Contacts of the helix formed by residues 8 - 34 (chain B) in PDB entry 3OOY
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 8 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B MET* 1.3 62.5 + - - +
10B GLN* 3.4 3.8 - - - +
11B LYS* 3.6 18.4 - - - +
12B LEU* 3.2 33.7 + - - +
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Residues in contact with MET 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 1.3 76.5 - - - +
10B GLN* 1.3 66.3 + - - +
11B LYS 3.2 0.2 - - - -
12B LEU* 3.5 11.6 + - + +
13B GLN* 3.2 22.9 + - - +
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Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 3.4 1.9 - - - +
9B MET* 1.3 76.9 - - - +
11B LYS* 1.3 56.7 + - - +
13B GLN* 3.4 6.7 + - - +
14B ALA* 2.9 29.0 + - - +
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Residues in contact with LYS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 3.6 21.8 + - - +
9B MET 3.2 0.2 - - - -
10B GLN* 1.3 77.3 - - - +
12B LEU* 1.3 67.9 + - + +
14B ALA* 3.2 5.1 + - + +
15B LEU* 3.0 35.5 + - + +
53B PHE 2.7 29.0 + - - -
54B HIS* 3.7 26.1 - - + +
284B ILE* 3.3 28.0 - - + +
285B LEU 5.3 0.4 + - - -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 3.2 22.4 + - - +
9B MET* 3.9 10.8 - - + +
10B GLN 3.4 0.2 - - - -
11B LYS* 1.3 78.4 - - + +
13B GLN* 1.3 63.2 + - - +
15B LEU* 3.3 9.4 + - + +
16B LYS* 3.1 33.1 + - - +
221B VAL* 4.1 17.2 - - + +
222B GLU* 3.6 41.5 - - + +
225B CYS* 4.6 14.8 - - + -
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B MET 3.2 14.8 + - - +
10B GLN* 3.7 5.6 - - - +
12B LEU* 1.3 80.7 - - - +
14B ALA* 1.3 56.9 + - - +
16B LYS* 3.3 27.8 + - - +
17B ASP* 2.9 63.0 + - - +
277B GLN 4.4 5.1 + - - -
279B GLN* 3.4 42.1 + - + +
280B SER* 6.3 0.4 - - - -
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN 2.9 18.3 + - - +
11B LYS* 3.2 8.5 + - + +
13B GLN* 1.3 75.0 - - - +
15B LEU* 1.3 52.5 + - - +
17B ASP* 3.6 11.7 - - - +
18B THR* 2.7 38.3 + - - -
21B ARG* 4.2 1.5 + - - +
280B SER* 6.3 1.6 - - - -
282B LYS 4.9 9.4 - - - +
284B ILE* 3.8 22.7 - - + -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LYS* 3.0 32.4 + - + +
12B LEU* 3.6 13.0 - - + +
14B ALA* 1.3 73.5 - - - +
16B LYS* 1.3 59.0 + - - +
18B THR* 3.3 3.9 + - - +
19B ALA* 2.8 28.6 + - - +
49B ALA* 3.6 35.2 - - + +
50B VAL* 4.2 6.3 - - + -
53B PHE* 3.7 14.6 - - + +
54B HIS* 4.1 11.9 - - + +
221B VAL* 4.1 15.0 - - + -
225B CYS* 4.1 25.8 - - - -
284B ILE* 3.6 19.7 - - + -
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 3.1 20.6 + - - +
13B GLN* 3.3 31.4 + - - +
15B LEU* 1.3 71.5 - - - +
17B ASP* 1.3 66.0 + - - +
19B ALA* 3.4 7.9 + - - +
20B ASN* 3.1 31.9 + - - +
46B GLU* 5.3 2.2 - - + +
221B VAL* 3.7 31.0 - - + -
222B GLU* 3.6 20.9 + - - -
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 2.9 52.7 + - - +
14B ALA* 3.6 8.5 - - - +
15B LEU 3.3 0.2 - - - -
16B LYS* 1.3 75.7 - - - +
18B THR* 1.3 57.8 + - - +
20B ASN* 3.3 4.1 + - - +
21B ARG* 2.9 51.1 + - - +
