Contacts of the helix formed by residues 60 - 89 (chain C) in PDB entry 4O9U
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 LEU 60 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C THR* 3.3 4.4 + - - +
59C GLY* 1.3 77.3 - - - +
61C GLU* 1.3 63.4 + - + +
62C LYS 3.5 0.9 - - - -
63C LEU* 3.8 14.6 + - + +
64C ILE* 3.7 36.2 - - + +
105D LEU* 5.1 7.4 - - + -
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 5.9 0.2 - - - -
56C ALA* 3.9 16.4 - - + +
57C GLU* 3.6 9.7 + - - +
58C THR* 2.9 41.5 + - - +
60C LEU* 1.3 76.2 - - - +
62C LYS* 1.3 63.6 + - - +
63C LEU 3.2 3.1 + - - -
64C ILE* 3.9 0.7 + - - -
65C GLY* 3.7 15.1 + - - -
102D VAL* 4.1 25.9 - - + +
105D LEU* 3.7 37.1 - - + +
106D LYS* 3.4 35.1 - - - +
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Residues in contact with LYS 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 3.4 23.2 - - + +
56C ALA* 3.6 26.5 - - + +
57C GLU 4.0 12.9 + - - +
58C THR 3.5 19.8 + - - +
59C GLY* 4.8 7.2 - - - +
60C LEU 3.5 0.4 - - - +
61C GLU* 1.3 77.0 - - - +
63C LEU* 1.3 60.5 + - - +
65C GLY 4.3 0.2 - - - -
66C PHE* 3.6 8.5 + - - +
54D ASN* 3.4 25.8 - - - +
57D LEU* 4.2 14.6 - - + +
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLY 4.5 9.6 + - - +
60C LEU* 3.8 16.0 + - + +
61C GLU 3.2 0.8 - - - -
62C LYS* 1.3 75.9 - - - +
64C ILE* 1.3 78.1 + - + +
65C GLY 3.1 1.8 - - - -
66C PHE* 3.0 17.6 + - + +
67C LEU* 2.9 43.2 + - + +
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 3.7 31.6 - - + +
61C GLU 3.9 1.4 + - - -
63C LEU* 1.3 88.1 - - + +
65C GLY* 1.3 57.1 + - - +
67C LEU* 3.3 11.7 - - + +
68C GLY 2.8 22.2 + - - -
98D THR* 3.6 33.4 - - + +
101D ALA* 4.6 16.6 - - + -
102D VAL* 4.5 9.6 - - + -
105D LEU* 4.8 14.4 - - + -
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Residues in contact with GLY 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 4.0 5.5 - - - +
52C VAL* 4.9 5.4 - - - -
53C LEU* 4.0 23.6 - - - -
61C GLU 3.7 10.5 + - - -
63C LEU 3.1 0.6 - - - -
64C ILE* 1.3 76.1 - - - +
66C PHE* 1.3 58.2 + - - +
67C LEU 3.2 0.2 - - - -
68C GLY* 3.2 2.7 + - - -
69C VAL* 3.0 34.0 + - - +
98D THR* 5.4 1.8 - - - -
102D VAL* 4.4 8.7 - - - +
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Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 3.8 10.3 - - + +
62C LYS 3.6 15.6 + - - +
63C LEU* 3.0 21.4 + - + +
65C GLY* 1.3 74.1 - - - +
67C LEU* 1.3 65.4 + - + +
70C ILE* 3.5 41.6 + - + +
57D LEU* 3.5 32.5 - - + -
60D LEU* 4.3 14.8 - - + -
61D ALA* 3.5 21.4 - - + +
64D LEU* 3.6 24.7 - - + -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 2.9 32.2 + - + +
64C ILE* 3.3 18.6 - - + +
66C PHE* 1.3 81.5 - - + +
68C GLY* 1.3 61.3 + - - +
70C ILE* 3.4 9.5 + - + +
71C LEU* 3.2 50.9 + - + +
98D THR* 5.0 1.3 - - + -
129D PHE* 6.5 0.4 - - + -
