Contacts of the helix formed by residues 56 - 86 (chain C) in PDB entry 5W69
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 GLY 56 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLN 3.8 1.7 + - - -
55C GLU* 1.3 79.1 - - - +
57C PRO* 1.4 75.3 - - - +
58C GLU* 3.2 4.9 - - - -
59C TYR* 3.2 15.4 + - - +
60C TRP* 3.3 14.3 + - - -
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Residues in contact with PRO 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 6.2 0.4 - - - +
56C GLY* 1.4 81.6 - - - +
58C GLU* 1.3 53.6 + - + +
60C TRP* 3.3 8.3 + - + +
61C ASP* 2.9 48.5 + - - +
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLY* 3.2 2.4 - - - -
57C PRO* 1.3 78.7 - - + +
59C TYR* 1.3 62.0 + - - +
61C ASP* 4.0 6.3 - - - +
62C ARG* 3.1 51.8 + - - +
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Residues in contact with TYR 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 5.1 1.2 + - - -
33C PHE* 4.2 8.8 - - - -
34C VAL* 5.9 0.3 - - - +
52C VAL* 4.2 6.0 - - + +
55C GLU* 3.5 32.5 - - + -
56C GLY* 3.2 14.3 + - - +
58C GLU* 1.3 76.8 - - - +
60C TRP* 1.4 92.3 + + - +
62C ARG* 3.2 19.1 + - - +
63C GLU* 2.9 64.1 + - + +
167C TRP* 3.7 30.7 - + - -
171C TYR* 2.7 33.4 + + - -
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Residues in contact with TRP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 4.3 0.4 - + - -
34C VAL* 3.6 29.4 - - + -
44C ARG* 3.9 17.3 - - - +
45C GLY* 3.3 28.7 - - - -
46C GLU 3.8 1.1 - - - -
47C PRO* 3.5 42.2 - - + +
52C VAL* 3.2 37.7 + - + -
53C GLU* 4.3 5.6 + - - +
55C GLU 4.0 6.9 + - - -
56C GLY 3.3 21.0 + - - -
57C PRO* 3.3 9.5 + - + +
59C TYR* 1.4 101.9 - + - +
61C ASP* 1.3 57.7 + - - +
63C GLU* 3.5 7.7 + - + +
64C THR* 2.7 38.4 + - - -
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Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 3.7 20.9 + - - +
57C PRO* 2.9 32.1 + - - +
58C GLU* 4.0 5.8 + - - +
60C TRP* 1.3 70.6 - - - +
62C ARG* 1.4 57.2 + - - +
64C THR* 3.5 6.1 + - - +
65C GLN* 3.1 34.3 + - + +
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU* 3.1 54.0 + - - +
59C TYR* 3.2 20.4 + - - +
61C ASP* 1.4 73.8 - - - +
63C GLU* 1.4 66.6 + - - +
65C GLN* 3.5 7.1 + - - +
66C LYS* 3.1 44.9 + - + +
167C TRP* 5.8 5.7 - - - -
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 4.2 15.4 + - - -
34C VAL* 5.8 1.1 - - + -
45C GLY* 5.4 0.4 - - - -
59C TYR* 2.9 56.0 + - + +
60C TRP* 4.0 14.6 - - + +
62C ARG* 1.4 76.6 - - - +
64C THR* 1.4 65.8 + - - +
66C LYS* 2.9 48.1 + - - +
67C TYR* 3.0 36.3 + - + -
167C TRP* 6.0 1.4 - - - -
171C TYR* 5.7 0.4 - - - -
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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
----------------------------------------------------------
43C PRO 4.1 0.2 - - - +
44C ARG* 3.4 42.7 + - + +
45C GLY* 3.1 23.8 + - - +
60C TRP 2.7 22.0 + - - -
61C ASP* 3.6 6.5 - - - +
62C ARG 3.3 0.2 - - - -
63C GLU* 1.4 74.3 - - - +
65C GLN* 1.3 61.1 + - - +
67C TYR* 3.3 5.8 + - - +
68C LYS* 2.8 51.7 + - + +
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Residues in contact with GLN 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASP* 3.1 20.0 + - + +
62C ARG* 3.7 7.4 - - - +
63C GLU 3.3 0.2 - - - -
64C THR* 1.3 78.3 - - - +
66C LYS* 1.3 63.1 + - + +
68C LYS* 3.9 28.4 - - - +
69C ARG* 3.1 45.0 + - - +
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Residues in contact with LYS 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 3.1 30.7 + - + +
63C GLU* 2.9 43.9 + - - +
65C GLN* 1.3 76.8 - - + +
67C TYR* 1.4 57.5 + - + +
69C ARG* 3.6 5.0 + - - +
70C GLN* 3.0 30.8 + - - +
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Residues in contact with TYR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 3.6 15.5 + + - -
