Contacts of the helix formed by residues 66 - 90 (chain B) in PDB entry 1WB7
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 ASP 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ARG* 5.0 0.8 - - - +
65B TYR* 1.3 83.0 + - - +
67B ILE* 1.3 60.0 + - - +
68B GLN* 3.3 3.1 - - + +
69B GLY* 2.8 26.5 + - - +
70B ILE* 3.4 11.2 + - - +
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.2 22.2 - - + -
55B VAL* 4.8 4.9 - - + -
65B TYR* 3.7 29.7 + - + -
66B ASP* 1.3 71.7 - - - +
68B GLN* 1.3 70.6 + - + +
70B ILE* 3.1 10.2 + - + +
71B ILE* 2.8 48.0 + - + +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASP* 3.1 2.3 + - + -
67B ILE* 1.3 91.0 - - + +
69B GLY* 1.3 58.2 + - - +
71B ILE* 4.6 16.5 - - - +
72B ARG* 2.9 49.5 + - - +
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.9 2.9 - - - +
66B ASP* 2.8 15.0 + - - +
68B GLN* 1.3 78.6 - - - +
70B ILE* 1.3 57.2 + - - +
72B ARG* 5.0 1.1 - - - -
73B GLY* 3.0 24.4 + - - -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.1 21.4 - - + +
51B ARG* 4.0 33.4 - - + +
52B LEU* 4.1 23.3 - - + -
55B VAL* 3.9 27.4 - - + -
65B TYR* 4.2 17.5 - - + -
66B ASP 3.4 7.4 + - - +
67B ILE* 3.1 12.2 + - + +
69B GLY* 1.3 75.0 - - - +
71B ILE* 1.3 60.8 + - + +
73B GLY* 3.3 1.4 + - - -
74B LEU* 2.9 50.2 + - + +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.7 20.0 - - + -
67B ILE* 2.8 46.0 + - + +
68B GLN* 4.3 16.2 - - - +
70B ILE* 1.3 73.2 - - - +
72B ARG* 1.3 62.7 + - - +
74B LEU* 3.2 10.7 + - + +
75B THR* 3.1 21.5 + - - +
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO* 4.5 11.5 - - + +
153A GLU* 2.7 42.5 + - - -
68B GLN* 2.9 32.8 + - - +
69B GLY* 4.5 1.6 - - - +
71B ILE* 1.3 77.6 - - - +
73B GLY* 1.3 65.8 + - - +
75B THR* 3.1 17.8 - - + +
76B PHE* 3.1 22.0 + - - +
156B PHE* 3.5 28.0 - - + -
157B GLN* 4.0 9.3 - - - +
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO* 5.9 3.1 - - - -
48B LEU* 3.3 16.8 - - - -
69B GLY 3.0 20.1 + - - -
72B ARG* 1.3 77.1 - - - +
74B LEU* 1.3 56.9 + - - +
76B PHE* 3.6 6.0 - - - +
77B ASN* 2.9 37.4 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 3.6 15.7 - - - +
48B LEU* 3.5 24.2 - - + +
49B LEU* 4.1 20.4 - - + +
52B LEU* 3.8 30.5 - - + -
70B ILE* 2.9 29.2 + - + +
71B ILE* 3.5 12.8 - - + +
72B ARG 3.1 0.2 - - - -
73B GLY* 1.3 75.1 - - - +
75B THR* 1.3 59.1 + - - +
77B ASN* 4.9 0.4 - - - -
78B ILE* 2.8 57.0 + - + +
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Residues in contact with THR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 3.1 12.2 + - - +
72B ARG* 3.1 26.2 - - + +
74B LEU* 1.3 77.2 - - - +
76B PHE* 1.3 66.5 + - - +
78B ILE* 4.8 2.7 - - - -
79B ASN* 2.9 46.1 + - - +