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Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 3.5 12.6 - - - +
64C ILE 2.8 12.1 + - - -
65C GLY* 3.2 4.2 + - - -
67C LEU* 1.3 77.9 - - - +
69C VAL* 1.3 54.9 + - - +
71C LEU* 4.2 0.7 - - - -
72C GLY* 3.0 20.4 + - - -
95D ALA* 3.2 16.8 - - - +
98D THR* 3.7 28.7 - - - -
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C VAL* 3.8 17.7 - - + -
49C ALA* 3.3 32.8 - - + +
50C MET* 3.9 7.4 - - + +
53C LEU* 3.8 13.9 - - + -
65C GLY 3.0 15.5 + - - +
67C LEU 3.3 0.2 - - - -
68C GLY* 1.3 77.2 - - - +
70C ILE* 1.3 56.8 + - - +
72C GLY 4.3 0.2 - - - +
73C ALA* 2.8 32.2 + - - +
58D ILE* 4.0 2.9 - - + +
61D ALA* 3.6 12.6 - - + -
62D LEU* 3.6 35.0 - - + +
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Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 3.5 43.2 + - + +
67C LEU* 3.4 10.4 + - + +
69C VAL* 1.3 76.0 - - - +
71C LEU* 1.3 62.8 + - + +
74C ALA* 2.9 29.3 + - + +
61D ALA* 3.3 23.1 - - - +
64D LEU* 3.8 23.6 - - + +
65D GLY* 3.2 11.8 - - - +
68D VAL* 6.4 1.3 - - + -
91D MET* 4.9 7.9 - - + -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.2 42.9 + - + +
68C GLY* 4.0 4.0 - - - +
70C ILE* 1.3 77.2 - - + +
72C GLY* 1.3 53.0 + - - +
74C ALA* 3.3 0.9 + - - +
75C ASN* 2.8 29.6 + - - +
91D MET* 2.9 62.7 - - + +
94D GLY* 3.6 11.9 - - - +
95D ALA* 3.6 21.3 - - + +
98D THR* 4.5 3.4 - - + -
129D PHE* 3.9 20.2 - - + -
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Residues in contact with GLY 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLY 3.8 1.4 - - - +
45C VAL* 3.8 23.8 - - - -
46C VAL* 3.4 18.1 - - - +
68C GLY 3.0 19.7 + - - -
69C VAL 3.7 0.7 - - - -
70C ILE 3.3 0.2 - - - -
71C LEU* 1.3 73.4 - - - +
73C ALA* 1.3 54.3 + - - +
75C ASN* 3.0 5.6 + - - +
76C ALA* 2.7 30.0 + - - +
95D ALA* 3.8 0.4 - - - +
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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
----------------------------------------------------------
46C VAL* 3.5 14.9 - - + +
69C VAL 2.8 20.0 + - - +
72C GLY* 1.3 71.2 - - - -
74C ALA* 1.3 54.3 + - - +
76C ALA* 3.5 9.4 - - + +
77C ALA* 2.8 35.9 + - - +
62D LEU* 3.3 34.1 - - + +
65D GLY* 3.6 4.3 - - - -
66D SER* 3.5 10.4 - - - +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 2.9 22.6 + - + +
71C LEU 3.5 0.7 - - - +
72C GLY 3.1 0.4 - - - -
73C ALA* 1.3 75.1 - - - +
75C ASN* 1.3 60.3 + - - +
76C ALA 3.2 0.2 - - - -
78C GLY 3.2 17.7 + - - -
65D GLY* 3.2 17.2 + - - +
68D VAL* 5.8 3.1 - - + -
69D ALA* 3.2 12.1 - - + +
88D TYR* 3.2 18.3 - - + -
91D MET* 3.4 28.0 - - + -
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Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN 2.8 22.4 + - - +
40C PHE* 4.0 2.8 - - - -
42C HIS* 2.7 34.6 + - - +
43C GLY* 3.5 4.8 - - - -
