Contacts of the helix formed by residues 60 - 83 (chain D) in PDB entry 3IT8
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 PRO 60 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 3.7 28.0 - - + +
7D TYR* 5.3 2.5 - - - +
53D ILE* 5.1 4.7 - - - +
58D HIS 3.6 7.7 - - - +
59D THR* 1.3 98.3 - - + +
61D GLY* 1.3 63.6 + - - +
63D ASP* 4.6 0.5 + - - -
64D TYR* 3.4 32.2 + - + +
65D ASN* 3.8 15.5 - - - +
154D TYR 6.0 1.1 - - - +
158D PHE* 4.1 16.4 - - + -
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D THR 3.5 2.3 + - - -
60D PRO* 1.3 73.0 - - - +
62D ASN* 1.3 77.8 + - - +
63D ASP 3.2 1.6 - - - -
65D ASN* 2.9 23.8 + - - +
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Residues in contact with ASN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLY* 1.3 74.1 - - - +
63D ASP* 1.3 79.1 + - - +
65D ASN* 2.9 26.5 + - - +
66D PHE* 3.4 5.9 + - - +
67D ASN* 5.0 6.1 + - - +
154D TYR* 5.0 4.6 + - - -
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Residues in contact with ASP 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 3.6 17.0 - - + +
42D GLY 5.2 7.8 - - - +
43D ASN* 6.3 0.7 - - - -
44D VAL* 3.6 24.0 - - - +
47D ARG* 4.9 6.6 + - - +
60D PRO 4.6 0.4 + - - -
61D GLY 3.2 0.8 - - - -
62D ASN* 1.3 81.6 - - - +
64D TYR* 1.3 77.5 + - - +
66D PHE* 3.0 20.6 + - + +
67D ASN* 5.9 0.5 + - - -
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Residues in contact with TYR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 3.7 16.2 - + - -
7D TYR* 2.7 36.5 + - + +
21D PHE* 3.2 33.9 - + + -
23D ASP* 2.9 30.3 + - - -
31D THR* 3.0 34.5 + - + -
33D ILE* 3.8 5.6 - - + -
47D ARG* 3.5 11.4 + - - -
51D PHE* 4.1 4.9 - - - -
53D ILE* 4.0 12.9 - - + +
59D THR* 3.4 27.6 - - + +
60D PRO* 3.4 17.7 + - + -
61D GLY 3.2 6.5 + - - -
62D ASN 3.2 0.6 - - - -
63D ASP* 1.3 81.3 - - - +
65D ASN* 1.3 73.5 + - - +
66D PHE 3.0 0.7 + - - -
170D TYR* 4.0 0.9 + - - -
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Residues in contact with ASN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D PRO* 3.8 18.0 - - - +
61D GLY 2.9 21.9 + - - +
62D ASN* 2.9 27.2 + - - +
64D TYR* 1.3 75.8 - - - +
66D PHE* 1.3 63.4 - - - +
67D ASN 3.5 2.5 - - - -
68D PHE* 3.3 13.9 + - + +
69D TRP* 3.1 35.2 + - + +
154D TYR* 3.5 45.5 + - + +
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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
----------------------------------------------------------
7D TYR* 4.5 14.1 - + + -
19D GLY* 3.9 12.8 - - - -
20D VAL 3.9 12.1 - - - -
21D PHE* 3.7 28.3 - - + -
33D ILE* 3.6 20.0 - - + -
34D SER 4.1 1.6 - - - -
35D TYR* 3.8 28.5 - + + -
42D GLY* 3.7 31.6 - - - -
62D ASN 3.4 3.3 + - - +
63D ASP* 3.0 21.5 + - + +
64D TYR* 3.0 3.5 - - + -
65D ASN* 1.3 73.4 - - - +
67D ASN* 1.3 67.8 + - - +
69D TRP* 3.2 1.2 + - - +
70D TYR* 2.7 51.6 + - + +
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Residues in contact with ASN 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TYR* 5.4 1.4 - - - -
40D ARG 5.7 0.2 - - - -
41D HIS* 3.6 19.3 + - - +
42D GLY* 3.0 28.6 + - - -
