Contacts of the helix formed by residues 55 - 84 (chain C) in PDB entry 4GUP
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 55 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASN 3.7 5.0 + - - +
54C LEU* 1.4 76.2 - - - +
56C PRO* 1.4 67.3 - - + +
57C ASP* 3.0 30.7 + - + +
58C HIS* 3.1 19.6 + - + +
59C TRP* 3.7 3.1 - - - -
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Residues in contact with PRO 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU 3.9 1.5 - - - +
55C ALA* 1.4 84.5 - - + +
57C ASP* 1.3 63.8 + - - +
58C HIS 3.3 0.4 - - - -
59C TRP* 3.5 15.2 + - + +
60C GLU* 3.2 42.7 + - - +
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Residues in contact with ASP 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 3.0 20.6 + - + +
56C PRO* 1.3 78.1 - - - +
58C HIS* 1.3 58.1 + - - +
60C GLU* 3.6 9.5 + - - +
61C ARG* 3.0 48.9 + - - +
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Residues in contact with HIS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TYR* 5.6 2.8 + - - -
34C THR* 5.6 1.8 - - + -
43C LYS* 5.2 7.2 - - - -
50C MET* 5.5 0.7 - - + -
54C LEU* 3.5 39.7 - - + +
55C ALA* 3.1 14.6 + - + +
57C ASP* 1.3 76.2 - - - +
59C TRP* 1.3 81.4 + + + +
61C ARG* 4.0 14.4 - - - +
62C TYR* 3.2 66.4 + + + +
164C TRP* 3.5 33.5 - + - -
168C PHE* 5.0 7.4 - + - -
301C 6FP 5.9 0.6 - + - -
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Residues in contact with TRP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C THR* 3.5 34.1 - - + -
42C GLN* 5.1 4.7 - - - +
43C LYS* 3.8 36.1 - - + +
44C GLU 3.9 9.9 - - - -
45C PRO* 3.7 30.8 - - + +
50C MET* 3.6 30.4 + - + -
51C ALA* 4.8 3.0 + - - +
54C LEU* 3.6 30.8 + - + +
55C ALA 3.7 13.5 - - - -
56C PRO* 3.5 13.8 + - + +
58C HIS* 1.3 81.5 - + - +
60C GLU* 1.3 55.7 + - + +
62C TYR* 3.5 2.7 + - - +
63C THR* 2.8 42.3 + - - -
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Residues in contact with GLU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLN* 5.4 7.0 - - - +
56C PRO* 3.2 34.3 + - - +
57C ASP* 3.9 8.2 - - - +
59C TRP* 1.3 78.1 - - + +
61C ARG* 1.3 61.4 + - - +
63C THR* 3.4 4.9 + - - -
64C GLN* 3.1 38.1 + - - +
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ASP* 3.0 40.7 + - - +
58C HIS* 4.0 27.6 - - - +
60C GLU* 1.3 76.3 - - - +
62C TYR* 1.3 71.5 + - + +
64C GLN* 3.6 7.9 + - - +
65C LEU* 3.3 35.4 + - + +
164C TRP* 5.4 4.2 - - - -
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Residues in contact with TYR 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS* 3.7 21.5 - - + -
58C HIS* 3.2 55.3 + + - +
59C TRP 4.2 0.7 - - - +
61C ARG* 1.3 92.2 - - + +
63C THR* 1.3 64.3 + - - +
65C LEU* 3.7 27.9 - - + +
66C LEU* 3.1 31.6 + - + +
69C TRP* 4.6 4.5 - + - -
152C TYR* 5.0 2.9 + - - -
156C TRP* 4.8 1.6 + - - -
160C GLU* 3.3 23.2 + - - -
164C TRP* 4.3 9.8 + + - -
301C 6FP 3.4 42.7 + + - -
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Residues in contact with THR 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TYR* 4.2 1.5 - - + -
41C ARG 3.4 13.9 - - - +
42C GLN* 3.6 28.8 + - - +
43C LYS* 3.0 24.5 + - - +
59C TRP 2.8 23.6 + - - -
60C GLU* 3.7 5.4 - - - -
61C ARG 3.4 0.2 - - - -
62C TYR* 1.3 78.5 - - - +
64C GLN* 1.4 66.4 + - - +
66C LEU* 3.2 3.3 + - - +
67C ARG* 3.0 55.1 + - - +
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Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLN* 5.7 1.0 - - - +
60C GLU* 3.1 29.0 + - - +
61C ARG* 3.8 8.1 - - - +
62C TYR 3.5 0.2 - - - -
63C THR* 1.4 83.5 - - - +
65C LEU* 1.4 63.3 + - - +
67C ARG* 3.4 42.9 + - - +
68C GLY* 3.5 4.9 + - - -
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG* 3.3 22.5 + - + +
62C TYR* 3.7 36.8 - - + +
