Contacts of the helix formed by residues 60 - 83 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E TYR* 3.7 27.4 - - + +
7E TYR* 5.3 2.5 - - - +
53E ILE* 5.1 4.9 - - - +
58E HIS 3.5 6.9 - - - +
59E THR* 1.3 100.6 - - + +
61E GLY* 1.3 62.6 + - - +
63E ASP* 4.7 0.5 + - - -
64E TYR* 3.5 31.4 + - + +
65E ASN* 3.8 15.3 - - - +
154E TYR 6.0 0.9 - - - +
158E PHE* 4.1 16.4 - - + -
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Residues in contact with GLY 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E THR 3.5 2.9 + - - -
60E PRO* 1.3 71.6 - - - +
62E ASN* 1.3 78.1 + - - +
63E ASP 3.3 2.2 - - - -
65E ASN* 2.9 24.3 + - - +
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Residues in contact with ASN 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLY* 1.3 73.7 - - - +
63E ASP* 1.3 79.8 + - - +
65E ASN* 2.9 29.8 + - - +
66E PHE* 3.4 3.6 + - - +
67E ASN* 5.0 6.2 + - - +
154E TYR* 5.0 4.2 + - - -
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Residues in contact with ASP 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ILE* 3.6 17.8 - - + +
42E GLY* 5.2 9.1 - - - +
44E VAL* 3.6 23.3 - - - +
47E ARG* 4.9 6.5 + - - +
60E PRO 4.7 0.6 + - - -
61E GLY* 3.3 1.0 - - - -
62E ASN* 1.3 81.5 - - - +
64E TYR* 1.3 76.6 + - - +
66E PHE* 2.9 19.9 + - + +
67E ASN* 5.9 0.3 + - - -
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Residues in contact with TYR 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E TYR* 3.6 16.6 - + - -
7E TYR* 2.6 36.5 + - + +
21E PHE* 3.2 33.2 - + + -
23E ASP* 2.8 30.4 + - - -
31E THR* 3.0 34.5 + - + -
33E ILE* 3.9 5.6 - - + -
47E ARG* 3.5 12.3 + - - -
51E PHE* 4.2 5.2 - - - -
53E ILE* 4.1 12.1 - - + +
59E THR* 3.5 26.6 - - + +
60E PRO* 3.5 17.5 + - + -
61E GLY 3.3 6.3 + - - -
62E ASN 3.2 0.2 - - - -
63E ASP* 1.3 80.2 - - - +
65E ASN* 1.3 75.0 + - - +
66E PHE 3.0 0.9 + - - -
170E TYR* 4.0 0.9 + - - -
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Residues in contact with ASN 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E PRO* 3.8 17.3 - - - +
61E GLY 2.9 18.0 + - - +
62E ASN* 2.9 31.2 + - - +
64E TYR* 1.3 75.5 - - - +
66E PHE* 1.3 64.2 + - - +
67E ASN 3.5 2.0 - - - -
68E PHE* 3.3 13.7 + - + +
69E TRP* 3.1 34.6 + - + +
154E TYR* 3.5 44.6 + - + +
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Residues in contact with PHE 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 4.5 13.0 - + + -
19E GLY* 3.8 24.0 - - - -
20E VAL 3.9 13.5 - - - -
21E PHE* 3.7 27.1 - - + -
33E ILE* 3.6 21.1 - - + -
34E SER 4.1 1.6 - - - -
35E TYR* 3.8 17.7 - + + -
42E GLY* 3.7 30.5 - - - -
62E ASN 3.4 3.5 + - - +
63E ASP* 2.9 21.0 + - + +
64E TYR* 3.0 3.3 - - + +
65E ASN* 1.3 73.2 - - - +
67E ASN* 1.3 69.0 + - - +
69E TRP* 3.2 1.2 + - - +
70E TYR* 2.7 52.0 + - + +
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Residues in contact with ASN 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E TYR* 5.3 1.4 - - - -
40E ARG 5.6 0.4 - - - -
41E HIS* 3.6 19.1 - - - +
42E GLY* 3.0 28.4 + - - +
62E ASN* 5.0 6.6 + - - +
63E ASP* 5.9 0.8 + - - -
65E ASN 3.5 0.4 - - - -
66E PHE* 1.3 82.8 - - - +
68E PHE* 1.3 63.6 + - - +
70E TYR* 3.9 4.9 - - - +
