Contacts of the helix formed by residues 40 - 77 (chain c) 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 c).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37c LYS* 3.1 27.9 + - + +
38c PRO 3.2 0.4 - - - -
39c SER* 1.3 76.9 + - - +
41c PRO* 1.3 65.3 - - - +
42c ALA* 2.9 21.3 + - - +
43c LEU* 3.2 33.8 + - + +
44c LEU* 2.9 32.1 + - - +
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Residues in contact with PRO 41 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39c SER 3.2 11.2 - - - +
40c ASP* 1.3 91.5 - - - +
42c ALA* 1.3 55.2 + - - +
44c LEU* 3.7 10.8 - - + +
45c ALA* 2.9 32.7 + - - +
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Residues in contact with ALA 42 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40c ASP* 2.9 15.9 + - - +
41c PRO* 1.3 81.5 - - - +
43c LEU* 1.3 58.1 + - + +
45c ALA* 4.1 3.9 - - - +
46c ALA* 3.1 30.8 + - - +
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Residues in contact with LEU 43 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30c ALA* 4.8 6.1 - - + +
33c LYS* 3.5 56.5 - - + +
34c LEU* 3.5 19.2 - - + +
37c LYS* 3.7 22.9 - - + +
40c ASP* 3.2 26.2 + - + +
42c ALA* 1.3 76.5 - - + +
44c LEU* 1.3 60.0 + - - +
46c ALA* 4.1 4.0 - - + +
47c TYR* 2.9 34.5 + - - +
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Residues in contact with LEU 44 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34c LEU* 3.6 22.0 - - + -
38c PRO* 3.2 28.7 - - + +
39c SER* 4.5 5.2 - - - +
40c ASP 2.9 20.0 + - - +
41c PRO* 3.7 9.2 - - + +
43c LEU* 1.3 76.5 - - - +
45c ALA* 1.3 57.2 + - - +
47c TYR* 4.1 1.1 - - + +
48c GLN* 2.9 35.4 + - - +
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Residues in contact with ALA 45 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41c PRO 2.9 17.7 + - - +
42c ALA* 4.1 4.3 - - - +
44c LEU* 1.3 76.6 - - - +
46c ALA* 1.3 59.3 + - - +
48c GLN* 4.1 4.1 - - - +
49c SER* 3.0 32.7 + - - -
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Residues in contact with ALA 46 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30c ALA* 4.8 5.4 - - + -
42c ALA 3.1 18.9 + - - +
43c LEU* 4.1 6.1 - - + +
45c ALA* 1.3 78.3 - - - +
47c TYR* 1.3 62.5 + - - +
49c SER* 3.7 3.7 - - - -
50c LYS* 3.1 41.9 + - - +
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Residues in contact with TYR 47 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27c VAL* 3.4 40.2 - - + -
30c ALA* 3.8 14.8 - - + +
31c LEU* 3.6 39.5 - - + +
34c LEU* 3.3 27.4 - - + -
43c LEU 2.9 21.3 + - - +
44c LEU* 4.1 1.6 - - + +
46c ALA* 1.3 78.7 - - - +
48c GLN* 1.3 54.5 + - + +
50c LYS* 3.2 2.9 + - - +
51c LEU* 2.7 68.7 + - + +
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Residues in contact with GLN 48 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44c LEU 2.9 20.2 + - - +
45c ALA* 4.2 4.2 - - - +
47c TYR* 1.3 82.3 - - + +
49c SER* 1.3 62.5 + - - +
51c LEU* 3.6 10.7 - - + +
52c SER* 2.9 40.3 + - - -
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Residues in contact with SER 49 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45c ALA 3.0 20.4 + - - -
46c ALA* 3.7 6.3 - - - -
48c GLN* 1.3 84.5 + - - +
50c LYS* 1.3 59.2 + - - +
52c SER* 2.8 21.3 + - - -
53c GLU* 3.6 15.2 + - - +
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Residues in contact with LYS 50 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23c LEU* 3.5 12.4 - - + +
26c GLN* 2.9 55.0 + - + +
27c VAL* 3.8 15.2 - - + +
30c ALA* 4.9 3.6 - - + -
46c ALA* 3.1 31.2 + - - +
47c TYR 3.9 2.9 - - - +
49c SER* 1.3 77.4 - - - +
51c LEU* 1.3 60.9 + - - +
52c SER 3.4 0.2 - - - -
