Contacts of the helix formed by residues 59 - 88 (chain C) in PDB entry 1TKP
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 GLU 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU 5.1 0.6 + - - -
57C GLY 3.1 0.8 - - - -
58C ALA* 1.3 93.8 + - - +
60C PHE* 1.3 65.2 + - - +
61C ARG 3.4 2.4 + - - -
62C ASP* 3.9 10.5 + - + +
63C LEU* 3.4 35.7 + - + +
115C ILE* 5.2 8.5 - - - +
169C TYR* 6.1 2.9 - - + -
502C NA 2.5 28.4 - - - -
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Residues in contact with PHE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 3.6 27.8 - - + +
56C GLU* 3.6 24.9 + - - +
57C GLY 3.0 19.8 + - - +
58C ALA 3.5 1.0 + - - -
59C GLU* 1.3 77.4 - - - +
61C ARG* 1.3 90.6 + - + +
63C LEU* 3.1 1.0 + - - +
64C HIS* 2.7 52.5 + + + +
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU 3.4 0.6 - - - -
60C PHE* 1.3 107.4 - - + +
62C ASP* 1.3 65.2 + - - +
64C HIS* 3.4 6.3 - - + +
65C LEU* 3.0 48.2 + - + +
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Residues in contact with ASP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 3.9 12.2 - - + +
61C ARG* 1.3 81.3 - - - +
63C LEU* 1.3 56.5 + - - +
65C LEU* 3.2 9.2 + - - +
66C PHE* 2.9 27.4 + - - +
169C TYR* 2.7 34.2 + - - -
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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
----------------------------------------------------------
55C VAL* 3.8 16.2 - - + -
59C GLU* 3.4 29.3 + - + +
60C PHE 3.1 8.1 + - - +
62C ASP* 1.3 76.2 - - - +
64C HIS* 1.3 59.5 + - - +
65C LEU 3.0 0.4 - - - -
66C PHE* 4.3 5.4 - - + -
67C LEU* 2.8 42.9 + - + +
115C ILE* 3.7 27.1 - - + -
119C LEU* 4.0 17.0 - - + -
169C TYR* 3.4 50.3 - - + -
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Residues in contact with HIS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C HIS* 2.6 71.6 + + - -
53C TRP* 5.1 1.9 + - - -
55C VAL* 3.9 13.4 + - + +
60C PHE* 2.7 38.0 + + + +
61C ARG* 3.4 9.6 - - + +
63C LEU* 1.3 72.2 - - - +
65C LEU* 1.3 72.2 + - + +
67C LEU* 4.8 0.7 - - - -
68C GLY 3.0 9.5 + - - -
83D GLU* 3.4 21.7 + - + -
301D FE 4.4 1.0 - - - -
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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
----------------------------------------------------------
52C HIS* 5.3 0.2 - - - -
61C ARG* 3.0 50.6 + - + +
62C ASP* 3.2 8.0 + - - +
63C LEU 3.0 0.2 - - - -
64C HIS* 1.3 88.8 - - + +
66C PHE* 1.3 60.0 + - - +
68C GLY* 3.4 1.7 + - - -
69C GLU* 3.0 41.8 + - - +
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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
----------------------------------------------------------
62C ASP 2.9 16.9 + - - +
63C LEU* 3.8 2.9 - - + +
65C LEU* 1.3 76.7 - - - +
67C LEU* 1.3 77.5 + - + +
69C GLU* 3.1 16.9 + - + +
70C ALA* 2.8 41.2 + - + +
119C LEU* 5.7 0.2 - - + -
162C ASP* 3.6 27.4 - - - -
165C HIS* 3.4 46.7 - + + -
166C ILE* 3.8 21.5 - - + -
169C TYR* 3.6 30.3 - + + +
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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
----------------------------------------------------------
48C LEU* 3.9 29.5 - - + +
51C HIS* 3.6 32.8 - - + +
52C HIS* 3.7 20.6 - - + +
55C VAL* 4.2 7.9 - - + -
63C LEU* 2.8 42.0 + - + +
66C PHE* 1.3 88.4 - - + +
68C GLY* 1.3 61.0 + - - +
70C ALA* 3.9 2.4 - - - +
71C ALA* 2.8 29.8 + - - +
115C ILE* 4.4 1.1 - - + -
119C LEU* 3.8 27.1 - - + -
122C ASP* 4.4 2.9 - - - +
166C ILE* 5.3 0.9 - - + -
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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 LYS* 5.9 2.4 + - - -