9C ASP* 5.9 0.4 - - - -
22C PHE* 4.2 6.8 - + - -
24C SER* 3.2 34.2 + - - -
26C GLY 5.1 0.2 + - - -
34C VAL* 3.3 43.6 - - + +
35C ARG 4.8 0.9 + - - -
36C PHE* 3.5 45.6 - + + -
45C GLY* 4.2 11.2 - - - -
63C GLU* 3.0 39.0 + - + -
64C THR 3.5 5.2 - - - +
66C LYS* 1.4 74.2 - - + +
68C LYS* 1.3 60.4 + - - +
70C GLN* 3.3 4.4 + - + +
71C ALA* 2.8 33.3 + - - +
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Residues in contact with LYS 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 4.2 18.4 - - + -
42C SER 5.1 0.2 - - - -
43C PRO* 2.9 41.6 + - + +
64C THR* 2.8 34.2 + - - +
65C GLN* 3.5 24.4 + - - +
67C TYR* 1.3 71.4 - - - +
69C ARG* 1.4 61.7 + - + +
71C ALA* 3.6 4.7 - - - +
72C GLN* 3.3 22.3 + - - +
75C ARG* 5.1 0.3 + - - -
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLN* 3.1 32.9 + - - +
66C LYS* 4.0 4.0 - - - +
68C LYS* 1.4 74.9 - - + +
70C GLN* 1.4 58.8 + - - +
72C GLN* 3.2 9.1 + - - +
73C ALA* 3.0 26.4 + - - +
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Residues in contact with GLN 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASP* 4.7 7.9 - - - +
22C PHE* 4.4 15.0 - - + -
66C LYS 3.0 18.2 + - - +
67C TYR* 4.0 3.8 - - + +
69C ARG* 1.4 71.1 - - - +
71C ALA* 1.3 57.2 + - - +
72C GLN 3.1 0.2 - - - -
73C ALA* 3.8 15.2 - - - +
74C ASP* 2.8 66.2 + - - +
77C ASN* 4.0 5.1 - - - +
97C TRP* 4.7 6.6 - - + +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.6 36.8 - - + +
36C PHE* 4.1 9.9 - - + -
38C SER* 4.7 0.9 - - - -
67C TYR 2.8 21.6 + - - +
68C LYS* 3.6 7.2 - - - +
70C GLN* 1.3 72.0 - - - +
72C GLN* 1.3 60.0 + - - +
74C ASP* 3.6 2.6 + - - +
75C ARG* 3.1 44.7 + - - +
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Residues in contact with GLN 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU* 4.3 5.3 + - - +
68C LYS 3.3 10.0 + - - +
69C ARG* 3.2 11.8 + - - +
70C GLN 3.1 0.6 - - - -
71C ALA* 1.3 77.7 - - - +
73C ALA* 1.3 62.5 + - - +
75C ARG* 2.8 57.5 + - - +
76C VAL* 3.5 14.4 + - - +
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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
----------------------------------------------------------
69C ARG 3.0 14.1 + - - +
70C GLN* 3.2 26.9 + - - +
72C GLN* 1.3 74.3 - - - +
74C ASP* 1.4 56.7 + - - +
76C VAL* 3.0 13.2 + - - +
77C ASN* 2.9 32.0 + - - +
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Residues in contact with ASP 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASP* 4.8 0.2 - - - +
11C ALA* 3.8 20.4 + - + +
22C PHE* 3.2 26.4 - - + -
70C GLN* 2.8 35.4 + - - +
71C ALA 4.1 4.0 - - - +
73C ALA* 1.4 69.1 - - - +
75C ARG* 1.3 59.9 + - + +
77C ASN* 2.7 30.7 + - - +
78C LEU* 2.9 36.2 + - - +
95C LEU* 3.9 6.1 - - + +
97C TRP* 3.2 27.4 + - - -
----------------------------------------------------------
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Residues in contact with ARG 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 6.4 0.2 - - + -
19C GLU* 3.2 35.1 + - - -
20C PRO* 2.8 61.8 + - + +
22C PHE* 4.4 3.0 - - + +
38C SER* 3.4 24.2 + - - -
68C LYS 5.1 0.4 + - - -
71C ALA* 3.1 37.6 + - - +
72C GLN* 2.8 52.6 + - - +
73C ALA 3.2 0.6 - - - -
74C ASP* 1.3 76.7 - - - +
76C VAL* 1.3 62.2 + - + +
78C LEU* 3.5 4.4 + - - +
79C ARG* 3.3 18.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLN* 3.6 15.0 - - - +
73C ALA* 3.0 10.3 + - - +
75C ARG* 1.3 74.0 - - + +
77C ASN* 1.3 62.6 + - - +
79C ARG* 3.0 10.0 + - + +
80C LYS* 2.9 35.1 + - + +
----------------------------------------------------------
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Residues in contact with ASN 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLN* 4.0 7.1 - - - +