53c GLU* 3.4 13.5 + - - +
54c TYR* 2.8 26.5 + - - +
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Residues in contact with LEU 51 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27c VAL* 3.7 14.8 - - + -
47c TYR* 2.7 58.8 + - + +
48c GLN* 3.3 11.9 + - + +
50c LYS* 1.3 70.5 - - - +
52c SER* 1.3 59.9 + - - +
53c GLU 3.1 1.1 - - - -
54c TYR* 3.0 20.8 + - + +
55c ASN* 2.8 42.3 + - - +
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Residues in contact with SER 52 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X SER* 5.8 0.3 - - - -
48c GLN* 2.9 27.6 + - - +
49c SER* 2.8 23.0 + - - -
51c LEU* 1.3 76.2 - - - +
53c GLU* 1.3 60.1 + - - +
55c ASN* 3.5 26.5 + - - +
56c LEU* 4.1 9.5 + - - +
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Residues in contact with GLU 53 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X PRO* 5.8 1.4 - - - +
39X SER* 3.5 33.3 + - - +
23c LEU* 3.7 27.2 - - + +
26c GLN* 5.8 0.2 - - - +
49c SER* 3.6 16.0 + - - +
50c LYS* 3.4 15.6 + - - +
51c LEU 3.1 0.2 - - - -
52c SER* 1.3 79.1 + - - +
54c TYR* 1.3 59.1 + - - +
55c ASN 3.0 2.0 - - - -
56c LEU* 2.9 23.6 + - - +
57c TYR 3.0 8.5 + - - -
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Residues in contact with TYR 54 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W PRO* 4.6 9.0 - - + +
23c LEU* 3.9 6.3 - - + +
24c GLN* 4.0 22.3 + - + +
27c VAL* 3.8 23.1 - - + -
28c THR* 6.0 0.7 - - - -
50c LYS 2.8 17.2 + - - +
51c LEU* 3.0 27.1 + - + +
53c GLU* 1.3 72.5 - - - +
55c ASN* 1.3 67.3 + - - +
57c TYR* 3.1 47.5 + + + +
58c ARG* 2.9 44.8 + - + +
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Residues in contact with ASN 55 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51c LEU* 2.8 23.6 + - - +
52c SER* 3.5 26.8 + - - +
53c GLU 3.0 0.2 - - - -
54c TYR* 1.3 80.5 - - - +
56c LEU* 1.3 58.5 + - + +
58c ARG* 3.7 3.0 + - - +
59c ASN* 3.1 28.6 + - - +
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Residues in contact with LEU 56 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X PRO* 3.7 31.2 - - + +
39X SER* 3.8 20.2 - - - -
44X LEU* 4.8 9.2 - - + -
16c PHE* 3.6 3.7 - - - -
52c SER 4.3 9.9 - - - +
53c GLU 2.9 9.2 + - - +
55c ASN* 1.3 77.9 - - + +
57c TYR* 1.3 66.2 + - - +
58c ARG 3.0 2.2 - - - -
59c ASN* 3.7 15.5 - - + +
60c ALA* 2.9 43.6 + - + +
61c GLN 3.4 2.9 + - - -
63c ASN* 6.2 0.2 - - - +
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Residues in contact with TYR 57 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X PRO* 5.7 0.6 - - - +
16c PHE* 3.6 9.0 - - - -
17c ASP* 3.8 24.0 + - - +
20c VAL* 3.2 49.1 - - + -
21c ASP* 5.2 4.9 + - - -
23c LEU* 3.8 11.7 - - + -
24c GLN* 2.8 28.2 + - + +
53c GLU 3.0 5.6 + - - -
54c TYR* 3.1 45.5 - + + +
56c LEU* 1.3 76.7 - - - +
58c ARG* 1.3 82.3 + - - +
61c GLN* 2.7 37.9 - - - +
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Residues in contact with ARG 58 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W PRO* 3.5 39.4 + - + +
42W ALA* 3.6 21.4 - - - +
45W ALA* 3.9 14.6 - - + +
24c GLN* 3.6 22.4 - - - +
54c TYR* 2.9 44.0 + - + +
55c ASN* 4.3 3.4 - - - +
56c LEU 3.0 0.2 - - - -
57c TYR* 1.3 100.5 - - + +
59c ASN* 1.3 64.8 + - - +
61c GLN* 3.6 9.7 + - - +
62c SER* 3.1 25.8 + - - -
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Residues in contact with ASN 59 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55c ASN 3.1 20.2 + - - +
56c LEU* 4.2 12.4 - - + +
58c ARG* 1.3 77.3 - - - +
60c ALA* 1.3 64.1 + - - +
62c SER* 3.0 10.9 + - - -
63c ASN* 2.7 51.7 + - - +
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Residues in contact with ALA 60 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34X LEU* 6.2 2.5 - - + -
