Contacts of the helix formed by residues 59 - 88 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 5.1 2.0 - - + -
62A ASP* 5.5 1.8 - - - -
169A TYR* 5.4 0.4 - - - -
174A THR* 2.7 28.0 + - - -
175A LEU* 2.6 45.0 + - + +
176A VAL* 3.6 6.1 - - - +
501A NA 2.7 27.7 - - - -
56D GLU 5.3 0.2 + - - -
57D GLY 3.1 1.0 - - - -
58D ALA* 1.3 80.2 + - - +
60D PHE* 1.3 65.9 + - - +
61D ARG 3.2 3.2 + - - -
62D ASP* 3.7 11.0 + - + +
63D LEU* 3.2 35.2 + - + +
115D ILE* 4.8 1.0 - - - +
169D TYR* 5.9 1.1 - - + -
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS* 6.0 0.7 - + - -
165A HIS* 3.4 50.5 - + + -
168A HIS* 3.6 31.9 - - + -
169A TYR* 3.5 37.2 - + - -
55D VAL* 3.6 24.8 - - + +
56D GLU* 3.6 9.2 - - - +
57D GLY 3.0 23.9 + - - +
58D ALA 3.5 1.0 + - - -
59D GLU* 1.3 80.2 - - - +
61D ARG* 1.3 78.7 + - + +
63D LEU* 4.6 0.2 - - - -
64D HIS* 2.8 47.6 + + + +
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 2.4 50.0 + - - +
65A LEU* 4.2 13.1 - - - +
66A PHE* 3.8 31.9 - - - +
69A GLU* 3.9 26.3 + - - -
165A HIS* 4.8 8.0 - - + +
169A TYR* 3.0 30.4 - - + +
59D GLU 3.3 0.8 - - - -
60D PHE* 1.3 97.7 - - + +
62D ASP* 1.3 64.4 + - - +
64D HIS* 3.0 10.5 + - + +
65D LEU* 3.0 49.3 + - + +
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Residues in contact with ASP 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 3.6 19.7 + - + +
59D GLU* 3.9 11.0 - - + +
61D ARG* 1.3 79.9 - - - +
63D LEU* 1.4 55.6 + - - +
65D LEU* 3.4 9.8 + - - +
66D PHE* 2.9 26.0 + - - +
169D TYR* 2.5 35.8 + - - -
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.6 24.7 - - + -
55D VAL* 3.8 20.9 - - + -
56D GLU 5.8 0.4 - - - +
59D GLU* 3.2 28.0 + - + +
60D PHE* 4.6 0.2 - - - -
62D ASP* 1.4 73.4 - - - +
64D HIS* 1.3 61.5 + - - +
66D PHE* 4.2 5.2 - - + -
67D LEU* 2.8 39.7 + - + +
115D ILE* 3.7 22.0 - - + -
119D LEU* 4.0 21.3 - - + -
169D TYR* 3.7 39.5 - - + -
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Residues in contact with HIS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A HIS* 5.0 16.2 - + - -
83C GLU* 3.7 18.7 + - + -
52D HIS* 2.7 81.9 + + - +
53D TRP 5.3 0.6 + - - -
55D VAL* 3.7 13.8 - - + +
60D PHE* 2.8 32.7 + + + +
61D ARG* 3.0 10.5 + - + +
63D LEU* 1.3 78.3 - - - +
65D LEU* 1.3 75.0 + - + +
68D GLY 3.0 6.1 + - - -
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 5.0 0.4 - - - +
52D HIS* 6.3 0.2 - - + -
61D ARG* 3.0 51.6 + - + +
62D ASP* 3.6 11.0 - - - +
64D HIS* 1.3 88.4 - - + +
66D PHE* 1.4 70.6 + - - +
68D GLY* 3.5 1.3 + - - -
69D GLU* 3.0 39.7 + - - +
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Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ASP* 2.9 18.5 + - - +
