Contacts of the helix formed by residues 40 - 77 (chain b) in PDB entry 2LPZ
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 40 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37b LYS* 3.1 29.8 + - + +
38b PRO 3.2 0.8 - - - +
39b SER* 1.3 76.4 + - - +
41b PRO* 1.3 65.4 - - - +
42b ALA* 2.9 21.5 + - - +
43b LEU* 3.4 31.1 - - + +
44b LEU* 2.9 32.1 + - - +
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Residues in contact with PRO 41 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39b SER 3.2 11.6 - - - +
40b ASP* 1.3 90.7 - - - +
42b ALA* 1.3 55.5 + - - +
44b LEU* 3.7 11.0 - - + +
45b ALA* 2.9 32.9 + - - +
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Residues in contact with ALA 42 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40b ASP* 2.9 16.3 + - - +
41b PRO* 1.3 80.2 - - - +
43b LEU* 1.3 59.3 + - + +
45b ALA* 4.1 4.0 - - - +
46b ALA* 3.1 30.8 + - - +
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Residues in contact with LEU 43 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30b ALA* 4.8 6.5 - - + +
33b LYS* 3.5 56.1 - - + +
34b LEU* 3.5 19.2 - - + +
37b LYS* 3.7 24.5 - - + +
40b ASP* 3.2 24.9 + - + +
42b ALA* 1.3 75.6 - - + +
44b LEU* 1.3 60.4 + - - +
46b ALA* 4.1 4.4 - - + +
47b TYR* 2.9 34.7 + - - +
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Residues in contact with LEU 44 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34b LEU* 3.6 21.3 - - + -
38b PRO* 3.2 29.8 - - + +
39b SER* 4.5 4.7 - - - +
40b ASP 2.9 21.4 + - - +
41b PRO* 3.7 8.7 - - + +
43b LEU* 1.3 76.8 - - - +
45b ALA* 1.3 57.4 + - - +
47b TYR* 4.1 1.0 - - + +
48b GLN* 2.9 35.9 + - + +
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Residues in contact with ALA 45 (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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41b PRO 2.9 18.2 + - - +
42b ALA* 4.1 4.0 - - - +
44b LEU* 1.3 76.4 - - - +
46b ALA* 1.3 58.4 + - - +
48b GLN* 4.2 3.9 - - - +
49b SER* 3.0 33.5 + - - -
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Residues in contact with ALA 46 (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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30b ALA* 4.8 5.4 - - + -
42b ALA 3.1 19.7 + - - +
43b LEU* 4.1 5.6 - - + +
45b ALA* 1.3 78.7 - - - +
47b TYR* 1.3 61.7 + - - +
49b SER* 3.7 3.7 - - - -
50b LYS* 3.1 41.9 + - - +
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Residues in contact with TYR 47 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27b VAL* 3.4 40.8 - - + -
30b ALA* 3.8 15.5 - - + +
31b LEU* 3.6 39.7 - - + +
34b LEU* 3.3 28.5 - - + -
43b LEU 2.9 20.9 + - - +
44b LEU* 4.1 1.6 - - + +
46b ALA* 1.3 78.4 - - - +
48b GLN* 1.3 54.5 + - + +
50b LYS* 3.2 2.8 + - - +
51b LEU* 2.7 69.4 + - + +
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Residues in contact with GLN 48 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44b LEU 2.9 20.4 + - - +
45b ALA* 4.2 4.2 - - - +
47b TYR* 1.3 81.7 - - + +
49b SER* 1.3 63.0 + - - +
51b LEU* 3.6 11.3 - - + +
52b SER* 2.9 40.7 + - - +
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Residues in contact with SER 49 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45b ALA 3.0 20.7 + - - -
46b ALA* 3.7 5.6 - - - -
48b GLN* 1.3 84.5 + - - +
50b LYS* 1.3 61.8 + - - +
52b SER* 2.8 21.3 + - - -
53b GLU* 3.6 15.3 + - - +
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Residues in contact with LYS 50 (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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23b LEU* 3.5 12.8 - - + +
26b GLN* 2.9 55.0 + - + +
27b VAL* 3.8 14.7 - - + +
30b ALA* 4.9 3.6 - - + -
46b ALA* 3.1 29.4 + - - +
47b TYR* 3.9 2.9 - - - +
49b SER* 1.3 77.9 - - - +
51b LEU* 1.3 61.0 + - - +
52b SER 3.4 0.2 - - - -
53b GLU* 3.4 14.0 + - - +
54b TYR* 2.8 26.0 + - - +
