Contacts of the helix formed by residues 58 - 87 (chain C) in PDB entry 4KNF
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 TRP 58 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.7 19.3 - - + -
55C SER* 2.6 27.8 + - - +
57C LYS* 1.3 85.3 - - + +
59C LYS* 1.3 62.9 + - - +
60C THR 3.3 2.7 - - - -
61C SER* 3.1 28.8 + - - -
62C LEU* 3.3 7.4 + - - +
112C ILE* 6.3 1.1 - - + -
181C ALA* 4.0 23.6 - - + -
182C VAL* 5.1 7.6 - - + -
185C ALA* 4.8 12.6 - - + -
239C ILE* 4.6 17.3 - - + -
242C VAL* 3.4 32.3 - - + -
243C ALA* 3.6 34.5 - - + -
246C GLU* 3.1 32.4 + - + +
247C SER* 3.9 2.2 - - - -
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Residues in contact with LYS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 4.1 0.2 - - - -
52B ASP* 3.4 33.7 - - - +
53B GLN* 3.4 24.5 - - + +
51C ARG* 3.3 47.1 + - - +
52C ASP* 4.6 7.4 + - - +
54C VAL* 2.7 33.4 + - + +
55C SER* 3.1 18.6 + - - +
56C ALA* 3.9 3.7 + - - +
57C LYS 3.8 1.0 - - - -
58C TRP* 1.3 74.1 - - - +
60C THR* 1.3 57.6 + - - +
62C LEU* 3.1 5.1 + - - +
63C THR* 3.0 28.2 + - - -
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Residues in contact with THR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 4.4 13.0 - - + -
50B GLU* 2.7 26.8 + - - +
53B GLN* 3.3 11.4 + - - +
240B TRP* 3.7 29.3 - - + -
244B VAL* 5.8 1.2 - - - +
56C ALA 4.9 0.4 + - - -
57C LYS 5.2 2.0 + - - -
58C TRP 3.3 0.6 - - - -
59C LYS* 1.3 73.8 - - - +
61C SER* 1.3 60.0 + - - +
63C THR* 3.4 2.1 + - - -
64C VAL* 3.0 31.2 + - + +
111C LEU* 4.4 19.3 - - + -
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LYS 5.5 1.1 + - - -
58C TRP* 3.1 23.2 + - - -
60C THR* 1.3 78.2 - - - +
62C LEU* 1.3 58.8 + - - +
64C VAL* 3.3 5.3 + - - +
65C SER* 3.0 32.8 + - - -
108C GLU* 3.6 18.0 + - - +
111C LEU* 4.5 15.5 - - - +
112C ILE* 5.9 2.6 - - - +
239C ILE* 4.2 21.6 - - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 3.7 27.0 - - + +
48C PHE* 4.8 0.2 - - - -
50C GLU 3.7 20.6 - - - +
51C ARG* 3.6 17.9 - - + +
54C VAL* 3.6 33.9 - - + -
58C TRP 3.3 8.2 + - - +
59C LYS 3.1 8.1 + - - +
61C SER* 1.3 79.9 - - - +
63C THR* 1.3 63.3 + - - +
65C SER* 3.3 7.5 + - - +
66C GLY* 3.0 19.9 + - - -
236C GLY 4.9 0.9 - - - +
239C ILE* 4.9 6.1 - - + -
240C TRP* 3.9 40.8 - - + +
243C ALA* 5.1 2.5 - - + -
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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
----------------------------------------------------------
46B PHE* 3.7 40.6 - - + -
49B VAL* 3.6 6.7 - - + +
50B GLU* 2.9 18.0 + - + +
48C PHE* 3.6 22.6 - - + -
51C ARG* 2.9 28.4 + - - +
59C LYS 3.0 4.5 + - - -
60C THR* 3.6 8.5 - - - -
61C SER 3.3 0.4 - - - -
62C LEU* 1.3 74.3 - - - +
64C VAL* 1.3 52.3 + - - +
66C GLY* 3.2 2.8 + - - -
67C LEU* 2.8 38.9 + - + +
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 4.6 13.5 - - + -
60C THR* 3.0 27.6 + - + +
61C SER 3.8 3.8 - - - +
62C LEU 3.3 0.2 - - - -
63C THR* 1.3 71.9 - - - +
