Contacts of the helix formed by residues 58 - 83 (chain A) in PDB entry 1GN3
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 ALA 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP 5.0 0.8 + - - -
56A HIS* 3.2 0.8 - - - +
57A SER* 1.3 84.0 + - - +
59A ILE* 1.3 63.7 + - - +
60A LEU* 3.1 4.0 - - - -
61A LEU* 2.8 31.9 + - + +
62A ASN* 3.0 23.8 + - - +
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Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.6 6.7 - - + -
56A HIS* 3.2 29.2 + - + +
57A SER 3.3 3.1 - - - +
58A ALA* 1.3 75.2 - - - +
60A LEU* 1.3 60.0 - - - +
62A ASN* 3.0 7.9 + - - +
63A GLU* 2.9 69.3 + - + +
112B GLN* 4.2 26.9 - - + +
115B ALA* 3.8 15.9 - - + +
116B ALA* 3.9 16.8 - - - +
119B THR* 3.5 29.4 - - + +
141B GLN* 5.3 0.9 - - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER 4.9 0.4 + - - -
58A ALA* 2.9 1.9 + - - -
59A ILE* 1.3 81.8 - - + +
61A LEU* 1.3 64.7 - - + +
64A LYS* 3.2 26.8 + - + +
119B THR* 3.6 24.9 - - - +
121B GLN* 3.2 43.5 - - + +
141B GLN* 3.8 25.0 - - - +
143B TYR* 4.1 13.7 - - + +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 2.8 22.5 + - + +
60A LEU* 1.3 85.1 - - + +
62A ASN* 1.3 64.3 + - - +
64A LYS* 3.4 7.7 + - + -
65A ASN* 3.0 51.6 + - - +
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Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 4.1 5.4 - - - +
46A LYS* 4.1 22.1 - - - +
47A LEU* 3.2 35.3 - - + +
50A ALA* 4.3 12.8 - - - +
56A HIS* 5.4 1.2 + - - -
58A ALA* 3.0 29.6 + - - +
59A ILE* 3.0 8.7 + - - +
61A LEU* 1.3 81.5 - - - +
63A GLU* 1.3 62.3 + - - +
65A ASN* 3.9 5.9 - - - +
66A LEU* 2.8 30.7 + - - +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.7 3.4 - - - -
59A ILE* 2.9 45.7 + - + +
60A LEU 4.2 0.2 - - - +
62A ASN* 1.3 77.4 - - + +
64A LYS* 1.3 62.3 + - - +
66A LEU* 4.4 5.9 - - - +
67A ALA* 2.9 29.6 + - - +
112B GLN* 3.6 8.5 + - - -
116B ALA* 4.3 2.0 - - - +
139B ILE* 2.7 44.6 - - - +
140B PHE* 3.4 9.3 - - - -
141B GLN* 3.9 34.8 + - + +
148B ASN* 3.8 4.0 + - - -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.2 26.2 + - + +
61A LEU* 3.4 9.6 + - + +
62A ASN 3.2 0.6 - - - -
63A GLU* 1.3 78.3 - - - +
65A ASN* 1.3 69.5 + - - +
67A ALA* 3.9 1.0 - - - +
68A PHE* 3.0 29.4 + - + +
146A GLN* 3.8 22.5 - - - +
143B TYR* 3.8 32.3 - - - +
148B ASN* 4.1 11.4 - - - +
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Residues in contact with ASN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 3.7 16.3 - - + +
61A LEU* 3.0 47.9 + - - +
62A ASN* 4.2 4.9 - - - +
64A LYS* 1.3 78.7 - - - +
66A LEU* 1.3 69.3 + - - +
68A PHE* 4.6 3.8 - - - +
69A ASN* 3.1 38.9 + - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 5.5 1.1 - - + +
40A ALA* 4.6 3.5 - - - +
43A ALA* 3.4 14.1 - - + +
44A VAL* 3.4 37.9 - - + +
47A LEU* 4.1 15.7 - - + -
62A ASN 2.8 19.8 + - - +
63A GLU* 4.4 4.7 - - - +
65A ASN* 1.3 78.6 - - - +
67A ALA* 1.3 62.6 + - - +
69A ASN* 5.7 0.2 - - - -
70A LEU* 3.2 31.8 + - + +
138B LEU* 4.4 21.1 - - + -
139B ILE 3.9 21.1 - - - +
140B PHE* 4.2 19.1 - - + -
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU 2.9 19.7 + - - +
64A LYS 4.0 1.8 - - - +
