Contacts of the helix formed by residues 35 - 70 (chain D) in PDB entry 2FIF
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 CYS 35 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D CYS* 3.3 10.5 - - + +
23D CYS* 3.8 6.5 - - - -
25D TYR* 4.1 16.8 - - + -
26D TYR 3.4 21.5 - - - +
31D TRP* 3.9 4.3 - - - -
34D PHE* 1.3 74.0 - - - +
36D SER* 1.3 54.8 + - - +
37D LYS* 3.7 10.1 - - - -
38D CYS* 3.3 16.1 + - - -
39D TRP* 2.7 34.1 + - - +
902D ZN 2.5 33.2 - - - -
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Residues in contact with SER 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TRP* 3.6 32.8 - - - -
35D CYS* 1.3 75.7 - - - +
37D LYS* 1.3 68.1 + - - +
39D TRP* 4.0 6.5 - - - +
40D ARG* 3.4 31.5 + - - +
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Residues in contact with LYS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D CYS* 3.3 9.6 - - - -
36D SER* 1.3 84.6 + - - +
38D CYS* 1.3 62.2 + - - +
40D ARG* 3.4 38.0 + - - +
41D GLU* 3.4 37.3 + - - +
----------------------------------------------------------
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Residues in contact with CYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D CYS* 3.9 8.1 - - - -
21D LYS* 3.5 31.9 - - + -
23D CYS* 3.9 10.5 - - - -
34D PHE* 4.2 7.0 - - + -
35D CYS* 3.3 6.0 + - - +
37D LYS* 1.3 79.5 - - - +
39D TRP* 1.3 61.3 + - - +
40D ARG 3.3 0.4 - - - -
41D GLU* 3.4 11.3 + - - +
42D GLU* 3.1 33.1 + - - +
902D ZN 2.3 35.2 - - - -
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Residues in contact with TRP 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLN* 5.7 9.2 - - - -
63C LYS* 6.1 2.7 - - - -
30D ALA 5.5 0.4 - - - -
31D TRP* 3.3 71.8 - + + +
34D PHE* 3.8 17.8 - + + +
35D CYS 2.7 22.3 + - - +
36D SER* 4.0 7.2 - - - +
37D LYS 3.5 0.2 - - - -
38D CYS* 1.3 73.7 - - - +
40D ARG* 1.3 67.7 + - + +
42D GLU* 3.8 2.6 - - + +
43D TYR* 2.9 57.6 + + + +
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D SER* 3.4 11.6 + - - +
37D LYS* 3.4 64.3 + - - +
38D CYS 3.3 0.4 - - - -
39D TRP* 1.3 88.8 - - + +
41D GLU* 1.3 63.7 + - - +
43D TYR* 3.5 10.1 + - + +
44D HIS* 3.1 27.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LYS* 4.2 21.4 + - - +
37D LYS* 3.4 30.2 + - - +
38D CYS* 3.4 10.9 + - - +
39D TRP 3.3 0.6 - - - -
40D ARG* 1.3 82.2 + - + +
42D GLU* 1.3 61.2 + - - +
44D HIS* 3.4 8.1 + - - +
45D LYS* 3.2 29.9 + - + +
----------------------------------------------------------
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Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LYS* 3.1 25.2 + - - -
34D PHE* 3.7 41.3 - - + -
38D CYS 3.1 20.4 + - - +
39D TRP* 4.0 4.0 - - + +
41D GLU* 1.3 73.0 - - - +
43D TYR* 1.3 60.3 + - - +
45D LYS* 2.9 37.3 + - - +
46D ALA* 3.1 29.2 + - - +
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Residues in contact with TYR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASN* 5.0 5.1 + - - -
