Contacts of the helix formed by residues 36 - 75 (chain A) in PDB entry 2C7M
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 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 3.5 7.4 - - - -
24A CYS* 3.8 9.4 - - - -
26A TYR* 4.0 16.8 - - + -
27A TYR 3.4 21.8 - - - +
32A TRP* 3.9 4.5 - - - -
35A PHE* 1.3 74.0 - - - +
37A SER* 1.3 70.0 + - - +
38A LYS* 3.6 7.9 - - - -
39A CYS* 3.6 12.5 - - - +
40A TRP* 2.9 23.4 + - - +
500A ZN 2.5 33.9 - - - -
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 3.4 30.7 - - - -
36A CYS* 1.3 78.6 - - - +
38A LYS* 1.3 64.1 + - - +
40A TRP* 3.9 3.7 - - - +
41A ARG* 3.1 39.5 + - - +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A CYS* 5.9 4.5 - - - -
26A TYR* 6.6 0.2 - - + -
36A CYS* 3.1 8.1 - - - -
37A SER* 1.3 82.0 + - - +
39A CYS* 1.3 64.7 + - - +
41A ARG* 3.4 26.9 + - - +
42A GLU* 3.1 46.1 + - - +
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Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 3.8 8.7 - - - -
22A LYS* 3.8 21.1 - - + +
24A CYS* 3.8 9.2 - - - -
35A PHE* 4.1 11.9 - - + -
36A CYS* 3.4 6.1 + - - +
38A LYS* 1.3 79.6 - - - +
40A TRP* 1.3 59.4 + - - +
42A GLU* 3.4 16.9 + - - +
43A GLU* 3.1 31.2 + - - +
500A ZN 2.3 35.9 - - - -
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Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA 5.1 2.7 - - - -
32A TRP* 3.4 69.7 - + + +
33A GLN* 4.1 28.0 - - + -
35A PHE* 3.9 19.7 - + + +
36A CYS 2.9 19.0 + - - +
37A SER 3.9 3.4 - - - +
39A CYS* 1.3 74.0 - - - +
41A ARG* 1.3 66.1 + - + +
43A GLU* 3.4 11.0 + - + +
44A TYR* 2.9 49.1 + + + +
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 3.1 31.7 + - - +
38A LYS* 3.4 33.4 + - - +
40A TRP* 1.3 81.2 - - + +
42A GLU* 1.3 56.4 + - + +
44A TYR* 3.7 12.4 - - + +
45A HIS* 3.0 29.0 + - + +
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 6.0 2.6 - - - +
38A LYS* 3.1 42.0 + - + +
39A CYS* 3.6 17.6 - - - +
40A TRP 3.2 0.6 - - - -
41A ARG* 1.3 75.5 - - + +
43A GLU* 1.3 65.2 + - - +
45A HIS* 3.3 6.8 + - - +
46A LYS* 3.1 40.2 + - - +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.3 33.7 + - - +
35A PHE* 3.9 27.7 - - + -
39A CYS 3.1 14.6 + - - +
40A TRP* 3.7 20.2 - - + +
42A GLU* 1.3 73.1 - - - +
44A TYR* 1.3 67.5 + - - +
46A LYS* 3.3 31.1 + - - +
47A ALA* 2.9 25.5 + - - +
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Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 2.9 42.5 + + + +
41A ARG* 3.7 13.7 - - + +
43A GLU* 1.3 78.6 - - - +
45A HIS* 1.3 64.5 + - - +
47A ALA* 3.3 7.5 + - + +
48A ARG* 3.1 63.1 + - + +
62B GLN* 3.7 26.0 + - - +
63B LYS* 3.8 19.0 + - - -
65B SER* 5.4 2.8 + - - -
----------------------------------------------------------
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Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 3.0 18.5 + - + +
42A GLU* 3.8 6.3 - - - +
43A GLU 3.2 0.4 - - - -
44A TYR* 1.3 74.7 - - - +