65C SER* 1.3 60.4 + - - +
67C LEU* 3.2 11.0 + - + +
68C ILE* 2.8 41.3 + - + +
104C LEU* 3.6 38.1 - - + +
107C VAL* 4.8 13.0 - - + -
108C GLU* 4.0 15.0 - - + +
111C LEU* 4.8 4.0 - - + -
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 3.8 25.8 - - - -
61C SER 3.0 14.8 + - - -
62C LEU* 3.6 10.1 - - - +
64C VAL* 1.3 77.5 - - - +
66C GLY* 1.3 57.6 + - - +
68C ILE* 3.3 9.2 + - - +
69C THR* 2.9 32.1 + - - +
108C GLU* 2.9 29.8 + - - -
232C LYS 5.4 0.8 - - - +
236C GLY* 3.9 15.5 + - - -
239C ILE* 5.1 1.0 - - - +
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Residues in contact with GLY 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 3.4 7.5 - - - +
47C PHE* 3.8 17.6 - - - +
48C PHE* 3.7 19.8 - - - -
62C LEU 3.0 11.4 + - - -
63C THR 3.6 3.4 - - - -
65C SER* 1.3 72.7 - - - +
67C LEU* 1.3 55.1 + - - +
69C THR* 2.8 10.2 + - - -
70C GLY* 2.7 33.1 + - - -
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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
----------------------------------------------------------
42B ALA* 3.7 31.2 - - + +
45B VAL* 3.6 32.5 - - + -
46B PHE* 3.8 34.8 - - + +
48C PHE* 3.7 9.2 - - + -
63C THR* 2.8 15.7 + - + +
64C VAL* 3.4 13.0 - - + +
66C GLY* 1.3 77.6 - - - +
68C ILE* 1.3 55.9 + - - +
70C GLY* 3.3 2.2 + - - -
71C ILE* 3.0 39.1 + - - +
104C LEU* 4.5 17.0 - - + -
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 2.8 28.0 + - + +
65C SER* 3.4 8.3 - - - +
67C LEU* 1.3 72.4 - - - +
69C THR* 1.3 67.7 + - + +
72C ALA* 3.2 20.4 + - - +
101C THR* 3.5 26.4 - - + +
104C LEU* 3.7 23.7 - - + +
105C LEU* 3.6 44.2 - - + +
108C GLU* 3.9 7.2 - - - +
232C LYS* 3.7 37.7 - - + +
301C RET 5.1 0.4 - - + -
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Residues in contact with THR 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 2.9 30.7 - - + +
43C ALA* 3.9 10.5 - - + -
44C THR* 2.8 33.6 + - - -
47C PHE* 3.6 22.9 - - + -
65C SER 2.9 16.4 + - - +
66C GLY* 2.8 19.6 + - - -
68C ILE* 1.3 72.3 - - - +
70C GLY* 1.3 50.7 - - - +
73C PHE* 2.8 32.2 + - - +
232C LYS* 4.1 17.0 - - + +
233C ILE* 4.6 0.4 - - + -
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Residues in contact with GLY 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C THR* 3.8 15.3 - - - -
48C PHE* 5.9 0.2 - - - -
66C GLY 2.7 22.6 + - - -
67C LEU* 3.3 2.7 + - - -
68C ILE 3.3 0.2 - - - -
69C THR* 1.3 69.2 + - - +
71C ILE* 1.3 65.8 + - - +
73C PHE* 3.2 13.8 - - - +
74C TRP* 3.1 25.8 - - - -
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 5.1 11.0 - - + +
41B LEU* 6.4 2.7 - - + -
42B ALA* 4.0 26.0 - - + -
67C LEU 3.0 17.8 + - - +
70C GLY* 1.3 71.7 - - - +
72C ALA* 1.3 65.6 + - - +
74C TRP* 3.3 8.1 + - + -
75C HIS* 2.7 52.9 + - + +
97C ASN* 3.5 9.0 - - - +
100C LEU* 4.1 21.3 - - + +
101C THR* 4.0 13.7 - - + -
104C LEU* 4.3 19.5 - - + -
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 3.0 37.2 - - + -
68C ILE 3.2 11.1 + - - +
69C THR 3.5 0.2 - - - +