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Residues in contact with LEU 51 (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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27b VAL* 3.7 15.0 - - + +
47b TYR* 2.7 59.9 + - + +
48b GLN* 3.3 11.2 + - + +
50b LYS* 1.3 71.1 - - - +
52b SER* 1.3 59.1 + - - +
53b GLU 3.1 1.8 - - - -
54b TYR* 3.0 20.7 + - + +
55b ASN* 2.8 42.3 + - - +
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Residues in contact with SER 52 (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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39W SER* 5.8 0.3 - - - -
48b GLN* 2.9 27.1 + - - -
49b SER* 2.8 22.9 + - - -
51b LEU* 1.3 75.8 - - - +
53b GLU* 1.3 62.3 + - - +
55b ASN* 3.5 26.7 + - - +
56b LEU* 4.1 9.7 + - - +
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Residues in contact with GLU 53 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38W PRO* 5.8 1.0 - - - +
39W SER* 3.5 33.0 + - - +
23b LEU* 3.7 27.9 - - + +
26b GLN* 5.8 0.3 - - - +
49b SER* 3.6 15.9 + - - +
50b LYS* 3.4 14.7 + - - +
51b LEU 3.1 0.4 - - - -
52b SER* 1.3 78.4 + - - +
54b TYR* 1.3 59.4 + - - +
55b ASN 3.0 1.8 - - - -
56b LEU* 2.9 24.0 + - - +
57b TYR 3.0 8.3 + - - -
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Residues in contact with TYR 54 (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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41V PRO* 4.6 9.6 - - + +
23b LEU* 3.9 6.3 - - + +
24b GLN* 4.0 21.2 + - + +
27b VAL* 3.8 22.7 - - + -
28b THR* 6.0 0.4 - - - -
50b LYS 2.8 18.3 + - - +
51b LEU* 3.0 27.1 + - + +
53b GLU* 1.3 73.1 - - - +
55b ASN* 1.3 66.8 + - - +
56b LEU 3.2 0.2 - - - -
57b TYR* 3.1 47.5 + + + +
58b ARG* 2.9 45.0 + - + +
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Residues in contact with ASN 55 (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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51b LEU* 2.8 24.7 + - - +
52b SER* 3.5 26.5 + - - +
53b GLU 3.0 0.4 - - - -
54b TYR* 1.3 80.1 - - - +
56b LEU* 1.3 60.0 + - + +
58b ARG* 3.7 2.6 + - - +
59b ASN* 3.1 29.0 + - - +
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Residues in contact with LEU 56 (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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38W PRO* 3.7 31.9 - - + +
39W SER* 3.8 20.0 - - - +
44W LEU* 4.8 9.2 - - + -
16b PHE* 3.6 3.4 - - - -
52b SER 4.3 9.9 - - - +
53b GLU 2.9 10.1 + - - +
55b ASN* 1.3 77.3 - - + +
57b TYR* 1.3 66.1 + - - +
58b ARG 3.0 2.2 - - - -
59b ASN* 3.7 15.3 - - + +
60b ALA* 2.9 45.2 + - + +
61b GLN 3.4 2.4 + - - -
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Residues in contact with TYR 57 (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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38W PRO* 5.7 1.0 - - - +
16b PHE* 3.6 9.2 - - - -
17b ASP* 3.8 23.9 + - - +
20b VAL* 3.2 49.8 - - + -
21b ASP* 5.1 4.7 + - - -
23b LEU* 3.8 11.0 - - + -
24b GLN* 2.8 27.9 + - + +
53b GLU 3.0 5.5 + - - -
54b TYR* 3.1 46.2 + + + +
56b LEU* 1.3 76.7 - - - +
58b ARG* 1.3 82.4 + - - +
61b GLN* 2.7 37.1 - - - +
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Residues in contact with ARG 58 (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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41V PRO* 3.5 40.8 + - + +
42V ALA* 3.6 22.4 - - - +
45V ALA* 3.9 14.1 - - - +
24b GLN* 3.6 22.2 + - - +
54b TYR* 2.9 42.4 + - + +
55b ASN* 4.3 4.0 - - - +
56b LEU 3.0 0.4 - - - -
57b TYR* 1.3 103.2 - - + +
59b ASN* 1.3 63.9 + - - +
60b ALA 3.6 0.2 - - - -
61b GLN* 3.6 8.7 + - - +
62b SER* 3.1 26.0 + - - -
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Residues in contact with ASN 59 (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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55b ASN 3.1 19.8 + - - +
56b LEU* 4.2 13.0 - - + +