71C LEU 2.8 14.5 + - - +
72C GLY* 3.3 9.4 - - - +
74C ALA* 1.3 76.1 - - - +
76C ALA* 1.3 64.1 + - - +
79C GLY* 3.4 12.5 + - - -
88D TYR* 3.0 41.7 + - - +
91D MET* 4.0 0.6 - - - +
92D GLY* 3.3 16.4 - - - +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE* 3.0 31.8 - - - -
43C GLY* 3.7 19.7 - - - +
46C VAL* 3.8 5.8 - - + -
72C GLY 2.7 19.2 + - - +
73C ALA* 3.5 11.2 - - + +
74C ALA 3.2 0.2 - - - -
75C ASN* 1.3 71.5 - - - +
77C ALA* 1.3 64.4 + - - +
78C GLY 3.1 5.0 + - - -
79C GLY 3.3 2.3 + - - -
80C TYR 3.3 0.3 + - - -
39D MET* 4.3 15.5 - - + -
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE* 5.4 0.2 - - - -
73C ALA 2.8 15.1 + - - +
76C ALA* 1.3 74.4 - - + +
78C GLY* 1.3 60.0 + - - +
80C TYR* 4.0 5.1 - - - +
81C ALA* 3.6 10.4 + - - +
66D SER* 3.4 37.2 - - - +
70D TRP* 3.5 40.2 - - + -
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Residues in contact with GLY 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA 3.2 20.0 + - - -
76C ALA 3.1 1.2 - - - -
77C ALA* 1.3 76.9 - - - +
79C GLY* 1.3 60.1 + - - +
80C TYR 3.3 0.4 - - - -
82C VAL* 3.1 27.5 + - - +
69D ALA* 3.7 11.3 - - - +
73D ALA* 3.6 2.3 - - - +
88D TYR* 3.1 28.8 - - - -
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Residues in contact with GLY 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER 3.7 3.4 - - - +
39C ASN* 4.4 1.6 - - - -
40C PHE* 3.4 32.2 - - - +
75C ASN 3.4 8.3 + - - -
76C ALA 3.3 4.0 + - - -
78C GLY* 1.3 75.7 - - - +
80C TYR* 1.3 59.4 + - - +
81C ALA 3.5 0.2 - - - -
82C VAL* 3.3 19.7 - - - +
83C THR* 3.3 16.1 - - - +
88D TYR* 3.9 7.6 - - - -
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Residues in contact with TYR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE* 3.4 35.8 - + + -
76C ALA 3.3 8.1 + - - +
77C ALA* 4.0 7.0 - - - +
78C GLY 3.3 0.6 - - - -
79C GLY* 1.3 77.8 - - - +
81C ALA* 1.3 57.8 + - - +
83C THR* 3.3 10.2 - - + +
84C VAL* 3.0 53.9 + - + +
32D ILE* 3.9 18.6 + - + +
33D VAL* 5.6 1.6 - - - -
36D GLY* 3.5 26.9 - - - -
40D VAL* 6.4 0.4 - - + -
70D TRP* 3.6 33.7 - + + -
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA 3.6 12.2 + - - +
78C GLY 3.7 0.2 + - - -
79C GLY 3.5 0.2 - - - -
80C TYR* 1.3 79.3 - - - +
82C VAL* 1.3 63.5 + - - +
83C THR 3.6 0.3 + - - -
84C VAL* 4.2 5.9 - - - +
85C ARG* 3.6 25.6 + - - +
70D TRP* 4.0 18.6 - - + +
73D ALA* 3.4 26.3 - - + +
74D VAL* 3.7 21.4 - - + +
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER* 3.2 20.7 + - - +
39C ASN* 5.0 2.7 - - - +
78C GLY 3.1 15.4 + - - +
79C GLY* 3.3 14.8 - - - +
81C ALA* 1.3 76.9 - - - +
83C THR* 1.3 57.0 + - - +
85C ARG* 4.7 1.9 - - - +
86C MET* 3.3 29.2 + - - +
73D ALA* 3.5 29.6 - - + +
78D MET* 5.9 0.2 - - - +
81D MET* 3.8 33.1 - - + +
84D MET* 4.2 9.0 - - + -
85D VAL* 5.9 2.5 - - + -
88D TYR* 3.7 18.2 - - + -