277B GLN 4.0 0.9 - - - +
278B ILE* 3.6 15.0 - - + +
279B GLN 3.0 22.6 + - - -
280B SER* 3.1 28.9 + - - +
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 2.7 26.2 + - - -
15B LEU* 3.5 7.4 - - - -
17B ASP* 1.3 74.7 - - - +
19B ALA* 1.3 66.1 + - - +
21B ARG* 3.2 20.5 + - - +
22B LEU* 2.9 33.0 + - + +
49B ALA* 4.1 10.3 - - + -
53B PHE* 3.9 28.7 - - + -
88B GLU* 3.9 21.1 + - + +
284B ILE* 3.8 15.2 + - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU 2.8 16.9 + - - +
16B LYS* 3.5 10.3 - - - +
18B THR* 1.3 71.7 - - - +
20B ASN* 1.3 57.5 + - - +
22B LEU* 3.2 7.6 + - - +
23B ARG* 3.1 23.2 + - - +
45B ALA* 3.4 28.5 - - - +
46B GLU* 3.6 40.6 - - + +
49B ALA* 3.8 3.3 - - + +
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 3.1 21.9 + - - +
17B ASP* 3.8 4.0 - - - +
19B ALA* 1.3 75.3 - - - +
21B ARG* 1.3 65.1 + - - +
22B LEU 3.2 1.1 - - - -
23B ARG* 2.9 36.7 + - - +
24B ILE* 3.1 26.5 + - - +
46B GLU* 5.4 0.8 + - - -
247B GLY* 6.1 0.2 - - - -
274B ILE* 3.6 21.9 - - + +
277B GLN* 4.1 24.3 + - - +
278B ILE* 3.9 16.4 - - + +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 4.2 2.0 + - - +
17B ASP* 2.9 29.4 + - - +
18B THR* 3.5 31.4 + - - +
20B ASN* 1.3 70.3 - - - +
22B LEU* 1.3 64.5 + - + +
24B ILE* 3.2 8.6 + - + +
25B SER* 3.1 24.4 + - - -
88B GLU* 2.8 31.1 + - - +
275B TYR* 6.3 1.1 - - + -
278B ILE* 3.9 20.8 - - + +
280B SER 2.9 24.9 + - - -
281B LYS* 3.8 17.6 - - - +
282B LYS 3.7 20.4 + - - -
283B LYS* 3.8 19.6 - - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B THR* 2.9 24.2 + - + +
19B ALA 3.3 7.6 - - - +
21B ARG* 1.3 78.6 - - - +
23B ARG* 1.3 61.1 + - - +
25B SER* 3.6 2.7 + - - -
26B SER* 3.1 26.9 + - - -
45B ALA 3.9 19.5 - - - +
48B MET* 4.1 8.3 - - + -
49B ALA* 4.1 10.8 - - - +
81B ILE* 3.9 16.1 - - + +
84B ALA* 3.5 42.4 - - + +
85B VAL* 3.5 27.8 - - + +
88B GLU* 4.7 9.6 - - + -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA 3.1 11.3 + - - +
20B ASN* 2.9 41.2 + - - +
22B LEU* 1.3 72.6 - - - +
24B ILE* 1.3 68.5 + - - +
26B SER* 3.2 6.2 + - - -
27B ILE* 3.0 28.8 + - - +
41B CYS* 6.2 0.2 - - - -
42B CYS* 3.2 34.1 + - - +
45B ALA* 3.6 16.3 - - + +
46B GLU* 2.8 43.2 + - - -
81B ILE* 5.6 0.4 - - - -
219B HIS* 3.9 0.2 + - - -
246B ARG* 3.1 49.7 + - - +
247B GLY* 4.7 4.9 - - - -
274B ILE* 4.2 19.7 - - + -
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASN 3.1 16.9 + - - +
21B ARG* 3.2 10.3 + - + +
23B ARG* 1.3 78.0 - - - +
25B SER* 1.3 60.4 + - - +
27B ILE* 3.2 11.1 + - - +
28B GLN* 2.8 51.3 + - - +
271B ILE* 3.9 19.5 - - + +
274B ILE* 3.7 17.7 - - + -
275B TYR* 3.8 42.0 - - + +
278B ILE* 3.9 14.4 - - + -
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG 3.1 13.2 + - - -
22B LEU* 3.8 4.0 - - - -
24B ILE* 1.3 78.4 - - - +
26B SER* 1.3 60.5 + - - +
28B GLN* 3.9 13.9 + - - +
29B ALA* 2.8 33.3 + - - +
80B PRO 5.1 1.4 + - - -
84B ALA* 3.7 16.0 - - - +
97B LEU* 3.1 33.0 - - - +
98B LEU* 5.6 0.2 - - - +
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 3.1 16.9 + - - -