65A ASN 3.1 0.4 - - - -
66A LEU* 1.3 79.9 - - - +
68A PHE* 1.3 63.3 + - - +
70A LEU* 4.2 0.3 - - - +
71A ALA* 3.0 29.8 + - - +
146A GLN* 4.5 2.5 - - + -
140B PHE* 4.6 11.9 - - + -
148B ASN* 3.1 42.8 - - - +
149B PHE* 4.2 4.0 - - - +
150B PRO* 4.8 1.8 - - - +
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.6 30.9 - + - -
64A LYS* 3.0 24.7 + - + +
65A ASN* 4.2 3.8 - - - +
67A ALA* 1.3 77.4 - - - +
69A ASN* 1.3 75.2 + - - +
71A ALA* 4.0 4.1 - - - +
72A GLY* 3.0 20.3 + - - -
144A ASP* 5.1 4.9 - - + -
145A GLN* 3.5 21.7 - - + +
146A GLN* 3.7 30.6 - - - +
162A TRP* 4.2 16.8 - + - -
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 4.6 5.0 - - - +
36A TYR* 3.3 33.2 - - - +
39A GLY* 3.7 20.9 - - - -
40A ALA* 3.2 24.2 - - - +
65A ASN* 3.1 37.4 + - - +
68A PHE* 1.3 90.4 - - - +
70A LEU* 1.3 63.0 + - - +
71A ALA 3.0 1.6 - - - -
72A GLY 4.2 0.2 - - - +
73A HIS* 2.7 31.5 + - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.2 50.7 - - + +
40A ALA* 4.3 6.7 - - + +
66A LEU* 3.2 24.5 + - + +
67A ALA 4.2 0.7 - - - +
69A ASN* 1.3 78.9 - - - +
71A ALA* 1.3 53.5 + - - +
73A HIS* 3.3 5.4 - - + +
74A VAL* 2.6 42.6 + - + +
131B ASP* 4.2 11.9 - - - +
133B LEU* 4.7 0.9 - - + -
138B LEU* 4.3 9.9 - - + -
140B PHE* 4.2 19.1 - - + -
150B PRO* 3.6 26.2 - - + -
153B ILE* 4.8 0.2 - - + -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA 3.0 19.5 + - - +
68A PHE 4.0 2.0 - - - +
70A LEU* 1.3 75.3 - - - +
72A GLY* 1.3 69.0 + - - +
73A HIS 3.0 1.1 - - - -
74A VAL* 3.1 0.6 + - - -
75A ASN* 2.8 29.4 + - - +
145A GLN* 3.3 23.3 - - - +
146A GLN* 3.8 13.9 - - + -
150B PRO* 3.8 23.3 - - + +
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 4.0 12.8 - - - -
68A PHE 3.0 17.5 + - - -
69A ASN 3.9 0.9 - - - -
71A ALA* 1.3 76.8 - - - +
73A HIS* 1.3 58.1 + - - +
76A HIS* 2.8 39.0 + - - +
145A GLN* 3.2 30.7 - - - +
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Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.6 42.0 - + + +
5A THR 3.8 16.0 + - - -
7A PRO* 4.2 2.2 - - + -
33A HIS* 2.8 34.8 + - - -
36A TYR* 3.6 14.4 - - + +
37A VAL* 3.2 24.5 - - + +
40A ALA* 4.7 0.9 - - + -
69A ASN 2.7 19.5 + - - +
70A LEU* 3.3 7.2 - - + +
72A GLY* 1.3 79.2 - - - +
74A VAL* 1.3 64.6 + - - +
77A THR* 2.9 39.4 + - - -
133B LEU* 3.9 15.1 - - + +
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 2.6 36.2 + - + +
71A ALA* 3.1 4.0 + - - +
73A HIS* 1.3 75.2 - - - +
75A ASN* 1.3 71.7 + - - +
77A THR* 3.3 11.2 + - - -
78A ILE* 3.4 29.3 + - + +
155A PRO* 5.6 0.2 - - + -
131B ASP* 4.9 2.2 - - - +
133B LEU* 4.3 28.7 - - + -
150B PRO* 4.5 7.0 - - + -
151B LEU* 3.8 25.1 - - + +
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 2.8 23.0 + - - +
74A VAL* 1.3 77.6 - - - +
76A HIS* 1.3 62.1 + - - +
77A THR 3.2 0.3 + - - -
78A ILE* 3.3 2.3 + - - +
79A TRP* 2.8 22.3 + - - +
125A TRP* 3.4 28.9 - - + +
142A VAL* 5.4 2.8 - - - +
145A GLN* 3.0 44.7 + - - +
158A LEU* 3.2 26.1 - - + +
151B LEU* 4.0 21.4 + - - +
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Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 2.9 25.8 + + - -
33A HIS* 3.2 27.4 - + + +
36A TYR* 3.5 19.8 - + - -
72A GLY 2.8 32.5 + - - +