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Residues in contact with THR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PRO 3.5 12.0 + - - -
36C SER* 3.3 21.0 + - - +
37C GLY* 4.2 7.0 + - - -
40C PHE* 5.1 5.2 - - + -
79C GLY 3.3 10.8 - - - +
80C TYR* 3.3 15.7 - - + +
82C VAL* 1.3 80.2 - - - +
84C VAL* 1.3 59.5 + - + +
85C ARG 3.3 1.6 - - - -
86C MET* 3.6 3.6 - - - -
87C LEU* 2.7 52.1 + - - +
22D MET* 4.5 0.9 - - - +
32D ILE* 3.8 23.4 - - + +
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR* 3.0 51.3 + - + +
81C ALA* 4.2 6.7 - - - +
83C THR* 1.3 78.3 - - + +
85C ARG* 1.3 65.7 + - + +
87C LEU* 3.5 4.5 + - - +
88C GLU* 2.9 36.3 + - - +
32D ILE* 4.4 17.0 - - + +
70D TRP* 6.0 0.4 - - + -
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Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA 3.6 14.5 + - - +
82C VAL* 4.7 1.6 - - - +
83C THR 3.3 0.4 - - - -
84C VAL* 1.3 82.9 - - + +
86C MET* 1.3 60.6 + - - +
88C GLU* 3.5 10.5 + - + +
89C MET* 3.0 50.2 + - + +
73D ALA 4.1 5.1 + - - -
74D VAL* 2.8 49.8 + - + +
76D VAL 3.1 23.0 + - - -
77D ALA* 5.2 0.4 - - - +
78D MET* 4.7 21.0 - - - +
81D MET* 5.0 2.9 - - + +
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Residues in contact with MET 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C THR* 3.6 19.5 - - + +
33C PRO* 3.5 45.1 - - + +
36C SER* 4.8 5.6 - - - -
82C VAL 3.3 20.6 + - - +
83C THR* 3.2 9.0 + - - +
85C ARG* 1.3 77.3 - - - +
87C LEU* 1.3 61.6 + - - +
89C MET* 3.6 18.4 + - - +
90C PHE* 4.0 9.9 - - - -
78D MET* 4.0 15.7 - - + -
81D MET* 3.3 35.2 - - + -
85D VAL* 6.2 1.3 - - + -
343D VAL* 3.4 26.5 - - + -
352D TYR* 4.7 2.1 + - - -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 5.1 2.5 - - + -
33C PRO* 3.8 22.9 - - + +
83C THR* 2.7 43.5 + - - +
84C VAL 4.0 2.0 - - - +
86C MET* 1.3 69.4 - - - +
88C GLU* 1.3 63.1 + - - +
89C MET 3.2 1.8 - - - -
90C PHE* 3.3 43.3 - - + +
22D MET* 4.7 6.1 - - + -
28D ALA* 3.4 36.6 - - + +
29D LYS* 4.0 10.7 - - - +
32D ILE* 3.9 31.6 - - + -
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C VAL* 2.9 26.4 + - + +
85C ARG* 3.5 16.2 - - + +
87C LEU* 1.3 74.0 - - - +
89C MET* 1.3 55.7 + - + +
90C PHE* 2.7 24.3 + - - +
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Residues in contact with MET 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ARG* 3.0 36.6 - - + +
86C MET 3.7 10.5 - - - +
87C LEU 3.2 0.4 - - - -
88C GLU* 1.3 75.8 - - + +
90C PHE* 1.3 60.3 + - - +
78D MET* 3.7 43.5 - - + -
346D ALA* 3.6 37.9 - - + +
347D GLU* 4.2 12.8 - - + +
352D TYR* 2.7 32.1 + - - +
----------------------------------------------------------
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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).
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