46A LYS* 1.3 59.9 + - - +
48A ARG* 3.4 28.8 + - - +
49A GLN* 3.0 68.7 + - + +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 5.2 4.8 - - - +
42A GLU* 3.1 28.3 + - - +
43A GLU* 3.3 39.2 + - - +
45A HIS* 1.3 73.4 - - - +
47A ALA* 1.3 64.5 + - - +
49A GLN* 3.1 16.8 + - - +
50A LYS* 3.2 14.7 + - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU 2.9 17.4 + - - +
44A TYR* 3.7 7.6 - - + +
46A LYS* 1.3 76.9 - - - +
48A ARG* 1.3 57.6 + - + +
50A LYS* 3.5 12.3 + - + +
51A GLN* 3.0 28.1 + - - +
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Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 3.1 60.8 + - + +
45A HIS* 3.5 30.1 + - - +
46A LYS 3.2 0.2 - - - -
47A ALA* 1.3 77.3 - - + +
49A GLN* 1.3 75.1 + - - +
51A GLN* 3.3 16.9 + - - +
52A ILE* 3.0 35.5 + - + +
63B LYS 5.8 0.6 + - - -
64B GLU* 4.7 23.6 + - - +
65B SER* 5.4 6.7 - - - +
66B THR* 5.9 1.3 - - - +
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Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A HIS* 3.0 56.3 + - + +
46A LYS* 3.1 9.1 + - - +
48A ARG* 1.3 91.0 - - - +
50A LYS* 1.3 56.5 + - - +
52A ILE* 3.3 22.8 + - - +
53A GLN* 3.1 28.1 + - - +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS 3.2 11.8 + - - +
47A ALA* 3.7 14.1 - - - +
48A ARG 3.4 0.2 - - - -
49A GLN* 1.3 71.7 - - - +
51A GLN* 1.3 65.3 + - - +
53A GLN* 3.7 6.3 - - - +
54A GLU* 2.9 63.4 + - - +
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Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.0 17.7 + - - +
48A ARG* 3.6 22.5 - - - +
49A GLN 3.2 0.2 - - - -
50A LYS* 1.3 77.2 - - - +
52A ILE* 1.3 73.5 + - - +
54A GLU* 3.7 9.4 - - - +
55A ASP* 2.8 55.5 + - - +
45B PHE* 3.4 22.3 - - + -
46B ALA* 4.1 20.6 - - + -
65B SER* 6.0 0.3 - - - -
66B THR 3.2 23.5 + - - +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 3.0 26.4 + - + +
49A GLN* 3.7 28.7 - - - +
51A GLN* 1.3 98.5 - - - +
53A GLN* 1.3 59.1 + - - +
55A ASP* 3.3 2.4 + - - -
56A TRP* 2.8 31.6 + - + +
6B LYS* 5.0 11.2 - - + +
66B THR* 3.7 32.8 - - + +
68B HIS* 3.5 17.6 - - + -
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN 3.1 16.9 + - - +
50A LYS* 3.7 8.1 - - - +
52A ILE* 1.3 76.9 - - - +
54A GLU* 1.3 57.3 + - + +
56A TRP* 3.4 19.2 + - - +
57A GLU* 3.1 56.4 + - - +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 2.9 56.4 + - + +
51A GLN* 3.7 8.4 - - - +
53A GLN* 1.3 75.2 - - + +
55A ASP* 1.3 60.0 + - - +
57A GLU* 3.3 16.3 + - - +
58A LEU* 3.1 26.2 + - - +
61A ARG* 4.8 1.6 + - - -
47B GLY* 6.0 2.0 - - - +
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 2.8 36.5 + - - +
52A ILE* 3.7 2.2 - - - +
54A GLU* 1.3 74.4 - - - +
56A TRP* 1.3 61.0 + - - +
58A LEU* 3.7 3.7 - - - +
59A ALA* 2.8 30.5 + - - +
44B ILE* 3.7 18.1 - - + +
45B PHE* 3.4 5.4 - - - -
46B ALA* 2.7 22.5 + - - -
47B GLY* 2.7 29.3 + - - -
66B THR 4.4 1.6 - - - +
68B HIS* 3.7 18.6 - - + +
----------------------------------------------------------