73C ALA* 2.9 20.7 + - - +
74C ASP* 2.7 28.3 + - - +
76C VAL* 1.3 79.3 - - - +
78C LEU* 1.4 56.3 + - - +
80C LYS* 3.2 9.1 + - - +
81C LEU* 3.0 39.6 + - + +
95C LEU* 3.5 19.7 - - + +
97C TRP* 4.5 10.6 - - + +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA* 3.8 32.1 - - + +
13C SER* 4.1 13.0 - - - +
20C PRO* 3.8 28.5 - - + -
74C ASP 2.9 23.6 + - - +
75C ARG 3.8 4.7 - - - +
77C ASN* 1.4 70.8 - - - +
79C ARG* 1.3 62.1 + - - +
81C LEU* 3.6 5.6 + - - +
82C ARG* 3.1 22.9 + - - +
93C HIS* 3.6 38.0 - - + +
94C THR 4.2 1.1 - - - +
95C LEU* 4.1 18.4 - - + +
118C TYR* 4.4 7.6 + - + -
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Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ARG 3.3 9.9 + - - +
76C VAL* 3.0 12.9 + - + +
78C LEU* 1.3 77.6 - - - +
80C LYS* 1.4 60.2 + - - +
82C ARG* 3.2 38.2 + - - +
83C GLY* 3.0 19.2 + - - -
89C GLU* 5.0 8.7 + - - -
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Residues in contact with LYS 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 2.9 20.5 + - + +
77C ASN* 3.2 13.0 + - - +
79C ARG* 1.4 72.9 - - - +
81C LEU* 1.4 58.3 + - + +
83C GLY* 3.2 4.6 + - - -
84C TYR* 2.9 71.2 + - + +
146C LYS* 3.8 28.3 - - - +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASN* 3.0 23.4 + - + +
78C LEU* 4.2 2.0 - - - +
80C LYS* 1.4 71.2 - - + +
82C ARG* 1.3 66.1 + - - +
84C TYR* 3.9 12.6 - - + -
85C TYR* 3.0 35.7 + - + +
95C LEU* 3.9 30.5 - - + -
118C TYR* 3.5 42.0 - - + -
123C TYR* 3.2 48.2 - - + +
143C THR* 5.2 0.2 - - - +
----------------------------------------------------------
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Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU 3.1 15.3 + - - +
79C ARG* 3.4 51.2 + - - +
81C LEU* 1.3 76.0 - - - +
83C GLY* 1.3 58.8 + - - +
85C TYR 3.5 0.5 + - - -
86C ASN 2.9 9.4 + - - -
87C GLN* 2.9 76.0 + - + +
88C SER* 3.5 15.5 - - - +
89C GLU* 3.7 40.4 + - - +
91C GLY 5.6 1.1 - - - -
93C HIS* 4.9 9.6 - - + -
118C TYR* 3.9 3.5 + - - +
----------------------------------------------------------
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Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG 3.0 12.8 + - - -
80C LYS 3.5 4.9 - - - -
81C LEU 3.2 0.2 - - - -
82C ARG* 1.3 80.6 - - - +
84C TYR* 1.4 61.2 + - - +
86C ASN* 3.2 16.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LYS* 2.9 63.5 + - + +
81C LEU* 3.2 20.8 + - + +
83C GLY* 1.4 73.1 - - - +
85C TYR* 1.3 62.6 + - + +
86C ASN* 3.6 1.6 + - - +
123C TYR* 3.3 27.1 - - - -
139C ALA* 3.8 25.6 - - + +
142C ILE* 3.6 44.5 - - + +
143C THR* 3.5 12.8 + - - -
146C LYS* 4.8 7.6 - - - +
----------------------------------------------------------
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Residues in contact with TYR 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 3.0 30.8 + - + +
84C TYR* 1.3 76.3 - - + +
86C ASN* 1.3 62.2 + - - +
87C GLN* 3.7 18.6 - - + -
118C TYR* 3.5 33.6 - + - +
122C ASP 5.7 0.2 + - - -
123C TYR* 3.3 23.6 - + - -
137C ASP* 2.7 37.6 + - - -
139C ALA* 3.6 21.5 - - + -
191E HIS* 4.6 14.6 + + - -
254E GLU* 4.6 4.9 - - - +
274E TRP* 2.7 42.6 + + + -
----------------------------------------------------------
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Residues in contact with ASN 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ARG 2.9 8.7 + - - -
83C GLY* 3.2 13.1 + - - +
84C TYR 3.3 1.5 - - - +
85C TYR* 1.3 79.8 - - - +
87C GLN* 1.4 58.3 + - - +
88C SER 4.3 0.2 + - - -
252E GLY* 3.0 31.0 + - - +
254E GLU* 2.8 40.1 + - - +
255E GLN* 4.2 13.0 + - - +
274E TRP* 3.4 11.8 - - - +
----------------------------------------------------------
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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