52C HIS* 3.3 24.4 + - - -
64C HIS 3.0 12.7 + - - -
65C LEU* 3.4 2.0 + - - -
66C PHE 3.3 0.2 - - - -
67C LEU* 1.3 77.0 - - - +
69C GLU* 1.3 61.8 + - - +
71C ALA* 3.5 6.6 - - - +
72C GLU* 3.0 23.3 + - - +
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 3.0 30.4 + - - +
66C PHE* 3.4 13.8 + - + +
68C GLY* 1.3 78.8 - - - +
70C ALA* 1.3 56.9 + - - +
72C GLU* 3.2 15.8 + - - +
73C THR* 2.9 31.8 + - - +
162C ASP* 6.1 0.4 - - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.6 10.9 - - + +
66C PHE* 2.8 32.3 + - + +
67C LEU* 3.9 5.4 - - - +
69C GLU* 1.3 73.4 - - - +
71C ALA* 1.3 58.3 + - - +
73C THR* 3.4 3.2 + - - -
74C ALA* 2.9 29.1 + - - +
126C TYR* 3.5 19.8 + - - +
162C ASP* 3.7 26.1 - - - +
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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
----------------------------------------------------------
45C TYR* 3.4 18.1 - - + -
48C LEU* 3.6 22.3 - - + +
49C LYS* 3.8 31.2 - - + +
67C LEU 2.8 20.9 + - - +
68C GLY* 3.5 6.7 - - - +
70C ALA* 1.3 72.6 - - - +
72C GLU* 1.3 64.0 + - - +
74C ALA* 3.0 2.3 + - - +
75C GLU 2.8 19.8 + - - -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLY 3.0 11.4 + - - +
69C GLU* 3.2 18.2 + - - +
71C ALA* 1.3 80.9 - - - +
73C THR* 1.3 62.8 + - - +
75C GLU* 3.3 9.2 + - - +
76C GLU* 3.0 47.8 + - + +
311C FE 4.3 6.1 - - - -
312D FE 4.1 19.3 - - - -
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Residues in contact with THR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLU* 2.9 16.4 + - - +
70C ALA 3.5 7.4 - - - -
72C GLU* 1.3 73.7 - - - +
74C ALA* 1.3 65.3 + - - +
76C GLU* 3.1 11.9 + - - +
77C VAL* 2.9 24.5 + - + +
158C GLU* 3.6 36.0 + - + +
159C LEU* 4.4 10.8 - - + -
162C ASP* 3.6 21.0 + - - +
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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
----------------------------------------------------------
41C VAL* 3.1 26.5 - - + +
44C LEU* 4.4 9.4 - - + -
45C TYR* 4.2 22.2 - - - +
48C LEU* 4.3 7.0 - - + -
70C ALA 2.9 16.8 + - - +
71C ALA 3.0 4.5 + - - +
73C THR* 1.3 80.7 - - - +
75C GLU* 1.3 52.1 + - - +
77C VAL* 3.1 4.2 + - - -
78C ALA* 2.8 31.4 + - - +
126C TYR* 5.4 0.7 - - - +
159C LEU* 5.0 4.7 - - + -
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 4.5 5.0 + - + +
45C TYR* 3.8 16.2 - - + -
71C ALA 2.8 12.9 + - - +
72C GLU* 3.3 10.0 - - - +
74C ALA* 1.3 74.9 - - - +
76C GLU* 1.3 59.9 + - + +
78C ALA* 3.3 8.3 - - - +
79C ASP* 2.9 26.2 + - - +
311C FE 3.1 2.4 - - - -
45D TYR* 2.6 31.8 + - - +
49D LYS* 4.3 10.1 + - - +
75D GLU* 3.1 12.5 - - - +
312D FE 2.3 30.1 - - - -
323D FE 2.6 23.5 - - - -
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLU* 3.0 47.0 + - + +
73C THR* 3.7 7.9 + - - +
75C GLU* 1.3 76.2 - - + +
77C VAL* 1.3 65.7 + - + +
79C ASP* 3.4 7.3 + - - +
80C GLU* 3.1 28.9 + - + +
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL* 4.2 12.6 - - + -
73C THR* 2.9 23.8 + - + +
74C ALA* 3.1 7.8 + - - +
76C GLU* 1.3 74.1 - - + +
78C ALA* 1.3 66.3 + - - +
80C GLU* 3.2 7.8 + - + +
81C LEU* 2.9 45.9 + - + +
155C GLY* 4.1 26.5 - - - +
158C GLU* 5.3 2.0 - - + -
159C LEU* 4.1 26.9 - - + -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 3.3 16.5 - - + +
41C VAL* 3.8 13.4 - - + +
42C TYR* 3.7 37.9 - - + -
74C ALA 2.8 15.7 + - - +
75C GLU* 3.3 11.7 - - - +
77C VAL* 1.3 73.6 - - - +
79C ASP* 1.3 64.2 + - - +
81C LEU* 3.2 5.2 - - - +
82C ALA* 2.9 21.2 + - - +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 5.5 0.2 + - - -
75C GLU 2.9 17.0 + - - +
76C GLU* 3.7 9.2 - - - +
77C VAL 3.2 0.2 - - - -