62D ASN* 5.0 6.8 + - - +
63D ASP* 5.9 1.0 + - - -
65D ASN 3.5 0.6 - - - -
66D PHE* 1.3 81.0 - - - +
68D PHE* 1.3 63.7 + - - +
70D TYR* 3.9 5.0 - - - +
71D SER* 3.1 26.7 + - - -
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Residues in contact with PHE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ASN* 3.3 16.0 + - + +
66D PHE 3.1 0.6 - - - -
67D ASN* 1.3 79.9 - - - +
69D TRP* 1.3 99.0 + + - +
71D SER* 3.8 2.7 - - - -
72D LEU* 3.0 48.1 + - + +
147D LEU* 4.2 21.9 - - + +
150D ASP* 3.5 37.5 - - + -
151D VAL* 4.2 5.8 - - + -
154D TYR* 3.7 28.3 - + + -
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Residues in contact with TRP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TYR* 3.5 48.9 + + + -
64D TYR 3.8 1.6 - - - -
65D ASN* 3.1 32.2 + - + +
66D PHE 3.9 0.4 - - - +
68D PHE* 1.3 98.6 - + - +
70D TYR* 1.3 68.2 + - - +
72D LEU* 4.4 11.0 - - + +
73D MET* 2.7 45.9 + - + +
93D LEU* 3.7 30.3 - - + -
140D MET* 4.2 16.8 - - - -
151D VAL* 4.2 16.6 - - + -
154D TYR* 3.7 27.2 - - + +
155D LEU* 3.9 24.0 - - + -
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Residues in contact with TYR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR* 5.6 0.4 - - - -
9D VAL* 3.9 16.9 - - + +
17D TYR* 2.6 37.7 + - + +
18D ASP 4.0 3.1 - - - -
19D GLY* 3.8 26.5 - - - -
35D TYR* 3.5 57.4 - + + -
37D HIS* 4.3 1.2 - - - -
66D PHE* 2.7 37.6 + + + +
67D ASN* 3.9 4.3 - - - +
69D TRP* 1.3 72.5 - - - +
71D SER* 1.3 64.8 + - - +
73D MET* 3.7 1.7 - - - +
74D LYS* 2.8 56.2 + - + +
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ASN 3.1 15.7 + - - -
68D PHE* 3.8 3.6 - - - -
70D TYR* 1.3 88.6 - - - +
72D LEU* 1.3 58.0 + - - +
74D LYS* 3.2 8.2 + - - +
75D GLU* 3.0 27.3 + - - +
147D LEU* 6.2 0.3 - - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D PHE* 3.0 48.8 + - + +
69D TRP* 4.0 7.6 - - + +
71D SER* 1.3 76.5 + - - +
73D MET* 1.3 59.0 + - - +
75D GLU* 3.5 16.6 + - - +
76D THR* 2.9 28.9 + - - -
140D MET* 3.6 31.0 - - + +
145D ASN* 3.8 25.4 - - - +
147D LEU* 4.3 20.2 - - + -
151D VAL* 3.7 14.1 - - + -
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Residues in contact with MET 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TYR* 3.7 36.8 - - - +
9D VAL* 3.7 20.8 - - + +
69D TRP* 2.7 42.3 + - + +
70D TYR* 5.3 0.2 - - - -
72D LEU* 1.3 70.5 - - - +
74D LYS* 1.3 60.6 + - - +
76D THR* 3.2 1.6 + - - -
77D LEU* 2.8 31.4 + - - +
91D LEU* 3.4 39.4 - - + +
92D SER* 3.9 1.3 - - - -
93D LEU* 3.8 17.0 - - - +
140D MET* 3.2 30.1 - - + -
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Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.3 9.8 - - + +
17D TYR* 3.9 34.3 - - + +
35D TYR* 5.9 0.8 + - - -
70D TYR* 2.8 46.9 + - + +
71D SER* 3.4 7.9 - - - +
73D MET* 1.3 78.6 - - - +
75D GLU* 1.3 62.2 + - - +
77D LEU* 3.2 4.0 + - - +
78D GLU* 3.0 46.8 + - - +
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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
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71D SER 3.0 13.3 + - - +
72D LEU* 3.5 20.7 - - - +
74D LYS* 1.3 76.1 - - - +