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Residues in contact with TRP 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 2.8 19.0 + - + +
53A GLN* 3.4 26.0 - - - +
55A ASP* 1.3 76.1 - - - +
57A GLU* 1.4 62.5 + - + +
59A ALA* 3.1 3.3 + - - +
60A GLU* 2.9 64.1 + - + +
6B LYS* 5.0 13.0 - - - -
7B THR 3.8 15.0 - - - -
8B LEU* 3.4 39.7 - - + -
68B HIS* 3.5 30.0 - - - +
----------------------------------------------------------
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 3.1 43.6 + - - +
54A GLU* 3.5 15.3 + - - +
55A ASP 3.2 0.4 - - - -
56A TRP* 1.4 80.9 - - + +
58A LEU* 1.3 57.7 + - - +
60A GLU* 3.4 8.6 + - - +
61A ARG* 3.2 46.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU 3.1 15.8 + - - +
55A ASP* 3.7 6.1 - - - +
56A TRP 3.2 0.2 - - - -
57A GLU* 1.3 75.4 - - - +
59A ALA* 1.3 65.6 + - - +
61A ARG* 3.3 33.1 + - + +
62A LEU* 3.0 31.8 + - + +
44B ILE* 4.0 21.8 - - + -
47B GLY* 3.6 39.3 - - - +
48B LYS* 4.1 3.4 - - - +
49B GLN* 5.2 1.1 - - + +
----------------------------------------------------------
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP 2.8 17.8 + - - +
56A TRP 3.5 4.5 - - - +
58A LEU* 1.3 78.8 - - - +
60A GLU* 1.4 56.7 + - - +
62A LEU* 4.4 0.2 - - - -
63A GLN* 3.0 30.1 + - - +
8B LEU* 3.5 15.4 - - + +
44B ILE* 3.6 24.2 - - + +
68B HIS* 4.0 14.8 - - + -
69B LEU 5.3 0.2 - - - +
70B VAL* 3.4 16.8 - - + +
----------------------------------------------------------
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TRP* 2.9 56.1 + - + +
57A GLU* 3.4 10.3 - - - +
58A LEU 3.2 0.2 - - - -
59A ALA* 1.4 73.1 - - - +
61A ARG* 1.3 65.0 + - - +
63A GLN* 3.2 2.8 + - - +
64A ARG* 2.9 32.0 + - - +
8B LEU* 3.6 22.2 - - + +
----------------------------------------------------------
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU 4.8 1.0 + - - -
57A GLU* 3.2 43.8 + - - +
58A LEU* 3.3 43.8 + - + +
60A GLU* 1.3 76.2 - - - +
62A LEU* 1.3 62.8 + - - +
64A ARG* 3.3 37.8 + - - +
65A GLU* 3.1 27.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.0 23.2 + - + +
59A ALA 3.9 2.9 - - - +
60A GLU 3.1 0.2 - - - -
61A ARG* 1.3 79.8 - - + +
63A GLN* 1.3 60.1 + - - +
65A GLU* 3.5 19.6 + - + +
66A GLU* 3.2 29.5 + - - +
42B ARG* 4.0 32.1 - - + +
44B ILE* 3.8 27.4 - - + -
49B GLN* 3.9 32.1 - - + +
70B VAL* 4.3 8.5 - - + -
----------------------------------------------------------
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 3.0 17.9 + - - +
60A GLU* 3.2 3.6 + - - +
62A LEU* 1.3 76.4 - - - +
64A ARG* 1.4 63.5 + - - +
66A GLU* 3.2 6.2 + - - +
67A GLU* 3.2 48.7 + - - +
8B LEU* 3.6 24.5 - - + +
69B LEU 5.1 0.2 - - - +
70B VAL* 3.4 21.0 - - + +
71B LEU* 3.6 34.3 + - - +
73B LEU* 4.8 5.3 - - - +
----------------------------------------------------------
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 2.9 15.7 + - - +
61A ARG* 3.5 57.2 + - - +
63A GLN* 1.4 71.9 - - - +
65A GLU* 1.3 60.6 + - + +