156B PHE* 3.5 29.5 + - + +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PRO* 3.7 24.7 - - + -
132A GLY* 3.4 30.1 - - - -
41B PHE* 3.8 24.9 - + - -
72B ARG 3.1 14.0 + - - +
73B GLY* 3.6 5.2 - - - +
75B THR* 1.3 83.2 - - - +
77B ASN* 1.3 78.0 + - - +
80B GLY* 2.9 25.1 + - - -
154B ASN* 3.2 27.4 - - - -
155B HIS* 3.4 16.8 - + - +
156B PHE* 3.6 21.5 - + + -
172B PHE* 5.7 0.7 - + - -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLY 4.0 1.7 - - - +
41B PHE* 3.6 30.4 - - - +
44B GLY* 3.7 21.1 - - - -
45B ALA* 3.5 22.2 - - - +
48B LEU* 3.5 15.6 - - - +
73B GLY* 2.9 24.4 + - - +
74B LEU 4.3 0.4 - - - +
76B PHE* 1.3 92.1 - - - +
78B ILE* 1.3 61.9 + - - +
80B GLY* 3.6 0.5 - - - -
81B HIS* 2.9 29.1 + - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 3.6 35.9 - - + +
45B ALA* 4.1 12.3 - - + -
49B LEU* 5.2 4.7 - - + -
74B LEU* 2.8 47.4 + - + +
75B THR* 4.5 2.9 - - - +
77B ASN* 1.3 70.8 - - - +
79B ASN* 1.3 60.4 + - - +
81B HIS* 3.2 5.5 + - - +
82B LYS* 2.8 56.2 + - + +
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B THR* 2.9 40.9 + - - +
78B ILE* 1.3 79.0 - - - +
80B GLY* 1.3 61.1 + - - +
82B LYS* 4.4 10.3 - - - +
83B LEU* 2.8 41.1 + - + +
155B HIS* 3.3 26.7 - - + +
156B PHE* 3.5 12.1 + - - +
159B HIS* 3.1 22.0 + - - -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.7 20.5 - - - -
76B PHE 2.9 19.6 + - - -
77B ASN 3.2 2.9 + - - -
79B ASN* 1.3 80.0 - - - +
81B HIS* 1.3 60.1 - - - +
84B HIS* 2.5 32.0 + - - -
155B HIS* 3.9 16.6 - - - +
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Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 3.7 35.9 - + + +
10B GLU 3.4 26.3 + - - -
12B PRO* 3.6 9.6 - - + -
38B HIS* 2.8 41.9 + + - +
41B PHE* 3.6 9.5 - - + +
42B VAL* 3.6 18.4 - - + +
45B ALA* 5.6 1.3 - - + -
77B ASN 2.9 13.2 + - - +
78B ILE* 3.5 7.6 - - - +
80B GLY* 1.3 75.2 - - - +
82B LYS* 1.3 78.5 + - + +
84B HIS 3.3 1.2 + - - -
85B ALA* 3.0 25.3 + - + +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 4.2 19.9 + - - -
78B ILE* 2.8 43.9 + - + +
79B ASN* 4.1 11.0 - - - +
81B HIS* 1.3 83.3 - - + +
83B LEU* 1.3 61.4 + - + +
85B ALA* 3.2 7.8 + - - +
86B LEU* 3.0 35.4 + - + +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASN* 2.8 29.5 + - + +
80B GLY 4.5 0.2 - - - +
82B LYS* 1.3 71.4 - - + +
84B HIS* 1.3 60.3 + - - +
86B LEU* 3.3 7.9 + - + +
87B TYR* 2.8 27.0 + - - +
135B TRP* 3.6 44.4 - - + +
152B PHE* 3.9 14.8 - - + -
155B HIS* 3.4 27.1 - - + +
159B HIS* 4.2 6.3 - - + -
165B ILE* 3.8 21.5 - - + -
168B ILE* 3.6 23.0 - - + +
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Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B HIS* 3.2 22.9 + + - -