71C ILE* 1.3 75.3 - - - +
73C PHE* 1.3 50.4 + - - +
74C TRP 3.2 0.3 + - - -
75C HIS 3.2 1.2 + - - -
76C TYR* 2.6 45.1 + - + -
97C ASN* 3.3 25.9 + - - +
232C LYS* 4.0 10.1 - - + -
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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
----------------------------------------------------------
37C THR* 3.5 37.2 - - + -
40C MET* 3.9 12.4 - - + +
41C LEU* 3.6 46.4 - - + +
44C THR* 4.9 0.7 - - - +
69C THR 2.8 13.9 + - - +
70C GLY* 3.2 13.0 - - - +
72C ALA* 1.3 77.2 - - - +
74C TRP* 1.3 95.8 + + - +
76C TYR* 3.3 4.4 + - - +
77C LEU* 3.1 45.5 + - + +
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Residues in contact with TRP 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TRP* 6.0 2.2 - - + -
41B LEU* 4.1 27.0 - - + +
70C GLY* 3.1 27.1 + - - -
71C ILE* 3.3 9.0 + - + +
72C ALA 3.3 0.4 - - - -
73C PHE* 1.3 97.8 - + - +
75C HIS* 1.3 67.7 + - + +
77C LEU* 3.0 36.5 + - + +
78C TYR* 3.2 32.5 - + + -
----------------------------------------------------------
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Residues in contact with HIS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TRP* 2.9 35.6 + + - -
38B ALA* 4.7 5.8 - - + -
71C ILE* 2.7 35.8 + - + +
72C ALA 3.2 3.3 + - - +
74C TRP* 1.3 81.8 - - + +
76C TYR* 1.3 57.7 + - - +
78C TYR* 3.5 6.9 + - - +
79C MET* 2.8 33.5 + - - +
93C PHE* 4.1 20.2 - + - +
96C ILE* 3.5 14.6 - - + +
97C ASN* 3.5 30.0 + - + +
100C LEU* 3.4 24.0 - - + -
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Residues in contact with TYR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 3.7 22.4 - + - -
36C VAL* 3.3 33.6 - - + +
37C THR* 3.4 30.2 + - - +
40C MET* 4.9 1.6 - - + -
72C ALA* 2.6 36.5 + - + +
73C PHE 3.6 6.1 - - - +
75C HIS* 1.3 72.1 - - - +
77C LEU* 1.3 63.7 + - - +
79C MET* 3.8 14.0 - - - +
80C ARG* 3.0 25.8 + - - +
94C ARG* 2.8 18.0 + - - -
97C ASN* 4.3 9.2 - - - -
225C ASN* 3.0 21.3 + - - -
228C ASP* 2.7 38.9 + - + +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C THR* 3.8 18.8 - - + -
73C PHE* 3.1 43.5 + - + +
74C TRP* 3.0 28.6 + - + +
76C TYR* 1.3 74.5 - - - +
78C TYR* 1.3 64.5 + - + +
80C ARG* 3.5 6.0 + - + +
81C GLY* 3.0 24.4 + - - -
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TRP* 3.7 30.1 - + - -
74C TRP* 3.2 37.4 + + + -
75C HIS 3.8 5.8 - - - +
77C LEU* 1.3 81.1 - - + +
79C MET* 1.3 65.4 + - - +
81C GLY* 3.3 2.2 + - - -
82C VAL* 2.9 31.0 + - + +
93C PHE* 3.6 37.2 - + + -
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Residues in contact with MET 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PHE* 3.8 15.0 - - + -
75C HIS* 2.8 26.1 + - - +
76C TYR* 3.8 21.8 - - - +
78C TYR* 1.3 74.2 - - - +
80C ARG* 1.3 63.8 + - - +
82C VAL 3.2 0.5 + - - -
83C TRP* 3.1 20.1 + - - +
90C PRO* 3.4 32.8 - - + +
93C PHE* 3.8 13.9 - - + +
94C ARG* 2.7 81.7 - - + +
97C ASN* 5.3 3.4 - - + +
