Contacts of the helix formed by residues 59 - 88 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU 5.3 0.4 + - - -
57B GLY 3.2 0.6 - - - -
58B ALA* 1.3 96.4 + - - +
60B PHE* 1.3 65.2 + - - +
61B ARG 3.3 2.9 + - - -
62B ASP* 3.7 12.6 + - + +
63B LEU* 3.3 36.6 + - + +
115B ILE* 5.2 8.8 - - - +
169B TYR* 5.8 3.8 - - + -
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 3.5 32.3 - - + +
56B GLU* 3.5 26.0 - - - +
57B GLY 2.9 20.8 + - - +
58B ALA 3.3 1.2 - - - -
59B GLU* 1.3 80.6 - - - +
61B ARG* 1.3 92.4 + - + +
63B LEU 3.2 0.2 + - - -
64B HIS* 2.8 44.3 + + + +
327B FE 4.4 13.2 - - - -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU 3.3 1.0 - - - -
60B PHE* 1.3 105.9 - - + +
62B ASP* 1.3 67.7 + - - +
64B HIS* 3.1 8.0 + - + +
65B LEU* 3.0 46.3 + - + +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 3.7 11.7 + - + +
61B ARG* 1.3 81.5 - - - +
63B LEU* 1.3 56.8 + - - +
65B LEU* 3.3 11.1 + - - +
66B PHE* 2.8 26.9 + - - +
169B TYR* 2.6 36.2 + - - -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 3.9 26.2 - - + -
59B GLU* 3.3 34.7 + - + +
60B PHE 3.2 4.8 + - - +
62B ASP* 1.3 76.6 - - - +
64B HIS* 1.3 58.2 + - - +
66B PHE* 4.2 4.7 - - + +
67B LEU* 2.7 44.6 + - + +
115B ILE* 3.9 13.2 - - + -
119B LEU* 3.9 20.0 - - + -
169B TYR* 3.5 46.7 - - + -
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Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 3.9 16.9 + - + -
52B HIS* 2.7 78.8 + + - +
53B TRP* 5.0 0.2 - - - -
55B VAL* 3.7 12.3 - - + +
60B PHE* 2.8 28.7 + + + +
61B ARG* 3.3 12.1 - - + +
63B LEU* 1.3 80.9 - - - +
65B LEU* 1.3 71.7 + - + +
68B GLY 3.0 7.3 + - - -
327B FE 4.3 14.6 - - - -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B HIS* 5.4 0.7 - - - -
61B ARG* 3.0 49.5 + - + +
62B ASP* 3.6 8.7 - - - +
64B HIS* 1.3 88.2 - - + +
66B PHE* 1.3 62.9 + - - +
68B GLY* 3.9 0.7 - - - -
69B GLU* 3.1 39.5 + - + +
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 2.8 19.1 + - - +
63B LEU* 3.2 4.2 + - + +
65B LEU* 1.3 78.7 - - - +
67B LEU* 1.3 74.4 - - + +
69B GLU* 3.4 13.3 + - + +
70B ALA* 2.9 28.5 + - + +
119B LEU* 6.2 0.2 - - + -
162B ASP* 3.7 31.4 - - + -
165B HIS* 3.4 46.7 - + + -
166B ILE* 3.7 22.0 - - + -
169B TYR* 3.5 31.2 - + + +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.8 31.0 - - + +
51B HIS* 3.8 16.2 - - + +
52B HIS* 3.7 34.3 - - - +
55B VAL* 4.7 0.9 - - + -
63B LEU* 2.7 35.8 + - + +
66B PHE* 1.3 90.8 - - + +
68B GLY* 1.3 58.5 + - - +
70B ALA* 3.4 3.5 + - - +
71B ALA* 2.8 29.8 + - - +
115B ILE* 4.5 4.7 - - + -
119B LEU* 4.4 20.4 - - + -
122B ASP* 4.2 10.5 - - - +
166B ILE* 4.9 2.2 - - + -
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 5.6 3.3 + - - +
52B HIS* 3.3 28.1 + - - -
64B HIS 3.0 11.6 + - - -
65B LEU 3.9 0.9 - - - -
67B LEU* 1.3 76.1 - - - +
69B GLU* 1.3 54.7 + - - +
71B ALA* 3.4 6.5 + - - +
72B GLU* 2.9 27.7 + - - +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.1 31.8 + - + +
66B PHE* 3.5 15.9 - - + +
68B GLY* 1.3 72.9 - - - +
70B ALA* 1.3 54.0 + - - +
72B GLU* 3.0 17.1 + - - +
73B THR* 2.8 37.6 + - - -
162B ASP* 4.9 0.2 - - - -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.5 16.8 - - + +