71E SER* 3.1 26.5 + - - -
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Residues in contact with PHE 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ASN* 3.3 16.7 + - + +
66E PHE 3.1 0.4 - - - -
67E ASN* 1.3 79.1 - - - +
69E TRP* 1.3 105.9 + + - +
71E SER* 3.7 3.8 - - - -
72E LEU* 3.0 42.1 + - + +
147E LEU* 4.3 21.0 - - + +
150E ASP* 3.5 37.7 - - + -
151E VAL* 4.2 6.1 - - + -
154E TYR* 3.7 25.1 - + + -
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Residues in contact with TRP 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 3.5 47.8 + + + -
64E TYR 3.8 1.6 - - - -
65E ASN* 3.1 30.4 + - + +
66E PHE 3.9 0.7 - - - +
68E PHE* 1.3 100.6 - + - +
70E TYR* 1.3 68.5 + - - +
72E LEU* 4.4 12.1 - - + -
73E MET* 2.7 45.3 + - + +
93E LEU* 3.7 29.8 - - + -
140E MET* 4.2 17.0 - - - -
151E VAL* 4.2 16.8 - - + -
154E TYR* 3.7 27.5 - - + +
155E LEU* 3.9 23.1 - - + -
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Residues in contact with TYR 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 5.6 0.4 - - - -
9E VAL* 3.8 17.5 - - + +
17E TYR* 2.6 37.6 + - + +
18E ASP 4.0 3.4 - - - -
19E GLY* 3.8 25.8 - - - -
35E TYR* 3.5 55.7 - + + -
37E HIS* 4.3 1.4 - - - -
66E PHE* 2.7 36.8 + + + +
67E ASN* 3.9 4.5 - - - +
69E TRP* 1.3 72.4 - - - +
71E SER* 1.3 65.3 + - - +
73E MET* 3.8 1.3 - - - +
74E LYS* 2.8 56.0 + - + +
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Residues in contact with SER 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E ASN 3.1 15.7 + - - -
68E PHE* 3.7 4.0 - - - -
70E TYR* 1.3 89.8 - - - +
72E LEU* 1.3 56.9 + - - +
74E LYS* 3.2 8.2 + - - +
75E GLU* 3.0 26.9 + - - +
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE* 3.0 39.7 + - + +
69E TRP* 4.0 7.9 - - + +
71E SER* 1.3 76.5 + - - +
73E MET* 1.3 58.2 + - - +
75E GLU* 3.4 16.1 + - - +
76E THR* 2.9 30.2 + - - -
140E MET* 3.6 30.5 - - + +
145E ASN* 3.8 26.0 - - - +
147E LEU* 4.3 20.6 - - + +
151E VAL* 3.7 22.4 - - + -
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Residues in contact with MET 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 3.7 37.0 - - - +
9E VAL* 3.8 19.4 - - + +
69E TRP* 2.7 41.3 + - + +
72E LEU* 1.3 70.3 - - - +
74E LYS* 1.3 62.3 + - - +
76E THR* 3.6 1.4 - - - -
77E LEU* 2.8 31.5 + - - +
91E LEU* 3.3 39.1 - - + +
92E SER 3.9 1.8 - - - +
93E LEU* 3.7 16.6 - - - +
140E MET* 3.2 30.3 - - + -
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Residues in contact with LYS 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 4.4 9.8 - - + +
17E TYR* 3.9 33.2 - - + +
70E TYR* 2.8 47.4 + - + +
71E SER* 3.4 7.4 - - - +
73E MET* 1.3 77.5 - - - +
75E GLU* 1.3 62.5 + - - +
77E LEU* 3.2 3.8 + - - +
78E GLU* 3.1 47.8 + - - +
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Residues in contact with GLU 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E SER 3.0 13.6 + - - +
72E LEU* 3.5 21.0 - - - +
74E LYS* 1.3 77.1 - - - +
76E THR* 1.3 61.4 + - - +
78E GLU* 3.2 12.6 + - - +
79E GLU* 3.1 39.3 + - + +
139E GLY* 3.9 8.4 + - - -
145E ASN* 3.2 25.7 + - - -
146E THR* 6.0 1.7 - - - +
147E LEU* 5.3 4.5 - - - +
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Residues in contact with THR 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LEU 2.9 16.2 + - - -