58b ARG* 1.3 76.0 - - - +
60b ALA* 1.3 63.7 + - - +
62b SER* 3.0 10.6 + - - -
63b ASN* 2.7 53.0 + - - +
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Residues in contact with ALA 60 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W LEU* 6.2 2.5 - - + -
38W PRO* 4.9 3.8 - - + -
44W LEU* 5.5 9.4 - - + -
16b PHE* 4.0 17.3 - - + -
56b LEU* 2.9 34.4 + - + +
59b ASN* 1.3 75.5 - - - +
61b GLN* 1.3 63.3 + - - +
63b ASN* 3.5 11.1 - - - +
64b THR* 3.1 32.2 + - + +
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Residues in contact with GLN 61 (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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45V ALA* 4.6 16.6 - - - +
13b SER* 2.8 31.7 + - - +
16b PHE* 3.6 24.7 - - + +
17b ASP* 3.1 26.9 + - - +
56b LEU 3.4 3.6 + - - -
57b TYR* 2.7 36.0 - - - +
58b ARG* 3.6 19.4 + - - +
59b ASN 3.2 0.2 - - - -
60b ALA* 1.3 77.4 - - - +
62b SER* 1.3 62.1 + - - +
64b THR* 2.8 21.8 + - - -
65b VAL* 3.3 14.6 + - + +
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Residues in contact with SER 62 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45V ALA* 6.4 3.6 - - - -
48V GLN* 4.8 14.6 - - - +
58b ARG 3.1 11.6 + - - -
59b ASN* 3.0 16.8 + - - -
61b GLN* 1.3 78.4 - - - +
63b ASN* 1.3 63.1 + - - +
65b VAL* 3.8 7.2 - - - +
66b LYS* 3.0 28.8 + - - +
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Residues in contact with ASN 63 (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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56b LEU* 6.2 0.2 - - - +
59b ASN* 2.7 46.9 + - - +
60b ALA* 3.5 10.6 - - - +
61b GLN 3.2 0.2 - - - -
62b SER* 1.3 81.5 + - - +
64b THR* 1.3 62.8 + - + +
66b LYS* 3.3 12.9 + - - +
67b VAL* 3.1 28.4 + - + +
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Residues in contact with THR 64 (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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31W LEU* 4.4 10.7 - - + +
34W LEU* 5.4 4.3 - - + -
47W TYR* 3.9 35.2 - - + +
51W LEU* 5.6 1.6 - - + -
12b VAL* 4.1 13.4 - - - +
16b PHE* 4.8 14.2 - - + +
60b ALA* 3.1 15.2 + - + +
61b GLN* 2.8 22.5 + - - -
63b ASN* 1.3 77.0 - - + +
65b VAL* 1.3 61.2 + - - +
67b VAL* 3.3 7.4 + - - +
68b PHE* 3.0 33.7 + - - -
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Residues in contact with VAL 65 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V GLN* 5.0 8.1 - - - +
49V SER* 4.5 14.8 - - - +
52V SER* 4.3 13.5 - - - +
9b LEU* 3.4 34.7 - - + +
12b VAL* 3.9 22.7 - - + -
13b SER* 4.1 16.8 - - - +
61b GLN* 3.3 18.8 + - + +
62b SER* 3.8 7.2 - - - +
63b ASN 3.3 0.6 - - - -
64b THR* 1.3 80.3 + - - +
66b LYS* 1.3 66.0 + - - +
68b PHE 3.3 1.0 + - - -
69b LYS* 2.9 21.8 + - + +
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Residues in contact with LYS 66 (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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48V GLN* 6.1 4.3 - - - +
62b SER 3.0 18.7 + - - +
63b ASN* 3.4 12.6 - - - +
65b VAL* 1.3 77.9 - - - +
67b VAL* 1.3 52.9 + - + +
69b LYS* 3.0 8.0 + - + +
70b ASP* 2.6 70.0 + - - +
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Residues in contact with VAL 67 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51W LEU* 3.8 38.4 - - + -
54W TYR* 5.8 0.4 - - + -
55W ASN* 3.4 26.7 - - - +
63b ASN* 3.1 15.1 + - + +
64b THR* 3.7 7.9 - - - +
65b VAL 3.3 0.2 - - - -
66b LYS* 1.3 79.6 - - + +
68b PHE* 1.3 60.3 + - + +
70b ASP* 3.0 25.8 + - + +
71b ILE* 3.0 18.5 + - + +
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Residues in contact with PHE 68 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q PRO* 4.0 1.4 - - - +
27W VAL* 6.1 3.4 - - + -
28W THR* 6.5 0.7 - - - -
31W LEU* 3.8 26.2 - - + -
47W TYR* 3.6 23.3 - + - -
51W LEU* 4.9 5.6 - - + -
54W TYR* 3.8 23.6 - + - -
8b TYR* 3.4 34.8 - + + -
9b LEU* 3.5 19.7 - - + +