63D LEU* 3.8 3.8 - - + +
65D LEU* 1.4 78.4 - - - +
67D LEU* 1.3 78.1 + - + +
69D GLU* 3.1 12.3 + - + +
70D ALA* 2.9 38.4 + - + +
119D LEU* 5.6 0.7 - - + -
162D ASP* 3.7 34.1 - - + -
165D HIS* 3.5 37.5 - + + -
166D ILE* 3.7 21.1 - - + -
169D TYR* 3.5 30.3 - + - +
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.7 30.6 - - + +
51D HIS* 3.6 35.2 - - + +
52D HIS* 3.7 17.9 - - + +
55D VAL* 4.3 4.5 - - + -
63D LEU* 2.8 37.7 + - + +
66D PHE* 1.3 89.2 - - + +
68D GLY* 1.3 60.5 + - - +
70D ALA* 3.9 3.0 - - - +
71D ALA* 2.8 30.3 + - - +
115D ILE* 4.5 0.9 - - + -
119D LEU* 4.1 23.3 - - + -
122D ASP* 4.3 4.0 - - - +
166D ILE* 5.3 1.1 - - + -
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LYS* 5.7 3.2 + - - -
52D HIS* 3.3 25.5 + - - -
64D HIS 3.0 10.8 + - - -
65D LEU* 3.6 4.9 - - - -
67D LEU* 1.3 75.1 - - - +
69D GLU* 1.3 61.3 + - - +
71D ALA* 3.4 6.0 + - - +
72D GLU* 3.0 22.3 + - - +
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU* 3.0 30.4 + - - +
66D PHE* 3.6 13.3 - - + +
68D GLY* 1.3 76.3 - - - +
70D ALA* 1.3 57.4 + - - +
72D GLU* 3.1 17.6 + - - +
73D THR* 2.8 31.4 + - - +
162D ASP* 5.0 0.2 - - - -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.7 10.2 - - + +
66D PHE* 2.9 30.0 + - + +
67D LEU* 3.3 6.7 + - - +
69D GLU* 1.3 76.7 - - - +
71D ALA* 1.3 50.7 + - - +
73D THR* 3.1 3.3 + - - +
74D ALA* 2.7 35.7 + - - +
126D TYR* 3.4 22.8 + - - +
162D ASP* 3.5 25.0 - - - +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D TYR* 3.1 18.6 - - + -
48D LEU* 3.7 21.3 - - + +
49D LYS* 3.7 31.9 - - + +
67D LEU 2.8 18.5 + - - +
68D GLY* 3.4 6.3 - - - +
70D ALA* 1.3 73.0 - - - +
72D GLU* 1.3 56.2 + - - +
74D ALA* 3.3 2.8 + - - +
75D GLU* 2.7 30.1 + - - +
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Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C FE 3.9 11.1 - - - -
68D GLY 3.0 14.3 + - - +
69D GLU* 3.1 20.0 + - - +
71D ALA* 1.3 71.0 - - - +
73D THR* 1.3 68.7 + - - +
75D GLU* 3.1 4.3 + - - +
76D GLU* 3.0 44.1 + - + +
323D FE 3.5 25.4 - - - -
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLU* 2.8 19.1 + - - +
70D ALA 3.4 7.9 - - - +
72D GLU* 1.3 74.1 - - - +
74D ALA* 1.4 64.8 + - - +
76D GLU* 3.1 13.1 + - - +
77D VAL* 2.8 31.0 + - + +
158D GLU* 3.7 36.3 + - + +
159D LEU* 4.5 6.7 - - + -
162D ASP* 3.6 17.1 + - - +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D VAL* 3.2 17.0 - - + +
44D LEU* 4.0 22.2 - - + -
45D TYR* 3.9 25.4 - - + +
48D LEU* 4.1 2.9 - - + -
70D ALA 2.7 20.1 + - - +
71D ALA 3.5 5.6 - - - +
73D THR* 1.4 74.4 - - - +
75D GLU* 1.3 57.3 + - - +