62C GLN* 3.8 27.0 + - - +
63C LYS* 3.4 25.6 + - - -
39D TRP* 2.9 45.5 + + + +
40D ARG* 3.7 10.3 - - + +
42D GLU* 1.3 77.0 - - - +
44D HIS* 1.3 59.2 + - - +
46D ALA* 3.5 6.9 + - + +
47D ARG* 2.9 77.2 + - - +
----------------------------------------------------------
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Residues in contact with HIS 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ARG 3.1 16.6 + - - +
41D GLU* 3.6 7.6 - - - +
43D TYR* 1.3 76.6 - - - +
45D LYS* 1.3 65.7 + - + +
47D ARG* 3.2 9.6 + - - +
48D GLN* 2.9 60.3 + - + +
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LYS* 4.6 7.0 - - - +
41D GLU* 3.2 17.2 + - + +
42D GLU* 2.9 41.9 + - - +
44D HIS* 1.3 83.7 - - + +
46D ALA* 1.3 58.0 + - - +
48D GLN* 3.2 7.0 + - - +
49D LYS* 3.0 32.2 + - - +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D GLU 3.1 17.9 + - - +
43D TYR* 3.7 11.0 - - + +
45D LYS* 1.3 76.9 - - - +
47D ARG* 1.3 57.2 + - - +
49D LYS* 3.7 11.6 - - - +
50D GLN* 3.0 30.5 + - - +
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Residues in contact with ARG 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE* 4.3 5.9 - - - -
60C ASN 5.2 0.8 + - - -
62C GLN 4.1 0.4 + - - -
63C LYS* 2.7 30.3 + - - +
64C GLU* 3.4 8.7 + - - +
65C SER* 2.7 43.8 + - - +
66C THR* 5.9 0.7 - - - +
43D TYR* 2.9 60.9 + - - +
44D HIS* 3.2 16.8 - - - +
45D LYS 3.1 0.2 - - - -
46D ALA* 1.3 75.7 - - - +
48D GLN* 1.3 62.9 + - - +
50D GLN* 3.1 25.4 - - - +
51D ILE* 3.0 42.5 + - + +
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Residues in contact with GLN 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D HIS* 2.9 48.7 + - + +
45D LYS* 3.2 8.0 + - - +
47D ARG* 1.3 74.3 - - - +
49D LYS* 1.3 64.7 + - - +
51D ILE* 3.8 19.6 - - - +
52D GLN* 3.1 23.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 3.0 17.1 + - - +
46D ALA* 3.7 10.5 - - - +
48D GLN* 1.3 78.0 - - - +
50D GLN* 1.3 56.3 + - - +
52D GLN* 3.2 8.6 + - + +
53D GLU* 3.0 50.0 + - + +
----------------------------------------------------------
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE* 3.4 34.6 - - + -
46C ALA* 4.3 13.5 + - + -
66C THR 3.9 8.8 + - - +
46D ALA 3.0 19.2 + - - +
47D ARG* 3.1 42.0 + - - +
49D LYS* 1.3 72.4 - - - +
51D ILE* 1.3 72.1 + - - +
53D GLU* 3.9 7.4 - - - +
54D ASP* 2.9 60.1 + - - +
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Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LYS* 4.5 20.2 - - + +
66C THR* 3.6 35.0 - - + +
68C HIS* 3.4 20.8 - - + -
47D ARG* 3.0 30.8 + - + +
48D GLN* 3.8 22.0 - - - +
50D GLN* 1.3 87.9 - - - +
52D GLN* 1.3 62.6 + - - +
54D ASP* 4.6 2.7 - - - -
55D TRP* 3.1 20.1 + - + +
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Residues in contact with GLN 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLN 3.1 15.0 + - - +