67A GLU* 3.3 14.1 + - - +
68A GLU* 3.0 51.8 + - + +
----------------------------------------------------------
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 3.1 18.5 + - - +
62A LEU* 3.9 20.4 - - + +
63A GLN 3.1 0.4 - - - -
64A ARG* 1.3 76.9 - - + +
66A GLU* 1.3 59.4 + - + +
68A GLU* 3.9 13.1 - - - +
69A ALA* 3.0 29.8 + - + +
----------------------------------------------------------
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.2 22.7 + - + +
63A GLN* 3.2 11.6 + - - +
65A GLU* 1.3 76.0 - - + +
67A GLU* 1.3 61.1 + - - +
69A ALA* 4.0 5.1 - - - +
70A PHE* 2.9 30.5 + - - +
42B ARG* 2.7 42.4 + - - +
70B VAL* 4.4 5.8 - - + -
71B LEU 3.6 16.8 - - - +
72B ARG* 3.6 9.7 - - - +
73B LEU* 3.0 34.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 3.2 35.9 + - - +
64A ARG* 3.7 13.8 + - - +
66A GLU* 1.3 78.7 - - - +
68A GLU* 1.3 56.8 + - + +
70A PHE* 3.5 3.4 + - - +
71A ALA* 2.9 30.1 + - - +
73B LEU* 4.2 13.9 - - + -
----------------------------------------------------------
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Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.0 38.6 + - + +
65A GLU* 3.9 13.6 - - - +
67A GLU* 1.3 76.0 - - + +
69A ALA* 1.3 57.5 + - - +
71A ALA* 3.7 6.0 - - - +
72A SER* 2.9 31.8 + - - -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 3.0 21.0 + - + +
66A GLU* 4.0 6.3 - - - +
68A GLU* 1.3 76.1 - - - +
70A PHE* 1.3 63.2 + - - +
72A SER* 3.6 7.2 + - - -
73A SER* 3.1 23.2 + - - -
----------------------------------------------------------
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU 2.9 18.3 + - - +
67A GLU* 3.7 4.7 - - - +
69A ALA* 1.3 74.7 - - - +
71A ALA* 1.3 60.0 + - + +
73A SER* 3.0 25.8 - - - -
74A GLN* 3.0 52.8 + - + +
73B LEU* 4.0 28.5 - - + -
74B ARG 4.1 18.6 - - - -
----------------------------------------------------------
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU 2.9 18.5 + - - +
68A GLU* 3.2 7.6 + - - +
70A PHE* 1.3 77.1 - - + +
72A SER* 1.3 57.9 + - - +
74A GLN* 3.4 5.2 + - - +
75A SER* 2.8 29.6 + - - -
----------------------------------------------------------
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLU 2.9 17.4 + - - -
69A ALA* 3.6 9.7 + - - -
71A ALA* 1.3 75.7 - - - +
73A SER* 1.3 59.0 + - - +
75A SER* 3.4 25.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 3.1 15.5 + - - -
70A PHE* 3.0 22.6 + - - -
72A SER* 1.3 77.5 - - - +
74A GLN* 1.3 70.1 + - - +
75A SER* 4.0 4.7 - - - +
----------------------------------------------------------
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 3.0 56.4 + - + +
71A ALA* 3.6 4.5 - - - +
73A SER* 1.3 83.2 + - - +
75A SER* 1.3 63.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA 2.8 20.4 + - - -
72A SER* 3.4 22.4 + - - +
73A SER 3.4 6.9 - - - +
74A GLN* 1.3 81.0 - - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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