38X PRO* 4.9 4.0 - - + -
44X LEU* 5.5 9.4 - - + -
16c PHE* 4.0 17.3 - - + -
56c LEU* 2.9 34.0 + - + +
59c ASN* 1.3 75.8 + - - +
61c GLN* 1.3 63.3 + - - +
63c ASN* 3.5 11.9 - - - +
64c THR* 3.1 31.6 + - + +
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Residues in contact with GLN 61 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45W ALA* 4.6 16.2 - - - +
13c SER* 2.8 32.8 + - - +
16c PHE* 3.6 24.5 - - + -
17c ASP* 3.1 26.3 + - - +
56c LEU 3.4 3.0 + - - -
57c TYR* 2.7 35.7 - - - +
58c ARG* 3.6 19.5 + - - +
59c ASN 3.2 0.4 - - - -
60c ALA* 1.3 78.5 - - - +
62c SER* 1.3 61.4 + - - +
64c THR* 2.8 22.1 + - - -
65c VAL* 3.3 15.3 + - + +
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Residues in contact with SER 62 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45W ALA* 6.4 3.1 - - - -
48W GLN* 4.8 14.6 - - - +
58c ARG 3.1 11.8 + - - -
59c ASN* 3.0 16.6 + - - -
61c GLN* 1.3 78.8 - - - +
63c ASN* 1.3 62.8 + - - +
65c VAL* 3.6 7.2 + - - +
66c LYS* 3.0 29.1 + - - +
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Residues in contact with ASN 63 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56c LEU* 6.2 0.2 - - - +
59c ASN* 2.7 46.1 + - - +
60c ALA* 3.5 11.0 - - - +
61c GLN 3.2 0.2 - - - -
62c SER* 1.3 82.9 + - - +
64c THR* 1.3 63.0 + - + +
66c LYS* 3.3 12.5 + - - +
67c VAL* 3.1 28.5 + - + +
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Residues in contact with THR 64 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X LEU* 4.4 10.7 - - + +
34X LEU* 5.4 4.3 - - + -
47X TYR* 3.9 34.3 - - + +
51X LEU* 5.6 1.6 - - + -
12c VAL* 4.1 13.8 - - - +
16c PHE* 4.8 14.2 - - + +
60c ALA* 3.1 16.1 + - + +
61c GLN* 2.8 22.0 + - - -
63c ASN* 1.3 76.6 - - + +
65c VAL* 1.3 60.4 + - - +
67c VAL* 3.3 8.0 + - - +
68c PHE* 3.0 32.7 + - - -
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Residues in contact with VAL 65 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48W GLN* 5.0 7.9 - - - +
49W SER* 4.5 15.0 - - - +
52W SER* 4.3 13.2 - - - +
9c LEU* 3.4 35.0 - - + +
12c VAL* 3.9 22.0 - - + -
13c SER* 4.1 16.4 - - - +
61c GLN* 3.3 19.4 + - + +
62c SER* 3.8 7.2 - - - +
63c ASN 3.3 0.2 - - - -
64c THR* 1.3 80.5 + - - +
66c LYS* 1.3 64.7 + - - +
68c PHE 3.3 0.9 + - - -
69c LYS* 2.9 22.8 + - + +
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Residues in contact with LYS 66 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48W GLN* 6.1 4.3 - - - +
62c SER 3.0 18.3 + - - +
63c ASN* 3.4 12.3 - - - +
65c VAL* 1.3 77.4 - - - +
67c VAL* 1.3 53.7 + - + +
69c LYS* 3.0 9.0 + - + +
70c ASP* 2.6 68.1 + - - +
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Residues in contact with VAL 67 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X LEU* 3.8 38.8 - - + -
55X ASN* 3.4 26.5 - - - +
63c ASN* 3.1 15.5 + - + +
64c THR* 3.7 7.2 - - - +
65c VAL 3.3 0.2 - - - -
66c LYS* 1.3 79.8 - - + +
68c PHE* 1.3 61.2 + - + +
70c ASP* 3.0 27.1 + - + +
71c ILE* 3.0 18.5 + - + +
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Residues in contact with PHE 68 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R PRO* 4.0 1.2 - - - +
27X VAL* 6.1 3.4 - - + -
28X THR* 6.5 0.9 - - - -
31X LEU* 3.8 25.8 - - + -
47X TYR* 3.6 23.6 - + - -
51X LEU* 4.9 6.3 - - + -
54X TYR* 3.8 23.1 - + - -
8c TYR* 3.4 34.1 - + + -
9c LEU* 3.5 20.4 - - + -
12c VAL* 3.6 20.6 - - + -
64c THR* 3.0 27.6 + - - +
67c VAL* 1.3 79.6 - - + +
69c LYS* 1.3 56.4 + - - +
71c ILE* 3.1 32.9 - - + +
72c ASP* 2.9 17.8 - - - +