66B PHE* 2.9 27.3 + - + +
67B LEU* 3.6 8.7 - - - +
69B GLU* 1.3 72.9 - - - +
71B ALA* 1.3 59.5 + - - +
73B THR* 3.2 4.0 + - - -
74B ALA* 2.9 24.4 + - - +
126B TYR* 3.6 20.6 + - - +
162B ASP* 3.5 23.0 - - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 3.1 20.9 - - + +
48B LEU* 3.6 22.2 - - + +
49B LYS* 3.7 29.8 - - + +
67B LEU 2.8 18.9 + - - +
68B GLY* 3.6 5.6 - - - +
70B ALA* 1.3 74.9 - - - +
72B GLU* 1.3 60.1 + - - +
74B ALA* 3.2 1.4 + - - +
75B GLU* 2.9 24.8 + - - +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A FE 4.4 2.5 - - - -
316A FE 3.2 24.7 - - - -
324A FE 3.9 12.2 - - - -
68B GLY 2.9 14.1 + - - +
69B GLU* 3.0 17.7 + - - +
71B ALA* 1.3 77.2 - - - +
73B THR* 1.3 61.1 + - - +
75B GLU* 3.2 3.4 + - - +
76B GLU* 3.0 45.1 + - + +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU 2.8 16.9 + - - -
70B ALA 3.5 7.6 - - - -
72B GLU* 1.3 72.8 - - - +
74B ALA* 1.3 65.2 + - - +
76B GLU* 3.3 9.7 + - + +
77B VAL* 3.1 27.5 + - + +
158B GLU* 3.6 36.1 + - + +
159B LEU* 4.7 4.9 - - + -
162B ASP* 3.7 17.6 + - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 3.1 35.7 - - + +
44B LEU* 4.0 19.7 - - + -
45B TYR* 4.1 12.8 - - + -
48B LEU* 4.3 1.1 - - + -
70B ALA 2.9 15.4 + - - +
71B ALA 3.2 3.5 + - - +
73B THR* 1.3 76.8 - - - +
75B GLU* 1.3 58.9 + - - +
77B VAL* 3.2 3.1 + - - -
78B ALA* 2.8 26.9 + - - +
126B TYR* 5.7 0.2 - - - +
159B LEU* 4.6 6.3 - - + +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 2.2 46.3 + - - +
49A LYS* 4.1 12.6 + - - +
72A GLU* 5.9 0.2 - - - -
75A GLU* 2.8 11.2 - - - +
315A FE 2.5 11.2 - - - -
316A FE 2.4 30.3 - - - -
42B TYR* 4.1 7.6 + - + +
45B TYR* 3.8 14.6 - - + -
71B ALA 2.9 17.0 + - - +
72B GLU* 3.4 5.6 - - - +
73B THR 3.1 0.2 - - - -
74B ALA* 1.3 80.1 - - - +
76B GLU* 1.3 58.7 + - + +
78B ALA* 3.4 7.0 - - - +
79B ASP* 2.9 26.7 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLU* 3.0 37.7 + - + +
73B THR* 3.7 7.4 - - + +
75B GLU* 1.3 77.4 - - + +
77B VAL* 1.3 63.1 + - + +
79B ASP* 3.2 8.5 + - - +
80B GLU* 2.8 33.9 + - + +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 4.0 17.0 - - + -
73B THR* 3.1 19.4 + - + +
74B ALA* 3.6 6.7 - - - +
76B GLU* 1.3 74.3 - - + +
78B ALA* 1.3 68.1 + - - +
80B GLU* 3.0 8.2 + - - +
81B LEU* 2.9 43.2 + - + +
155B GLY* 4.1 24.5 - - - +
158B GLU* 5.5 1.3 - - + -
159B LEU* 4.1 25.8 - - + -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TRP* 5.0 0.7 - - - -
38B LEU* 3.4 26.9 - - + +
41B VAL* 4.0 9.9 - - + -
42B TYR* 3.7 26.5 - - + -
74B ALA 2.8 17.4 + - - +
75B GLU* 3.4 7.4 - - - +
77B VAL* 1.3 78.6 - - - +
79B ASP* 1.3 63.6 + - - +
81B LEU* 3.2 8.8 + - - +
82B ALA* 2.8 22.4 + - - +
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 3.3 21.1 + - - +
53A TRP* 3.0 28.2 + - - +
42B TYR* 5.4 0.4 - - - -
75B GLU 2.9 15.5 + - - +
76B GLU* 3.4 12.1 - - - +
77B VAL 3.2 0.2 - - - -
78B ALA* 1.3 78.3 - - - +
80B GLU* 1.3 68.0 + - - +
83B GLU* 3.1 34.9 + - - +
303B FE 2.2 31.5 - - - -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 2.8 23.0 + - + +
77B VAL* 3.0 7.1 + - - +
79B ASP* 1.3 76.9 - - - +