37B HIS* 4.8 0.4 - - - +
38B HIS* 3.6 25.8 - + + +
41B PHE* 3.4 25.9 - + - -
80B GLY 2.5 24.8 + - - +
81B HIS 3.3 2.2 + - - +
83B LEU* 1.3 74.6 - - - +
85B ALA* 1.3 65.9 + - - +
87B TYR* 3.0 7.4 + + - +
88B TRP* 2.9 40.3 + + - +
135B TRP* 3.5 20.2 - + - -
155B HIS* 3.7 9.2 - + - -
170B ASP* 3.5 2.7 + - - -
174B HIS* 3.7 2.6 + - - -
211B FE 2.1 30.8 - - - -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PRO* 4.1 15.2 - - + +
38B HIS* 3.6 15.0 - - + +
81B HIS* 3.0 21.2 + - + +
82B LYS* 3.4 12.6 - - - +
84B HIS* 1.3 77.1 - - - +
86B LEU* 1.3 62.3 + - + +
88B TRP* 4.0 5.7 - - - +
89B GLU* 3.5 26.9 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LYS* 3.0 20.3 + - + +
83B LEU* 3.6 14.4 - - + +
85B ALA* 1.3 75.4 - - + +
87B TYR* 1.3 60.1 + - - +
89B GLU* 3.3 6.7 + - + +
90B ASN* 2.9 31.2 + - - +
165B ILE* 3.7 40.2 - - + -
168B ILE* 3.8 11.7 - - + -
203B LYS* 3.5 23.8 - - + +
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.8 17.7 - - + +
30B ILE* 5.7 1.1 - - + +
33B HIS* 3.6 19.8 - + - -
83B LEU 2.8 14.2 + - - +
84B HIS* 3.0 13.4 + + - +
86B LEU* 1.3 76.8 - - - +
88B TRP* 1.3 96.3 + + - +
90B ASN* 3.1 11.8 + - - +
91B MET* 3.4 41.0 + - + +
135B TRP* 3.9 9.4 - + + -
168B ILE* 3.7 25.1 - - - +
170B ASP* 3.5 32.4 - - + +
175B ALA* 4.3 4.5 + - - +
187B TYR* 2.8 22.1 + - - -
191B TRP* 4.4 5.3 - - - -
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Residues in contact with TRP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PRO* 5.0 4.5 - - + -
13B PRO 5.8 0.4 - - - -
14B LEU* 3.8 14.4 - - + -
15B PRO* 3.8 21.8 - - + -
16B TYR* 2.7 29.2 + + - +
30B ILE* 4.1 22.0 - - + -
33B HIS* 3.5 42.0 - + + -
34B TYR* 3.7 37.9 - + + -
38B HIS* 2.8 32.6 + + - -
84B HIS* 2.9 33.7 + + + -
85B ALA* 4.0 5.8 - - - +
87B TYR* 1.3 98.7 - + - +
89B GLU* 1.3 62.6 + - + +
91B MET* 3.3 17.7 + - + +
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PRO* 6.0 1.6 - - - +
13B PRO 4.6 5.4 - - - +
15B PRO* 3.0 31.7 - - + +
85B ALA 3.5 17.2 + - - +
86B LEU* 3.3 6.8 + - + +
88B TRP* 1.3 77.1 - - + +
90B ASN* 1.3 57.8 + - - +
91B MET 3.2 5.4 + - - -
196B ASN* 3.6 19.9 + - - +
199B ALA* 3.8 10.9 - - + +
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU 2.9 17.7 + - - +
87B TYR* 3.1 7.3 + - - +
89B GLU* 1.3 77.3 - - - +
91B MET* 1.3 55.2 + - + +
166B ILE 3.1 22.1 + - - -
167B LEU* 3.3 17.0 - - - +
168B ILE* 2.9 43.1 + - + +
191B TRP* 4.3 2.1 + - - -
195B VAL* 3.6 5.4 - - - +
196B ASN* 2.7 39.4 + - - +
199B ALA* 5.4 1.6 - - - +
200B ALA* 4.6 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
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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