49D LYS* 3.4 11.4 - - - +
51D ILE* 1.3 77.0 - - - +
53D GLU* 1.3 64.7 + - + +
55D TRP* 3.4 24.0 + - - +
56D GLU* 3.2 41.5 + - - +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 6.2 1.1 - - - -
49D LYS* 3.0 45.1 + - + +
50D GLN* 3.3 7.1 + - - +
52D GLN* 1.3 75.8 - - + +
54D ASP* 1.3 63.3 + - - +
56D GLU* 3.4 16.9 + - - +
57D LEU* 2.9 28.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 3.9 17.3 - - + +
45C PHE* 3.5 7.4 - - - -
46C ALA* 2.9 22.3 + - - -
47C GLY* 2.9 26.9 + - - -
66C THR 4.4 2.9 - - - +
68C HIS* 3.7 19.8 - - + +
50D GLN* 2.9 33.4 + - - +
51D ILE* 4.0 1.3 - - - +
53D GLU* 1.3 77.2 - - - +
55D TRP* 1.3 54.3 + - - +
57D LEU* 3.5 6.3 - - - +
58D ALA* 2.7 36.0 + - - +
----------------------------------------------------------
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Residues in contact with TRP 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 5.9 2.5 - - - -
6C LYS* 6.1 2.0 - - - -
7C THR 5.6 2.2 + - - -
8C LEU* 3.9 15.5 + - + +
68C HIS* 3.6 24.4 - + + +
51D ILE* 3.1 18.3 + - + +
52D GLN* 3.5 26.0 - - - +
53D GLU 3.3 0.2 - - - -
54D ASP* 1.3 74.2 - - - +
56D GLU* 1.3 78.8 + - + +
58D ALA* 3.2 2.9 + - - +
59D GLU* 2.8 66.7 + - + +
----------------------------------------------------------
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLN* 3.2 31.9 + - - +
53D GLU* 3.6 20.0 - - - +
54D ASP 3.4 0.2 - - - -
55D TRP* 1.3 98.0 - - + +
57D LEU* 1.3 61.5 + - - +
59D GLU* 3.2 7.1 + - - +
60D ARG* 3.1 37.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ILE* 3.8 22.4 - - + -
47C GLY* 3.7 37.2 - - - +
48C LYS* 5.3 1.6 - - - -
49C GLN* 5.7 2.9 - - + +
53D GLU 2.9 17.0 + - - +
54D ASP* 3.5 6.7 - - - +
56D GLU* 1.3 74.5 - - - +
58D ALA* 1.3 56.2 + - - +
60D ARG* 3.3 25.1 + - + +
61D LEU* 2.9 52.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.6 18.1 - - + +
44C ILE* 4.9 4.7 - - + +
68C HIS* 4.1 17.0 - - + -
70C VAL* 3.4 30.4 - - + +
54D ASP 2.7 21.3 + - - +
55D TRP* 3.2 6.7 + - - +
57D LEU* 1.3 74.7 - - - +
59D GLU* 1.3 56.2 + - - +
61D LEU* 3.4 1.1 + - - -
62D GLN* 3.0 27.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 3.1 33.8 + - - -
8C LEU* 3.4 26.4 - - + +
55D TRP* 2.8 53.3 + - + +
56D GLU* 3.2 9.4 + - - +
58D ALA* 1.3 75.7 - - - +
60D ARG* 1.3 61.3 + - + +
62D GLN* 3.3 5.2 + - - +
63D ARG* 3.2 35.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU 5.6 0.2 + - - -
56D GLU* 3.1 25.8 + - - +
57D LEU* 3.7 42.8 - - + +
59D GLU* 1.3 74.4 - - + +
61D LEU* 1.3 66.1 + - + +
63D ARG* 3.4 35.0 + - - +
64D GLU* 3.2 33.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG* 3.5 28.0 + - - +
44C ILE* 5.1 6.5 - - + -
49C GLN* 3.4 34.8 - - + +
70C VAL* 4.1 15.9 - - + -
57D LEU* 2.9 49.2 + - + +
58D ALA* 3.6 5.8 - - - +
60D ARG* 1.3 77.9 - - + +
62D GLN* 1.3 56.1 + - - +
64D GLU* 3.4 24.6 + - - +
65D GLU* 3.0 29.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 5.8 7.9 - - - +