23B ARG* 3.2 10.9 + - - -
25B SER* 1.3 75.2 - - - +
27B ILE* 1.3 54.1 + - - +
29B ALA* 4.0 0.7 - - - +
30B THR* 2.7 40.5 + - - +
38B PRO* 4.7 7.0 - - - -
41B CYS* 3.2 37.0 - - - +
42B CYS* 5.2 0.9 - - - -
80B PRO* 4.3 11.2 - - - -
81B ILE* 3.6 16.5 - - - +
84B ALA* 5.1 0.8 - - - +
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG 3.0 20.5 + - - +
24B ILE* 3.5 6.7 - - - +
26B SER* 1.3 75.3 - - - +
28B GLN* 1.3 60.5 + - - +
30B THR* 3.2 5.8 + - - -
31B THR* 2.8 37.4 + - - +
38B PRO* 4.4 12.8 - - + -
42B CYS* 4.4 6.3 - - - -
248B ILE* 4.2 19.1 - - + -
262B LEU* 3.9 17.9 - - + -
267B ALA* 3.9 27.4 - - + -
270B ILE* 4.3 9.0 - - + -
271B ILE* 4.1 15.5 - - + -
274B ILE* 3.8 28.0 - - + -
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 2.8 36.8 + - - +
25B SER* 3.9 16.3 + - - +
27B ILE* 1.3 72.6 - - - +
29B ALA* 1.3 57.2 + - - +
31B THR* 3.8 4.5 - - - +
32B ALA* 2.9 31.5 + - - +
98B LEU* 3.9 21.1 - - + +
271B ILE* 3.4 24.7 - - + +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 2.8 22.2 + - - +
26B SER 4.1 2.9 - - - +
28B GLN* 1.3 75.0 - - - +
30B THR* 1.3 57.4 + - - +
32B ALA* 3.4 4.5 + - - +
33B ALA* 3.0 27.4 + - - +
80B PRO* 4.8 7.9 - - + +
97B LEU* 3.2 33.4 - - + +
98B LEU* 4.2 6.6 - - + +
100B LEU* 3.7 18.3 - - + +
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Residues in contact with THR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER 2.7 23.0 + - - +
27B ILE* 3.2 6.4 + - - -
29B ALA* 1.3 72.9 - - - +
31B THR* 1.3 60.3 + - - +
33B ALA 3.2 0.5 + - - -
34B GLY* 2.9 25.1 + - - -
35B SER 3.3 26.6 + - - +
36B GLY* 3.9 0.4 - - - -
37B HIS 3.8 20.2 - - - +
38B PRO* 3.5 29.2 - - + +
80B PRO* 3.9 11.7 - - + -
100B LEU* 3.7 16.4 - - + -
261B PRO* 3.7 7.1 - - - +
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 2.8 19.9 + - - +
28B GLN* 3.9 4.3 - - - +
30B THR* 1.3 75.0 + - - +
32B ALA* 1.3 65.2 + - - +
34B GLY* 3.5 10.0 + - - -
261B PRO* 4.5 3.6 - - - -
262B LEU* 2.6 36.2 + - - +
264B LYS* 4.0 28.5 - - + +
267B ALA* 3.5 16.9 - - + +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLN 2.9 17.8 + - - +
29B ALA* 3.7 6.1 - - - +
31B THR* 1.3 79.0 - - - +
33B ALA* 1.3 61.6 + - - +
34B GLY 3.5 0.2 + - - -
98B LEU* 3.7 29.4 - - + +
102B LYS* 3.6 13.0 + - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 5.0 8.7 - - - +
597A LYS* 5.3 5.4 + - - -
29B ALA 3.0 16.0 + - - +
30B THR 3.2 4.2 + - - +
32B ALA* 1.3 79.8 - - - +
34B GLY* 1.3 59.2 + - - +
35B SER* 3.3 16.3 + - - +
98B LEU 5.5 0.4 - - - -
100B LEU* 3.4 29.4 - - + +
101B ARG* 4.2 10.8 - - + -
102B LYS* 4.0 13.5 + - - +
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Residues in contact with GLY 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR 2.9 7.2 + - - -
31B THR 3.5 7.2 + - - -
32B ALA 3.3 3.2 - - - -
33B ALA* 1.3 76.3 - - - +
35B SER* 1.3 61.2 + - - +
261B PRO* 3.7 17.9 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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