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Residues in contact with LYS 69 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52W SER* 3.9 27.8 - - - +
55W ASN* 4.1 22.1 - - - +
56W LEU* 5.4 10.8 - - + +
9c LEU* 3.6 22.6 - - + +
65c VAL* 2.9 14.4 + - + +
66c LYS* 3.3 11.0 - - + +
68c PHE* 1.3 77.0 - - - +
70c ASP* 1.3 66.1 + - - +
71c ILE 3.3 0.2 - - - -
72c ASP* 3.2 12.8 - - + +
73c ALA* 3.0 38.4 + - - +
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Residues in contact with ASP 70 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55X ASN* 5.9 0.9 - - - +
66c LYS* 2.6 62.5 + - - +
67c VAL* 3.0 16.9 + - + +
69c LYS* 1.3 82.2 + - - +
71c ILE* 1.3 58.5 + - + +
73c ALA* 3.3 9.4 + - - +
74c ALA* 2.9 25.6 + - - +
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Residues in contact with ILE 71 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R PRO* 3.4 31.2 - - + -
54X TYR* 3.5 30.1 - - + +
55X ASN* 3.9 38.1 - - + +
58X ARG* 3.9 14.5 - - + +
67c VAL* 3.0 12.1 + - + +
68c PHE* 3.1 28.3 - - + +
70c ASP* 1.3 74.6 - - + +
72c ASP* 1.3 63.5 + - - +
74c ALA* 3.6 9.6 - - + +
75c ILE* 3.2 29.7 + - - +
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Residues in contact with ASP 72 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R SER* 2.7 39.6 - - - +
41R PRO* 3.2 19.2 - - - +
44R LEU* 3.4 25.2 - - + +
56W LEU* 4.5 10.9 - - + +
9c LEU* 4.2 2.6 - - - +
68c PHE 2.9 16.3 - - - +
69c LYS* 3.2 17.1 - - + +
70c ASP 3.2 0.4 - - - -
71c ILE* 1.3 76.7 - - - +
73c ALA* 1.3 63.9 + - - +
75c ILE* 3.3 4.0 + - - +
76c ILE* 3.1 30.0 + - - +
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Residues in contact with ALA 73 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56W LEU* 5.9 0.2 - - - +
69c LYS* 3.0 28.3 + - - +
70c ASP* 3.3 11.4 + - - +
72c ASP* 1.3 75.7 - - - +
74c ALA* 1.3 58.5 - - - +
76c ILE* 3.3 16.1 - - + +
77c GLN* 2.8 33.7 + - - +
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Residues in contact with ALA 74 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X ASN* 4.2 38.1 - - + +
62X SER* 3.8 10.2 + - - -
70c ASP 2.9 16.1 + - - +
71c ILE* 3.6 12.3 - - + +
72c ASP 3.2 0.2 - - - -
73c ALA* 1.3 77.1 - - - +
75c ILE* 1.3 61.2 + - + +
77c GLN* 3.4 17.3 - - - +
78c ASN* 3.8 5.7 + - - -
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Residues in contact with ILE 75 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R PRO* 3.4 34.3 - - + +
44R LEU* 3.7 37.2 - - + +
45R ALA* 3.9 14.6 - - + +
48R GLN* 4.3 14.9 - - + +
58X ARG* 4.2 27.1 - - + +
62X SER* 4.3 11.8 - - - -
71c ILE 3.2 18.2 + - - +
72c ASP 3.7 5.4 - - - +
73c ALA 3.2 0.4 - - - -
74c ALA* 1.3 77.7 - - - +
76c ILE* 1.3 60.5 + - + +
77c GLN 3.1 0.2 - - - -
78c ASN* 3.0 27.9 + - - +
79c PHE* 4.3 0.9 - - + -
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Residues in contact with ILE 76 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R LEU* 3.8 30.1 - - + -
56W LEU* 3.6 30.5 - - + -
59W ASN* 3.9 22.7 - - - +
60W ALA* 5.4 4.9 - - + +
63W ASN* 4.5 13.2 + - - +
69c LYS* 6.4 0.2 - - - +
72c ASP 3.3 11.7 - - - +
73c ALA* 3.3 25.1 - - + +
75c ILE* 1.3 72.8 - - + +
77c GLN* 1.3 61.2 + - - +
78c ASN 3.1 1.6 - - - -
79c PHE* 3.1 36.7 + - + +
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Residues in contact with GLN 77 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X LYS* 5.7 1.4 - - - -
73c ALA 2.8 19.8 + - - +
74c ALA* 3.4 11.7 - - - +
75c ILE 3.1 0.2 - - - -
76c ILE* 1.3 79.2 - - - +
78c ASN* 1.3 64.6 + - - +
79c PHE 3.3 1.8 + - - -
80c ARG* 5.8 1.2 - - - -
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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