37.5 + - + +
30N GLY* 3.7 5.4 - - - +
32N ALA* 1.3 76.5 - - - +
34N SER* 1.3 61.4 + - - +
36N LEU* 3.2 13.2 + - + -
37N ILE* 3.2 17.3 + - - +
57N VAL* 3.5 31.2 - - + +
60N ALA* 3.7 16.2 - - + -
61N HIS* 3.6 35.2 - - + +
64N VAL* 3.9 10.3 - - + -
112N LEU* 6.0 0.2 - - + -
36Y PRO* 3.5 24.2 - - + -
40Y VAL* 6.2 0.7 - - + -
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Residues in contact with SER 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N GLY 3.0 15.4 + - - -
31N THR* 2.7 24.1 + - - +
33N LEU* 1.3 75.3 - - - +
35N LEU* 1.3 66.6 + - - +
37N ILE* 3.3 11.1 + - - +
38N ARG* 3.1 26.2 + - - +
61N HIS* 3.6 15.7 + - - -
604N HEA 3.5 40.8 - - - +
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Residues in contact with LEU 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N THR* 2.9 12.4 + - + +
32N ALA* 3.2 6.7 + - - +
34N SER* 1.3 84.7 + - - +
36N LEU* 1.3 58.8 + - - +
38N ARG* 3.4 3.1 + - - +
39N ALA* 2.9 31.3 + - - +
458N SER* 3.6 37.9 - - - +
459N PHE* 4.2 17.3 - - + -
462N LEU* 3.6 30.1 - - + -
33Y PHE* 3.4 36.8 - - + -
37Y PHE* 4.7 0.9 - - + -
101Z DMU 3.9 18.1 - - + +
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Residues in contact with LEU 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N ALA 3.0 18.6 + - - +
33N LEU* 3.2 10.5 + - + +
35N LEU* 1.3 74.7 - - - +
37N ILE* 1.3 63.2 + - - +
39N ALA* 3.5 7.7 + - + +
40N GLU* 3.2 23.4 + - - +
47N LEU* 6.2 0.2 - - + -
48N LEU* 4.5 32.1 - - + +
57N VAL* 4.0 13.0 - - + -
36Y PRO* 3.9 28.5 - - + -
37Y PHE* 3.6 31.0 - - + +
40Y VAL* 3.9 24.0 - - + -
34Z LEU* 4.3 11.9 - - + -
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Residues in contact with ILE 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N LEU 3.2 14.3 + - - +
34N SER* 3.4 8.1 - - - +
35N LEU 3.2 0.4 - - - -
36N LEU* 1.3 77.8 - - - +
38N ARG* 1.3 62.2 + - - +
40N GLU* 3.2 4.7 + - - +
41N LEU* 3.1 25.8 + - + +
54N TYR* 3.5 30.0 - - + +
57N VAL* 4.1 11.4 - - + -
58N VAL* 4.0 26.2 - - + -
61N HIS* 3.9 31.0 - - + -
604N HEA 3.6 37.7 - - + -
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Residues in contact with ARG 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N SER 3.1 14.7 + - - +
35N LEU 3.4 2.2 + - - +
37N ILE* 1.3 77.6 - - - +
39N ALA* 1.3 58.7 + - - +
41N LEU* 3.4 23.7 - - - +
42N GLY* 2.8 14.6 + - - -
371N TYR* 4.3 4.6 - - - -
424N THR* 4.1 7.2 - - - -
428N GLN* 3.1 18.4 - - - +
431N LEU* 5.7 0.6 - - - +
451N ASN* 2.9 47.7 + - - +
454N SER* 3.1 21.8 + - - -
455N SER* 2.6 51.4 + - - +
458N SER* 3.5 26.7 - - - +
459N PHE* 5.9 2.5 - - + -
604N HEA 3.0 38.7 + - + +
104Q TYR* 4.0 0.2 + - - -
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Residues in contact with ALA 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N LEU 2.9 19.5 + - - +
36N LEU* 3.6 12.3 - - + +
37N ILE 3.2 0.2 - - - -
38N ARG* 1.3 76.2 - - - +
40N GLU* 1.3 64.7 + - - +
42N GLY 3.3 1.2 + - - -
47N LEU* 4.2 15.2 - - + +
459N PHE* 5.4 3.5 - - + -
99Q GLU* 4.0 15.9 - - - +
103Q VAL* 6.3 0.7 - - + -
104Q TYR* 2.6 38.0 + - + -
34Z LEU* 5.6 10.3 - - + -
101Z DMU 5.9 2.2 - - + -
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Residues in contact with GLU 40 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N LEU 3.2 11.3 + - - +
37N ILE 3.5 7.9 - - - +
39N ALA* 1.3 81.3 - - - +
41N LEU* 1.3 56.6 + - - +
43N GLN 3.6 7.6 - - - +
46N THR* 3.4 5.6 - - - -
47N LEU* 2.9 26.7 + - - +
48N LEU* 2.8 40.1 + - + +
49N GLY 4.2 4.0 + - - +
54N TYR* 3.6 27.1 - - + +
441N SER* 3.1 20.1 - - - +
603N NA 2.2 52.2 - - - -
104Q TYR* 5.5 0.3 - - - -
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Residues in contact with LEU 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N ILE* 3.1 22.3 + - + +
38N ARG* 3.4 30.5 - - - +
40N GLU* 1.3 73.6 - - - +
42N GLY* 1.3 59.0 + - - +
43N GLN 3.2 2.9 - - - -
54N TYR* 3.4 15.3 - - + +
371N TYR* 3.3 27.6 - - + +
436N MET* 4.2 4.0 - - + -
440N TYR 3.4 22.0 - - - +
441N SER* 3.9 12.1 - - - +
443N TYR* 2.7 48.6 + - + -
451N ASN* 3.5 15.4 - - - +
455N SER* 3.9 1.6 - - - -
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Residues in contact with GLY 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ARG 2.8 13.3 + - - -
39N ALA 3.3 3.4 + - - -
41N LEU* 1.3 77.5 - - - +
43N GLN* 1.3 61.7 + - - +
443N TYR* 4.2 0.7 - - - -
451N ASN 4.4 0.9 - - - -
452N THR* 3.3 27.9 + - - +
455N SER* 3.4 14.4 - - - -
104Q TYR* 3.2 21.9 - - - -
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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