63C THR 3.3 0.2 - - - -
64C GLN* 1.4 78.4 - - - +
66C LEU* 1.3 56.8 + - - +
68C GLY* 3.3 5.2 + - - -
69C TRP* 3.1 62.6 + - + +
152C TYR* 3.8 21.1 - - + +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 5.4 1.1 - - - +
22C PHE* 3.7 21.1 - - + -
24C SER* 3.6 31.6 - - - +
36C TYR* 3.8 26.5 - - + -
43C LYS* 3.9 29.8 - - + -
62C TYR* 3.1 21.3 + - + +
63C THR 3.7 2.7 - - - +
65C LEU* 1.3 74.7 - - - +
67C ARG* 1.4 54.7 + - - +
68C GLY 3.1 2.2 - - - -
69C TRP* 3.0 27.8 + - + +
70C GLN* 2.7 35.5 + - - +
301C 6FP 4.1 11.2 - - + +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TYR* 3.2 22.0 - - + +
41C ARG* 2.9 65.1 + - - +
42C GLN* 4.3 9.7 - - - +
63C THR* 3.0 36.2 + - - +
64C GLN* 3.5 32.3 + - - +
66C LEU* 1.4 75.1 - - - +
68C GLY* 1.3 56.2 + - - +
70C GLN* 3.4 14.9 - - - +
71C GLN* 3.8 11.8 + - - +
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Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLN 3.5 4.3 + - - -
65C LEU 3.3 7.7 + - - -
66C LEU 3.1 0.4 - - - -
67C ARG* 1.3 77.3 - - - +
69C TRP* 1.3 66.6 + - - +
70C GLN 3.1 1.3 - - - -
71C GLN* 3.1 17.6 + - - +
72C MET* 3.1 21.6 + - - +
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Residues in contact with TRP 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 3.1 48.7 + - - +
22C PHE* 4.1 7.7 - - + -
62C TYR* 4.6 1.6 - + - -
65C LEU* 3.1 43.1 + - + +
66C LEU* 3.0 32.0 + - + +
68C GLY* 1.3 75.2 - - - +
70C GLN* 1.3 62.4 + - - +
72C MET* 3.8 23.2 - - + +
73C PHE* 3.1 27.5 + - - +
152C TYR* 3.4 32.5 - + - -
301C 6FP 3.5 39.3 - + - -
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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
----------------------------------------------------------
21C GLU* 4.9 9.3 + - - +
22C PHE* 3.8 31.6 - - + +
36C TYR* 2.7 35.7 + - - -
38C SER* 3.3 36.8 + - - +
41C ARG* 3.9 19.7 + - - +
66C LEU 2.7 14.7 + - - +
67C ARG 3.4 9.2 - - - +
69C TRP* 1.3 76.6 - - - +
71C GLN* 1.3 68.3 + - + +
73C PHE* 3.4 5.0 + - - +
74C LYS* 3.3 21.5 + - - +
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Residues in contact with GLN 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLU* 5.8 1.8 + - - -
41C ARG* 5.5 5.2 - - - +
67C ARG 4.1 11.2 + - - +
68C GLY* 3.1 11.7 + - - +
70C GLN* 1.3 87.4 - - - +
72C MET* 1.3 63.1 + - - +
74C LYS* 3.4 19.6 + - - +
75C VAL* 3.2 32.7 + - + +
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Residues in contact with MET 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 6.1 1.8 - - - +
68C GLY 3.1 23.6 + - - +
69C TRP* 3.8 24.5 - - + +
71C GLN* 1.3 75.1 - - - +
73C PHE* 1.4 52.5 + - + +
75C VAL* 3.2 8.7 + - - +
76C GLU* 2.8 52.5 + - - +
144C GLU* 5.3 8.7 - - + +
145C ALA* 6.5 0.2 - - + -
148C HIS* 5.8 8.1 - - + -
149C GLU* 5.4 11.7 - - - +
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Residues in contact with PHE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 3.8 33.2 - - + -
10C LEU* 3.8 5.6 - - - -
11C GLY* 3.5 23.6 - - - -
22C PHE* 3.9 17.5 - + + -
69C TRP 3.1 15.6 + - - +
70C GLN 3.6 4.9 - - - +
71C GLN 3.3 0.2 - - - -
72C MET* 1.4 79.2 - - - +
74C LYS* 1.3 61.6 + - - +
76C GLU* 3.5 8.8 + - - +
77C LEU* 3.0 28.3 + - + +
92C TYR* 3.2 61.4 - + - -
93C GLN 4.2 0.7 - - - -
94C ARG* 3.9 24.7 - - + -
112C TYR* 4.3 7.2 - + - -
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Residues in contact with LYS 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLU* 3.7 36.1 - - - +
70C GLN 3.3 10.4 + - - +
71C GLN* 3.6 24.5 - - - +
72C MET 3.3 0.2 - - - -
73C PHE* 1.3 77.5 - - - +
75C VAL* 1.3 59.6 + - + +
77C LEU* 3.9 5.2 - - - +
78C LYS* 3.0 55.5 + - + +
----------------------------------------------------------