81B LEU* 1.3 57.6 + - + +
83B GLU* 3.8 12.9 - - - +
84B ARG* 3.0 27.9 + - - +
151B MET* 3.8 38.2 - - + +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.0 27.5 - - + +
37B ASP* 3.9 22.0 - - + +
38B LEU* 3.9 18.2 - - + +
41B VAL* 4.3 6.1 - - + -
77B VAL* 2.9 38.7 + - + +
78B ALA* 3.3 7.6 - - - +
80B GLU* 1.3 73.1 - - + +
82B ALA* 1.3 66.9 + - - +
84B ARG* 3.2 6.7 + - - +
85B VAL* 2.9 28.5 + - - +
151B MET* 4.6 8.3 - - + -
152B LEU* 3.9 28.3 - - + -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TRP* 3.3 45.1 - - + +
38B LEU* 3.6 10.7 - - + +
78B ALA 2.8 15.5 + - - +
81B LEU* 1.3 74.1 - - - +
83B GLU* 1.3 64.7 + - - +
85B VAL* 3.1 4.4 + - - +
86B GLN* 3.1 21.8 + - - +
92B PRO* 3.5 23.8 - - + +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 3.3 9.0 + - - -
53A TRP* 3.5 17.5 - - + -
64A HIS* 3.5 15.5 + - + -
79B ASP* 3.1 26.0 + - - +
80B GLU* 3.8 12.5 - - - +
82B ALA* 1.3 79.3 - - - +
84B ARG* 1.3 56.8 + - - +
86B GLN* 3.3 2.2 + - - -
87B ALA* 2.9 26.6 + - - +
303B FE 2.1 30.7 - - - -
326B FE 3.3 23.0 - - - -
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.4 30.8 - - - +
22B MET* 4.4 4.4 - - - +
34B LEU* 4.0 18.4 - - + -
80B GLU 3.0 17.3 + - - +
81B LEU* 3.5 5.4 - - - +
83B GLU* 1.3 73.9 - - - +
85B VAL* 1.3 66.2 + - - +
87B ALA* 3.0 8.9 + - - +
88B LEU* 2.8 40.2 + - + +
145B ASP* 2.6 31.7 + - - -
147B ALA* 3.4 23.8 - - - +
148B THR* 2.9 21.0 + - + +
151B MET* 3.3 28.7 - - + +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 3.8 16.4 - - + +
34B LEU* 3.6 28.0 - - + -
35B ASN* 3.9 22.9 - - - +
38B LEU* 5.1 0.2 - - + -
81B LEU 2.9 18.7 + - - +
82B ALA* 3.2 9.0 - - - +
84B ARG* 1.3 77.1 - - - +
86B GLN* 1.3 55.4 + - - +
88B LEU* 3.1 9.4 + - - +
90B GLY* 2.8 31.5 + - - -
91B VAL 3.5 16.6 - - - +
92B PRO* 3.4 29.6 - - + -
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Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TRP* 3.6 17.8 + - + +
54A ASN* 3.1 37.2 - - - +
56A GLU* 2.9 11.6 - - - +
112A VAL* 5.7 0.7 - - - +
82B ALA 3.1 8.5 + - - +
83B GLU* 3.6 8.5 - - - +
85B VAL* 1.3 77.6 - - - +
87B ALA* 1.3 71.2 + - - +
89B GLY* 2.9 15.2 + - - -
90B GLY 3.5 13.9 - - - +
92B PRO* 4.0 4.3 - - + -
317B FE 2.5 35.1 - - - -
326B FE 3.8 14.4 - - - -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER* 3.4 21.3 - - - -
20B LEU* 4.1 20.2 - - + +
83B GLU 2.9 16.5 + - - +
84B ARG* 3.0 18.3 + - - +
86B GLN* 1.3 81.2 - - - +
88B LEU* 1.3 58.9 + - - +
89B GLY* 3.3 3.6 + - - -
326B FE 4.4 0.2 - - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 3.7 2.8 - - - +
16B GLY* 3.1 26.2 + - - -
17B SER* 5.3 0.9 - - - -
20B LEU* 4.2 18.2 - - + -
22B MET* 4.2 25.6 - - + -
27B ALA* 3.4 14.1 - - + +
30B CYS* 3.8 22.9 - - + -
31B VAL* 3.6 20.4 - - + -
34B LEU* 4.5 6.5 - - + -
84B ARG* 2.8 29.4 + - - +
86B GLN 3.0 0.6 - - - -
87B ALA* 1.3 81.2 - - - +
89B GLY* 1.3 57.2 + - - +
90B GLY 3.3 0.9 - - - -
145B ASP* 3.5 20.6 - - - +
148B THR* 4.1 7.4 - - - +
----------------------------------------------------------
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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