77D VAL* 3.2 4.3 + - - +
78D ALA* 2.9 24.3 + - - +
159D LEU* 4.8 4.5 - - - +
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Residues in contact with GLU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 2.5 33.3 + - - +
49C LYS* 4.2 10.9 + - - +
75C GLU* 2.8 14.2 - - - +
311C FE 3.2 2.1 - - - -
42D TYR* 4.1 5.1 + - - +
45D TYR* 3.5 14.8 - - + -
71D ALA 2.7 21.0 + - - +
72D GLU* 3.1 6.4 + - - +
74D ALA* 1.3 73.0 - - - +
76D GLU* 1.3 52.6 + - - +
78D ALA* 3.1 8.5 + - - +
79D ASP* 2.7 35.4 + - - +
312D FE 2.5 23.6 - - - -
323D FE 2.2 29.3 - - - -
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Residues in contact with GLU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLU* 3.0 39.5 + - + +
73D THR* 3.5 12.0 + - + +
75D GLU* 1.3 74.7 - - + +
77D VAL* 1.4 62.4 + - + +
79D ASP* 3.1 8.4 + - - +
80D GLU* 2.8 36.3 + - + +
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Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D VAL* 4.2 13.9 - - + -
73D THR* 2.8 25.8 + - + +
74D ALA* 3.6 7.0 - - - +
76D GLU* 1.4 76.4 - - + +
78D ALA* 1.3 64.1 + - - +
80D GLU* 3.2 8.2 + - + +
81D LEU* 3.0 44.4 + - + +
155D GLY* 4.2 26.5 - - - +
158D GLU* 5.0 2.5 - - + -
159D LEU* 4.0 29.4 - - + -
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TRP* 5.1 0.7 - - - -
38D LEU* 3.3 19.7 - - + +
41D VAL* 3.8 15.7 - - + -
42D TYR* 3.8 34.5 - - + -
45D TYR* 5.9 0.2 - - + -
74D ALA 2.9 13.7 + - - +
75D GLU* 3.1 9.2 + - - +
77D VAL* 1.3 76.3 - - - +
79D ASP* 1.3 59.5 + - - +
81D LEU* 3.2 4.5 + - - -
82D ALA* 2.7 28.3 + - - +
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Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LYS* 3.1 23.9 + - - +
53C TRP* 2.9 27.2 + - - +
42D TYR* 5.5 0.4 + - - -
75D GLU 2.7 16.9 + - - +
76D GLU* 3.1 12.5 + - - +
78D ALA* 1.3 75.7 - - - +
80D GLU* 1.3 66.1 + - + +
82D ALA* 3.8 0.2 - - - +
83D GLU* 2.9 36.8 + - - +
301D FE 2.3 31.8 - - - -
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLU* 2.8 27.0 + - + +
77D VAL* 3.7 6.5 - - + +
79D ASP* 1.3 78.5 - - + +
81D LEU* 1.3 56.7 + - + +
83D GLU* 3.9 6.5 - - - +
84D ARG* 2.9 30.7 + - - +
151D MET* 3.7 38.8 - - + +
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LEU* 3.8 24.1 - - + +
37D ASP* 3.8 29.8 - - + -
38D LEU* 4.2 12.8 - - + +
41D VAL* 4.4 4.5 - - + -
77D VAL* 3.0 41.7 + - + +
78D ALA* 3.4 11.7 - - - +
80D GLU* 1.3 71.4 - - + +
82D ALA* 1.3 66.1 + - - +
84D ARG* 3.4 5.0 + - - +
85D VAL* 2.9 28.9 + - - +
151D MET* 4.8 7.4 - - + -
152D LEU* 3.7 30.3 - - + -
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TRP* 3.3 41.1 - - + +
38D LEU* 3.8 10.8 - - + -