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Residues in contact with ARG 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.5 28.5 - - - +
30C GLY* 2.7 33.1 + - - +
33C PHE* 3.6 34.7 - - + -
34C TRP* 3.6 37.1 - - - +
37C THR* 5.2 2.7 - - - +
76C TYR 3.0 17.0 + - - +
77C LEU* 3.8 6.7 - - + +
79C MET* 1.3 73.8 - - - +
81C GLY* 1.3 69.2 + - - +
83C TRP* 3.4 1.8 + - + +
84C ILE* 3.0 53.9 + - + +
93D PHE* 5.8 0.8 - - - -
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU 3.0 16.4 + - - -
78C TYR* 3.3 5.3 + - - -
80C ARG* 1.3 78.0 - - - +
82C VAL* 1.3 60.5 + - - +
84C ILE* 3.2 2.5 + - - +
85C ASP* 3.0 32.2 + - - +
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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
----------------------------------------------------------
21B GLY* 3.7 26.7 - - - +
22B ASP* 3.9 18.8 - - + +
78C TYR* 2.9 19.2 + - + +
79C MET* 4.1 0.7 - - - +
81C GLY* 1.3 71.7 - - - +
83C TRP* 1.3 70.0 + - - +
85C ASP* 4.6 3.4 - - - +
86C THR* 2.4 36.1 + - - +
87C GLY 3.5 0.5 + - - -
88C ASP* 3.7 11.6 - - + +
90C PRO* 3.5 30.3 - - + -
93C PHE* 4.0 16.8 - - + -
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Residues in contact with TRP 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 2.8 36.1 + - - -
29C VAL* 3.3 36.3 - - + +
30C GLY* 3.9 14.8 - - - -
33C PHE* 3.9 12.1 - + + -
79C MET 3.1 9.1 + - - +
80C ARG 3.7 6.7 - - - +
82C VAL* 1.3 80.8 - - - +
84C ILE* 1.3 61.4 + - + +
87C GLY* 2.5 56.7 + - - -
88C ASP 3.6 21.8 - - - +
89C THR* 4.1 8.7 - - - -
90C PRO* 4.7 3.4 - - + -
217C ALA* 4.5 18.4 - - + -
218C SER* 4.5 11.4 - - - -
221C ASN* 4.0 17.7 - - - -
----------------------------------------------------------
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Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 3.6 23.8 - - - +
30C GLY* 4.5 3.8 - - - -
80C ARG* 3.0 67.9 + - + +
81C GLY* 4.0 2.0 - - - +
83C TRP* 1.3 82.9 - - + +
85C ASP* 1.3 70.4 + - - +
86C THR 3.6 0.3 + - - -
87C GLY 4.7 0.3 + - - -
----------------------------------------------------------
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 5.4 9.0 + - - +
81C GLY* 3.0 21.1 + - - +
82C VAL* 4.3 3.4 - - - +
84C ILE* 1.3 86.3 - - - +
86C THR* 1.3 68.0 + - + +
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Residues in contact with THR 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY* 4.9 13.4 - - - -
22B ASP 5.5 0.3 + - - -
82C VAL* 2.4 36.7 + - - +
84C ILE 3.4 0.6 - - - -
85C ASP* 1.3 84.8 - - + +
87C GLY* 1.3 62.2 + - - +
88C ASP* 3.1 32.3 + - - +
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TRP* 2.5 54.5 + - - -
84C ILE 4.5 0.8 + - - -
86C THR* 1.3 72.6 + - - +
88C ASP* 1.3 61.7 + - - +
89C THR 4.0 0.2 + - - -
217C ALA* 5.3 2.8 - - - +
----------------------------------------------------------
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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).
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