78C ALA* 1.3 77.6 - - - +
80C GLU* 1.3 65.5 + - - +
82C ALA* 3.9 0.5 - - - +
83C GLU* 2.9 36.0 + - - +
49D LYS* 3.2 21.1 + - - +
52D HIS* 3.6 0.2 + - - -
53D TRP* 2.9 29.3 + - - +
302D FE 2.2 31.2 - - - -
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 5.5 2.6 - - - +
76C GLU* 3.1 18.5 + - + +
77C VAL* 3.2 9.4 + - + +
79C ASP* 1.3 81.4 - - + +
81C LEU* 1.3 58.0 + - + +
83C GLU* 3.4 10.7 + - - +
84C ARG* 2.9 29.6 + - - +
151C MET* 3.7 42.5 - - + +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 4.1 15.6 - - + +
37C ASP* 3.6 30.7 - - + -
38C LEU* 3.8 18.8 - - + +
41C VAL* 3.9 11.0 - - + -
77C VAL* 2.9 36.1 + - + +
78C ALA* 3.2 9.9 - - - +
80C GLU* 1.3 73.0 - - + +
82C ALA* 1.3 60.4 + - - +
84C ARG* 3.1 6.8 + - - +
85C VAL* 2.8 34.5 + - - +
151C MET* 4.9 7.9 - - + -
152C LEU* 3.9 28.0 - - + -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 3.5 20.9 - - + -
78C ALA 2.9 14.4 + - - +
81C LEU* 1.3 77.4 - - - +
83C GLU* 1.3 61.1 - - - +
85C VAL* 3.5 1.2 + - - +
86C GLN* 3.2 17.3 + - - +
92C PRO* 3.3 22.6 - - + +
53D TRP* 3.4 37.6 - - + +
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS* 4.6 7.2 - - + -
310A FE 4.5 10.1 - - - -
79C ASP* 3.0 25.6 + - - +
80C GLU* 3.9 9.8 - - - +
82C ALA* 1.3 74.9 - - - +
84C ARG* 1.3 59.8 + - - +
86C GLN* 3.4 7.3 + - - +
87C ALA* 2.9 29.0 + - - +
52D HIS* 2.7 11.4 + - - -
53D TRP* 3.4 19.5 - - + -
64D HIS* 3.7 12.5 + - + -
302D FE 1.9 32.8 - - - -
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 5.3 2.8 - - - +
160A GLU* 2.7 37.5 + - - +
20C LEU* 4.0 14.6 - - - +
22C MET* 4.3 2.4 - - - +
34C LEU* 3.7 21.5 - - + -
80C GLU 2.9 18.4 + - - +
81C LEU* 3.5 5.8 - - - +
83C GLU* 1.3 74.1 - - - +
85C VAL* 1.3 66.7 + - - +
87C ALA* 2.9 18.4 + - - +
88C LEU* 2.9 32.4 + - + +
145C ASP* 2.7 31.1 + - - -
147C ALA* 3.6 11.8 - - - +
148C THR* 2.6 16.2 + - + +
151C MET* 3.8 30.4 - - + +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 3.6 26.7 - - + -
34C LEU* 3.5 28.5 - - + -
35C ASN* 4.0 17.0 - - - +
38C LEU* 5.5 0.4 - - + -
81C LEU 2.8 24.8 + - - +
82C ALA* 3.7 5.8 - - - +
84C ARG* 1.3 73.7 - - - +
86C GLN* 1.3 63.3 + - - +
88C LEU* 3.0 8.9 + - - +
89C GLY 3.3 0.2 + - - -
90C GLY* 2.9 42.2 + - - -
91C VAL 3.6 7.0 - - - +
92C PRO* 3.7 16.4 - - + -
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS* 3.3 3.1 + - - -
168A HIS* 2.9 22.4 + - - -
310A FE 3.3 6.5 - - - -
82C ALA 3.2 11.1 + - - +
83C GLU* 3.5 9.6 - - - +
84C ARG 3.1 0.4 - - - -
85C VAL* 1.3 79.0 - - - +
87C ALA* 1.3 64.2 + - - +
89C GLY* 3.0 14.7 + - - -
90C GLY 3.6 13.5 - - - +
92C PRO* 4.3 3.4 - - + -
53D TRP 3.5 19.3 - - - +
54D ASN* 3.1 31.5 - - - +
56D GLU* 2.9 10.4 - - - +
309D FE 2.6 33.1 - - - -
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS* 3.6 38.5 - - + +
167A GLU* 4.6 1.2 - - - +
17C SER* 3.4 21.7 - - - -
20C LEU* 3.8 17.9 - - + +
83C GLU 2.9 17.1 + - - +
84C ARG* 2.9 17.8 + - - +
86C GLN* 1.3 78.3 - - - +
88C LEU* 1.3 57.9 + - - +
89C GLY 3.1 3.3 + - - -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 3.8 2.1 - - - +
16C GLY* 3.0 30.7 + - - -
17C SER* 4.8 0.7 - - - -
20C LEU* 4.8 4.3 - - + -
22C MET* 4.1 37.9 - - + -
27C ALA* 3.3 11.0 - - + +
30C CYS* 3.5 32.3 - - + -
31C VAL* 3.6 16.4 - - + -
34C LEU* 3.8 19.5 - - + -
84C ARG* 2.9 32.4 + - + +
85C VAL 3.0 7.8 + - - +
87C ALA* 1.3 78.0 - - - +
89C GLY* 1.3 59.5 + - - +
90C GLY 3.4 0.4 + - - -
145C ASP* 4.2 4.9 - - - +
----------------------------------------------------------
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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