75A ASN* 1.3 71.9 - - - +
77A THR* 1.3 53.8 - - - +
79A TRP* 3.4 8.0 + + - +
80A TRP* 2.7 40.5 + + - +
125A TRP* 3.5 14.1 - + - -
145A GLN* 3.3 27.6 - - - -
160A ASP* 2.9 4.6 + - - -
1200A FE 2.0 32.9 - - - -
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Residues in contact with THR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 4.3 13.2 - - + +
33A HIS* 3.3 9.6 - - - -
73A HIS* 2.9 42.5 + - - -
74A VAL* 3.5 7.1 - - - -
75A ASN 3.2 0.2 - - - -
76A HIS* 1.3 75.8 - - - +
78A ILE* 1.3 68.7 + - + +
80A TRP* 3.0 18.6 + - - +
81A LYS* 3.4 16.2 + - + +
193A ARG* 6.3 0.4 - - - +
133B LEU* 5.2 12.3 - - + +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.4 27.5 + - + +
75A ASN 3.3 4.6 + - - +
77A THR* 1.3 81.2 - - + +
79A TRP* 1.3 64.4 + - - +
81A LYS* 3.3 1.1 + - - +
82A ASN* 2.8 45.1 + - - +
155A PRO* 3.9 32.5 - - + -
156A LEU 4.5 5.6 - - - +
158A LEU* 4.3 20.0 - - + -
193A ARG* 4.2 30.7 - - - +
151B LEU* 5.9 0.2 - - + -
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Residues in contact with TRP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.7 8.1 - - + -
25A ASN* 5.1 1.2 + - - -
28A HIS* 3.8 18.7 + + - -
75A ASN 2.8 14.2 + - - +
76A HIS* 3.4 10.5 - + - +
77A THR 3.1 0.2 - - - -
78A ILE* 1.3 78.9 - - - +
80A TRP* 1.3 102.5 + + - +
82A ASN* 3.2 6.4 + - + +
83A LEU* 3.2 44.9 + - + +
125A TRP* 3.9 15.0 - + + -
158A LEU* 3.6 18.6 - - - +
159A LEU* 3.1 43.1 - - + -
160A ASP* 3.1 21.8 - - + -
165A ALA* 5.7 1.6 - - + -
177A PHE* 4.2 15.5 - + - -
181A PHE* 4.0 15.5 - + - -
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 4.5 8.7 - - + -
8A ASP 5.8 1.1 - - - +
9A LEU* 3.7 40.8 - - + -
10A ASP 6.3 0.2 - - - +
11A TRP* 3.8 16.9 + + + -
25A ASN* 3.5 24.7 - - - -
28A HIS* 3.6 38.1 - + + -
29A HIS* 3.5 34.3 - + + -
33A HIS* 2.9 31.2 + + + -
76A HIS* 2.7 21.7 + + - -
77A THR* 3.0 9.3 + - - +
79A TRP* 1.3 95.3 - + - +
81A LYS* 1.3 54.2 - - + +
83A LEU* 2.8 34.8 + - + +
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP 5.5 3.8 - - - -
10A ASP* 2.9 36.7 + - - +
77A THR* 3.4 12.7 + - + +
78A ILE 3.3 4.2 + - - +
80A TRP* 1.3 70.1 - - + +
82A ASN* 1.3 65.6 + - - +
83A LEU 3.1 2.9 - - - -
186A ASN* 3.2 22.3 + - - +
189A ASP* 2.8 28.2 - - - +
193A ARG* 3.6 18.6 - - - +
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 2.8 22.6 + - - +
79A TRP* 3.6 7.4 - - + +
81A LYS* 1.3 79.3 - - - +
83A LEU* 1.3 64.8 + - + +
156A LEU 3.3 16.4 + - - +
157A LEU* 3.0 24.1 - - + +
158A LEU* 2.7 36.4 + - - +
181A PHE* 5.8 0.4 - - + -
184A VAL 3.6 0.9 - - - +
185A VAL* 3.6 3.5 - - - -
186A ASN* 2.7 32.1 + - - +
189A ASP* 2.9 17.9 + - - -
190A VAL* 3.9 6.6 - - - +
193A ARG* 3.6 7.3 - - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.6 25.0 + - + -
16A LEU* 3.6 22.2 - - + -
20A ILE* 4.0 6.1 - - + -
25A ASN* 5.1 0.7 - - - +
79A TRP* 3.2 52.7 + - + +
80A TRP* 2.8 21.8 + - + +
81A LYS* 3.7 5.7 - - - +
82A ASN* 1.3 86.7 - - + +
84A SER* 1.3 64.6 + - - +
181A PHE* 4.3 20.2 - - + -
184A VAL* 3.6 25.4 - - + +
186A ASN* 3.7 2.3 + - - -
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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