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Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLN* 3.3 19.5 - - + +
72C MET* 3.2 10.6 + - - +
74C LYS* 1.3 73.5 - - + +
76C GLU* 1.4 66.3 + - - +
78C LYS* 3.2 9.4 + - - +
79C ARG* 3.1 50.3 + - + +
----------------------------------------------------------
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C MET* 2.8 36.3 + - - +
73C PHE* 3.7 9.9 - - - +
75C VAL* 1.4 71.7 - - - +
77C LEU* 1.4 59.6 + - - +
79C ARG* 3.5 27.5 + - - +
80C LEU* 3.4 25.3 + - - +
92C TYR* 3.7 27.6 + - + +
112C TYR* 4.1 8.7 + - - -
139C ILE* 5.7 5.6 - - + +
143C TRP* 3.2 41.8 - - + +
149C GLU* 5.3 0.9 - - - +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLY* 3.5 35.7 - - - +
12C VAL* 4.3 3.1 - - - +
13C SER* 3.4 13.9 - - - +
73C PHE* 3.0 18.5 + - + +
74C LYS* 3.9 4.3 - - - +
76C GLU* 1.4 72.3 - - - +
78C LYS* 1.4 68.7 + - - +
79C ARG 3.1 1.8 - - - -
80C LEU* 2.8 28.1 + - - +
81C GLN* 3.3 33.1 + - + +
90C HIS* 3.9 10.5 - - + +
92C TYR* 3.5 24.2 - - + +
114C TYR* 5.2 7.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LYS* 3.0 45.3 + - + +
75C VAL* 3.5 6.7 - - - +
77C LEU* 1.4 80.9 - - - +
79C ARG* 1.4 60.2 + - - +
81C GLN* 3.5 9.4 + - - +
82C ARG* 3.4 64.6 + - - +
----------------------------------------------------------
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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 VAL* 3.1 39.8 + - - +
76C GLU* 3.5 39.0 + - - +
78C LYS* 1.4 75.9 - - - +
80C LEU* 1.4 56.0 + - - +
82C ARG* 3.3 11.3 + - - +
83C HIS* 3.1 54.4 + - + +
139C ILE* 4.5 22.4 - - + +
142C ALA 5.4 3.1 + - - -
143C TRP* 5.1 14.1 - - - +
144C GLU* 5.4 9.3 - - - +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU 3.4 15.7 + - - +
77C LEU* 2.8 17.5 + - - +
79C ARG* 1.4 70.8 - - - +
81C GLN* 1.3 62.3 + - - +
83C HIS* 3.3 6.3 + - - +
84C TYR* 3.1 38.8 + - + -
92C TYR* 3.7 34.8 - - + +
114C TYR* 3.8 27.1 - - + -
119C PHE* 3.2 39.3 - - + -
135C VAL* 4.1 11.2 - - + -
139C ILE* 4.3 9.9 - - + -
----------------------------------------------------------
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Residues in contact with GLN 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 2.6 24.4 + - - -
77C LEU* 3.3 16.2 + - + +
78C LYS* 3.8 11.5 - - - +
79C ARG 3.4 0.2 - - - -
80C LEU* 1.3 78.4 - - - +
82C ARG* 1.3 59.2 + - + +
84C TYR 3.0 15.4 - - - +
85C ASN 3.8 0.5 - - - -
86C HIS* 3.0 42.2 + - + +
87C SER* 4.0 2.0 - - - +
88C GLY 3.4 15.0 + - - +
90C HIS* 2.9 26.9 + - - -
114C TYR* 3.2 28.5 - - + +
----------------------------------------------------------
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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 LYS* 3.4 58.0 + - - +
79C ARG* 3.3 10.8 + - - +
80C LEU 3.2 0.6 - - - -
81C GLN* 1.3 76.9 - - + +
83C HIS* 1.3 62.3 + - + +
84C TYR 2.9 15.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG* 3.1 47.3 + - + +
80C LEU* 3.3 2.4 + - - +
82C ARG* 1.3 78.7 - - + +
84C TYR* 1.3 64.4 + - - +
135C VAL* 3.6 33.1 - - + +
138C THR* 4.2 22.6 + - - -
139C ILE* 4.6 7.4 - - + +
----------------------------------------------------------
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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 LEU* 3.1 36.7 + - + +
81C GLN 3.0 5.5 - - - +
82C ARG* 2.9 17.7 - - - +
83C HIS* 1.3 76.3 - - - +
85C ASN* 1.3 61.1 + - - +
86C HIS* 3.3 27.4 - + + -
114C TYR* 3.6 37.2 - + - -
119C PHE* 3.4 14.5 - + - -
132C VAL* 5.2 0.7 - - - +
133C ASP* 2.7 35.0 + - - -
135C VAL* 3.5 17.9 - - + -
----------------------------------------------------------
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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