78D ALA 2.7 19.2 + - - +
79D ASP 3.8 0.2 - - - +
81D LEU* 1.3 73.8 - - - +
83D GLU* 1.4 61.2 + - - +
85D VAL* 3.3 4.1 + - - +
86D GLN* 3.0 27.0 + - - +
92D PRO* 3.6 21.7 - - + +
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C HIS* 2.8 17.0 + - - -
53C TRP* 3.4 20.6 - - + +
64C HIS* 3.4 14.9 + - + -
79D ASP* 2.9 28.4 + - - +
80D GLU* 4.0 6.9 - - - +
82D ALA* 1.4 74.6 - - - +
84D ARG* 1.3 56.0 + - - +
86D GLN* 3.1 7.9 + - + +
87D ALA* 2.8 29.8 + - - +
301D FE 2.1 27.3 - - - -
325D FE 3.5 6.9 - - - -
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Residues in contact with ARG 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.9 23.6 - - - +
22D MET* 4.6 2.4 - - - +
34D LEU* 3.6 22.7 - - + -
80D GLU 2.9 19.0 + - - +
81D LEU 3.7 3.4 - - - +
83D GLU* 1.3 73.4 - - - +
85D VAL* 1.3 67.5 + - - +
87D ALA* 3.1 8.8 + - - +
88D LEU* 2.9 39.3 + - + +
145D ASP* 2.8 31.1 + - - -
147D ALA* 3.4 23.3 - - - +
148D THR* 2.7 18.6 + - + +
151D MET* 3.6 29.7 - - + +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D VAL* 4.0 21.4 - - + +
34D LEU* 3.5 28.2 - - + +
35D ASN* 3.9 19.7 - - - +
38D LEU* 5.2 0.9 - - + -
81D LEU 2.9 20.6 + - - +
82D ALA* 3.4 9.0 - - - +
84D ARG* 1.3 78.3 - - - +
86D GLN* 1.3 62.6 + - - +
88D LEU* 3.3 6.1 + - - +
89D GLY 3.3 0.2 + - - -
90D GLY* 2.9 30.2 + - - -
91D VAL 3.6 9.0 - - - +
92D PRO* 3.4 30.7 - - + -
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TRP* 3.4 22.0 + - + +
54C ASN* 3.3 31.6 - - - +
55C VAL 5.8 0.4 + - - -
56C GLU* 2.9 12.5 - - - +
82D ALA 3.0 13.2 + - - +
83D GLU* 3.5 9.4 - - - +
84D ARG 3.1 0.4 - - - -
85D VAL* 1.3 77.0 - - - +
87D ALA* 1.3 59.7 + - - +
89D GLY* 2.9 20.6 + - - -
90D GLY 3.7 12.1 - - - +
92D PRO* 4.3 4.3 - - + -
314D FE 2.2 36.1 - - - -
325D FE 3.1 20.7 - - - -
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D SER* 3.3 22.9 - - - -
20D LEU* 3.6 22.2 - - + +
83D GLU 2.8 16.6 + - - +
84D ARG* 3.1 17.4 + - - +
86D GLN* 1.3 82.6 - - - +
88D LEU* 1.3 56.4 + - - +
89D GLY* 3.2 1.3 + - - -
325D FE 4.1 8.1 - - - -
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D VAL* 3.6 3.8 - - - +
16D GLY* 3.0 29.7 + - - -
17D SER* 4.7 0.2 - - - -
20D LEU* 4.4 10.5 - - + -
22D MET* 3.9 36.6 - - + -
27D ALA* 3.4 16.7 - - + +
30D CYS* 3.8 28.7 - - + -
31D VAL* 4.0 10.5 - - + -
34D LEU* 4.0 13.9 - - + -
84D ARG* 2.9 43.7 + - + +
85D VAL 4.0 2.9 - - - +
86D GLN 3.2 0.2 - - - -
87D ALA* 1.3 75.0 - - - +
89D GLY* 1.3 58.3 + - - +
90D GLY 3.4 2.2 - - - -
145D ASP* 4.0 6.5 - - - +
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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