12b VAL* 3.6 21.1 - - + -
64b THR* 3.0 25.8 + - - +
65b VAL 4.5 0.2 - - - -
66b LYS 3.3 0.2 - - - -
67b VAL* 1.3 78.5 - - + +
69b LYS* 1.3 56.9 + - - +
71b ILE* 3.1 32.7 - - + +
72b ASP* 2.9 16.6 - - - +
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Residues in contact with LYS 69 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52V SER* 3.9 28.5 - - - +
55V ASN* 4.1 21.4 - - - +
56V LEU* 5.4 11.3 - - + +
9b LEU* 3.6 22.4 - - + +
65b VAL 2.9 13.8 + - - +
66b LYS* 3.3 11.2 - - + +
68b PHE* 1.3 77.6 - - - +
70b ASP* 1.3 67.2 + - - +
71b ILE 3.3 0.4 - - - -
72b ASP* 3.2 12.7 - - + +
73b ALA* 3.0 37.7 + - - +
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Residues in contact with ASP 70 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55W ASN* 5.9 0.9 - - - +
66b LYS* 2.6 61.5 + - - +
67b VAL* 3.0 16.5 + - + +
69b LYS* 1.3 82.4 + - - +
71b ILE* 1.3 58.9 + - + +
73b ALA* 3.3 8.9 + - - +
74b ALA* 2.9 26.2 + - - +
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Residues in contact with ILE 71 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q PRO* 3.4 30.7 - - + -
54W TYR* 3.5 29.8 - - + +
55W ASN* 3.9 38.8 - - - +
58W ARG* 3.9 15.2 - - + +
67b VAL* 3.0 11.4 + - + +
68b PHE* 3.1 28.3 - - + +
70b ASP* 1.3 74.5 - - + +
72b ASP* 1.3 62.8 + - - +
74b ALA* 3.6 8.6 - - - +
75b ILE* 3.2 30.0 + - - +
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Residues in contact with ASP 72 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q SER* 2.7 38.6 - - - +
41Q PRO* 3.2 19.4 - - - +
44Q LEU* 3.4 24.4 - - + +
56V LEU* 4.5 12.1 - - + +
9b LEU* 4.2 2.8 - - - +
68b PHE 2.9 16.9 - - - +
69b LYS* 3.2 17.1 + - + +
71b ILE* 1.3 76.7 - - - +
73b ALA* 1.3 64.2 + - - +
75b ILE* 3.3 3.5 + - - +
76b ILE* 3.1 30.5 + - - +
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Residues in contact with ALA 73 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V LEU* 5.9 0.4 - - - +
69b LYS* 3.0 28.8 + - - +
70b ASP* 3.6 11.0 - - - +
72b ASP* 1.3 75.2 - - - +
74b ALA* 1.3 58.8 + - - +
76b ILE* 3.3 16.0 - - + +
77b GLN* 2.8 33.3 + - - +
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Residues in contact with ALA 74 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59W ASN* 4.2 37.7 - - + +
62W SER* 3.8 10.3 + - - -
70b ASP 2.9 15.9 + - - +
71b ILE* 3.6 12.3 - - + +
72b ASP 3.2 0.4 - - - -
73b ALA* 1.3 76.7 - - - +
75b ILE* 1.3 62.6 + - + +
77b GLN* 3.4 17.8 - - - +
78b ASN* 3.8 6.1 + - - -
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Residues in contact with ILE 75 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Q PRO* 3.4 35.0 - - + +
44Q LEU* 3.7 37.0 - - + +
45Q ALA* 3.9 14.1 - - + +
48Q GLN* 4.3 14.5 - - + +
58W ARG* 4.2 26.9 - - + +
62W SER* 4.3 12.2 - - - -
71b ILE 3.2 17.4 + - - +
72b ASP 3.3 6.0 + - - +
73b ALA 3.2 0.6 - - - -
74b ALA* 1.3 77.7 - - - +
76b ILE* 1.3 61.2 + - + +
77b GLN 3.1 0.2 - - - -
78b ASN* 3.0 27.0 + - - +
79b PHE* 3.6 1.4 + - + -
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Residues in contact with ILE 76 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q LEU* 3.8 29.4 - - + -
56V LEU* 3.6 31.0 - - + -
59V ASN* 3.9 22.2 - - - +
60V ALA* 5.4 4.9 - - + +
63V ASN* 4.5 14.0 + - - +
72b ASP 3.3 11.7 - - - +
73b ALA* 3.3 24.9 - - + +
75b ILE* 1.3 73.2 - - + +
77b GLN* 1.3 61.9 + - - +
78b ASN 3.1 1.3 - - - -
79b PHE* 3.1 36.2 + - + +
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Residues in contact with GLN 77 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66W LYS* 5.7 1.0 - - - -
73b ALA 2.8 18.9 + - - +
74b ALA* 3.4 12.8 - - - +
75b ILE 3.1 0.2 - - - -
76b ILE* 1.3 79.0 - - - +
78b ASN* 1.3 65.0 + - - +
79b PHE 3.3 1.6 + - - -
80b ARG* 5.8 1.0 - - - -
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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