76D THR* 1.3 61.0 + - - +
78D GLU* 3.2 12.6 + - - +
79D GLU* 3.1 39.1 + - + +
139D GLY* 3.9 8.2 + - - -
145D ASN* 3.2 25.4 + - - +
146D THR* 6.0 1.4 - - - +
147D LEU* 5.3 4.3 - - - +
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D LEU 2.9 15.9 + - - -
73D MET* 3.6 5.6 - - - -
75D GLU* 1.3 77.4 - - - +
77D LEU* 1.3 62.4 + - - +
79D GLU* 3.4 2.9 + - - +
80D ILE* 3.0 35.7 + - + +
91D LEU* 3.5 21.3 - - + -
110D VAL* 6.1 0.2 - - + -
138D VAL* 4.2 16.4 - - + +
139D GLY* 3.3 7.5 - - - -
140D MET* 2.8 38.0 + - + +
141D LEU* 4.5 7.0 - - + -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.6 36.8 - - + +
11D LEU* 4.5 1.3 - - + +
17D TYR* 3.8 22.9 - - + -
73D MET 2.8 20.1 + - - +
74D LYS 3.2 4.5 + - - +
76D THR* 1.3 73.1 - - - +
78D GLU* 1.3 63.4 + - - +
80D ILE* 3.3 10.1 + - + +
81D ASN* 3.0 47.7 + - - +
88D THR* 3.9 16.2 - - - +
89D THR 4.1 7.4 - - - +
90D SER* 4.1 21.8 - - - +
91D LEU* 4.0 10.3 - - + +
112D THR* 6.1 0.2 - - - +
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Residues in contact with GLU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D TYR* 3.4 30.1 - - + +
74D LYS* 3.0 46.5 + - - +
75D GLU* 3.5 11.2 - - - +
77D LEU* 1.3 76.1 - - - +
79D GLU* 1.3 68.6 + - + +
81D ASN* 3.1 15.3 + - - +
82D LYS* 3.4 17.3 + - - +
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Residues in contact with GLU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D GLU* 3.1 29.1 + - + +
76D THR 3.8 1.8 - - - +
78D GLU* 1.3 77.8 - - - +
80D ILE* 1.3 62.7 + - - +
82D LYS* 3.0 52.5 + - - +
83D ASN* 4.2 2.3 + - - +
138D VAL* 3.6 36.1 - - + +
139D GLY 4.4 7.8 + - - +
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Residues in contact with ILE 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D THR* 3.0 36.4 + - + +
77D LEU* 3.5 10.8 - - + +
78D GLU 3.3 0.2 - - - -
79D GLU* 1.3 76.3 - - - +
81D ASN* 1.3 66.1 - - - +
82D LYS 3.4 0.9 + - - -
83D ASN* 3.6 6.4 + - - +
86D THR* 3.4 48.5 - - + +
87D LYS 3.9 0.2 + - - -
88D THR* 4.4 7.2 - - - +
91D LEU* 4.1 15.5 - - + -
112D THR* 4.7 2.9 - - - +
117D LEU* 4.1 26.9 - - + -
136D PRO* 4.0 13.5 - - + -
138D VAL* 4.0 14.8 - - + -
141D LEU* 4.9 1.3 - - + -
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Residues in contact with ASN 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 3.9 18.5 - - - +
17D TYR* 4.5 6.0 + - - +
77D LEU* 3.0 40.9 + - - +
78D GLU* 3.1 6.9 + - - +
80D ILE* 1.3 77.7 - - - +
82D LYS* 1.3 63.3 + - - +
83D ASN 3.4 5.3 - - - +
84D ASP* 4.2 0.7 + - - -
87D LYS* 3.0 32.7 - - + +
88D THR* 2.6 39.8 + - - +
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D GLU* 3.4 14.6 + - - +
79D GLU* 3.0 38.8 + - - +
81D ASN* 1.3 75.4 - - - +
83D ASN* 1.3 60.5 + - - +
84D ASP* 3.0 10.2 + - - +
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLU 4.2 2.7 + - - +
80D ILE 3.6 5.2 + - - +
81D ASN 3.4 0.6 - - - -
82D LYS* 1.3 75.2 - - - +
84D ASP* 1.3 55.3 + - - +
85D SER* 2.7 34.9 + - - -
86D THR* 2.8 28.6 + - - +
87D LYS 3.5 6.1 + - - -
327D NAG 1.5 65.8 + - - +
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il