8C LEU* 3.6 24.5 - - + +
70C VAL* 3.7 9.2 - - + +
71C LEU* 3.5 39.7 + - - +
73C LEU* 4.2 14.6 - - - +
58D ALA 3.0 17.0 + - - +
59D GLU* 3.3 6.5 + - - +
61D LEU* 1.3 73.7 - - - +
63D ARG* 1.3 61.3 + - + +
65D GLU* 3.2 7.3 + - - +
66D GLU* 2.9 45.9 + - - +
----------------------------------------------------------
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLU* 3.2 16.7 + - - +
60D ARG* 3.4 41.8 + - - +
61D LEU 3.3 0.2 - - - -
62D GLN* 1.3 73.3 - - + +
64D GLU* 1.3 60.7 + - + +
66D GLU* 3.0 17.6 + - - +
67D GLU* 3.0 42.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG* 5.6 2.5 + - - +
60D ARG* 3.2 19.8 + - - +
61D LEU* 3.5 27.5 - - + +
62D GLN 3.3 0.2 - - - -
63D ARG* 1.3 78.4 - - + +
65D GLU* 1.3 60.3 + - + +
67D GLU* 3.5 12.5 + - - +
68D ALA* 3.5 17.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG* 2.8 40.1 + - - +
70C VAL* 4.5 6.7 - - + -
71C LEU 3.9 19.1 - - - +
72C ARG* 3.4 18.7 - - - +
73C LEU* 3.3 35.9 + - + +
61D LEU 3.0 16.7 + - - +
62D GLN* 3.4 15.0 - - - +
63D ARG 3.2 0.2 - - - -
64D GLU* 1.3 75.0 - - - +
66D GLU* 1.3 63.6 + - - +
68D ALA* 3.3 22.1 + - - +
69D PHE* 3.5 5.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG* 6.1 1.2 - - - -
63B ARG* 4.9 12.3 + - - -
73C LEU* 4.2 3.8 - - + -
62D GLN* 2.9 38.7 + - - +
63D ARG* 3.0 19.7 + - - +
65D GLU* 1.3 76.7 - - - +
67D GLU* 1.3 58.2 + - - +
68D ALA 3.3 0.2 - - - -
69D PHE* 3.2 23.0 - - + -
70D ALA* 2.8 37.5 + - + +
----------------------------------------------------------
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ARG* 3.0 34.5 + - - +
64D GLU* 3.6 13.7 + - - +
65D GLU 3.3 0.4 - - - -
66D GLU* 1.3 81.5 - - - +
68D ALA* 1.3 52.2 + - - +
70D ALA* 3.4 7.5 - - + +
71D SER* 2.6 37.0 + - - -
----------------------------------------------------------
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 6.4 0.4 - - + -
64D GLU 3.5 10.0 + - - +
65D GLU* 3.3 21.7 + - - +
66D GLU 3.3 0.4 - - - -
67D GLU* 1.3 79.5 - - - +
69D PHE* 1.3 57.7 + - - +
71D SER* 3.4 20.0 + - - -
----------------------------------------------------------
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Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 5.2 12.8 - - - -
73C LEU* 3.4 40.1 - - + +
65D GLU 3.5 3.4 + - - -
66D GLU* 3.2 38.4 - - + -
67D GLU 3.3 0.2 - - - -
68D ALA* 1.3 76.3 - - - +
70D ALA* 1.3 63.8 + - + +
71D SER* 3.0 8.7 + - - -
72D SER* 3.3 18.2 + - - -
----------------------------------------------------------
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D GLU* 2.8 23.3 + - + +
67D GLU* 3.4 10.7 + - + +
69D PHE* 1.3 83.1 - - + +
71D SER* 1.3 50.3 + - - +
72D SER* 2.6 19.7 + - - +
73D GLN 3.2 27.7 + - - +
----------------------------------------------------------
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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