73E MET* 3.2 6.7 + - - -
75E GLU* 1.3 77.2 - - - +
77E LEU* 1.3 60.5 + - - +
79E GLU* 3.4 3.4 + - - +
80E ILE* 3.0 34.5 + - + +
91E LEU* 3.5 20.9 - - + -
138E VAL* 4.2 16.6 - - + +
139E GLY* 3.4 8.0 - - - -
140E MET* 2.8 37.9 + - + +
141E LEU* 4.5 7.9 - - + -
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Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.6 35.7 - - + +
11E LEU* 4.5 0.7 - - + +
17E TYR* 3.8 22.2 - - + -
73E MET 2.8 19.7 + - - +
74E LYS 3.2 4.9 + - - +
76E THR* 1.3 73.3 - - - +
78E GLU* 1.3 63.5 + - - +
80E ILE* 3.3 10.3 + - + +
81E ASN* 3.0 48.2 + - - +
88E THR* 3.8 17.0 - - - +
89E THR 4.0 13.9 - - - +
90E SER* 4.1 14.4 - - - +
91E LEU* 4.1 11.2 - - + +
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Residues in contact with GLU 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E TYR* 3.3 30.3 - - + +
74E LYS* 3.1 46.1 + - - +
75E GLU* 3.5 11.3 - - - +
77E LEU* 1.3 76.1 - - - +
79E GLU* 1.3 68.4 + - - +
81E ASN* 3.1 14.0 + - - +
82E LYS* 3.4 18.4 + - - +
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Residues in contact with GLU 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E GLU* 3.1 28.7 + - + +
76E THR 3.8 1.8 - - - +
78E GLU* 1.3 77.6 - - - +
80E ILE* 1.3 63.6 + - - +
82E LYS* 3.0 51.9 + - - +
83E ASN* 4.2 2.9 + - - +
138E VAL* 3.5 35.6 - - + +
139E GLY 4.4 7.2 - - - +
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Residues in contact with ILE 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E THR* 3.0 36.3 + - + +
77E LEU* 3.6 11.2 - - + +
79E GLU* 1.3 77.4 - - - +
81E ASN* 1.3 66.6 + - - +
82E LYS 3.4 0.9 + - - -
83E ASN* 3.6 6.4 + - - +
86E THR* 3.3 48.8 + - + +
88E THR* 4.4 7.0 - - - +
91E LEU* 4.1 16.8 - - + -
112E THR* 4.7 2.5 - - - +
117E LEU* 4.1 26.0 - - + -
136E PRO* 4.0 13.5 - - + -
138E VAL* 4.0 15.0 - - + -
141E LEU* 4.9 1.1 - - + -
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Residues in contact with ASN 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 4.0 18.1 - - - +
17E TYR* 4.5 6.6 + - - +
77E LEU* 3.0 34.8 + - - +
78E GLU* 3.1 6.3 + - - +
79E GLU 3.1 0.6 - - - -
80E ILE* 1.3 76.7 - - - +
82E LYS* 1.3 64.8 + - - +
83E ASN 3.4 3.7 - - - -
84E ASP* 4.2 0.5 + - - -
87E LYS* 3.0 31.5 - - + +
88E THR* 2.6 45.6 + - - +
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Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E GLU* 3.4 14.6 + - - +
79E GLU* 3.0 39.8 + - - +
81E ASN* 1.3 76.8 - - - +
83E ASN* 1.3 61.4 + - - +
84E ASP* 3.0 9.7 + - - +
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Residues in contact with ASN 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E GLU 4.2 1.9 + - - +
80E ILE 3.6 5.9 + - - +
81E ASN 4.1 0.2 - - - -
82E LYS* 1.3 74.8 - - - +
84E ASP* 1.3 54.8 + - - +
85E SER* 2.7 36.5 + - - -
86E THR* 2.8 26.5 + - - +
87E LYS 3.5 6.2 + - - -
327E NAG 1.5 69.6 + - - +
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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) + - + + + + + -
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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