Contacts of the helix formed by residues 56 - 87 (chain B) in PDB entry 4WB7
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 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP 3.7 15.9 - - - +
53B VAL 3.2 4.5 + - - +
54B LEU 3.2 1.2 - - - -
55B SER* 1.3 80.2 + - - +
57B PRO* 1.3 63.3 - - - +
58B ARG* 3.2 32.4 + - - +
59B LYS* 3.0 28.1 + - + +
60B ARG* 2.7 34.2 + - - +
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Residues in contact with PRO 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASP* 5.9 3.8 - - - +
54B LEU 5.4 0.2 - - - +
55B SER 3.5 9.6 - - - +
56B ASP* 1.3 87.8 - - - +
58B ARG* 1.3 57.6 + - - +
60B ARG* 3.7 9.2 - - + +
61B GLU* 2.9 31.5 + - - +
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP* 3.2 25.0 + - - +
57B PRO* 1.3 80.0 - - - +
59B LYS* 1.3 90.4 + - - +
61B GLU* 3.2 13.8 + - - +
62B ILE* 3.1 39.0 + - + +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 4.0 25.5 + - - +
53B VAL* 3.6 28.8 - - + +
56B ASP* 3.0 18.2 + - + +
58B ARG* 1.3 102.5 - - - +
60B ARG* 1.3 66.0 + - - +
62B ILE* 3.5 9.8 + - + +
63B PHE* 3.1 23.4 + - - +
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 3.0 24.7 + - - +
12B ARG 3.2 24.5 + - - -
13B GLY* 3.8 2.8 - - - -
14B ALA 2.7 33.5 + - - +
15B SER* 4.8 0.6 - - - +
16B ASP* 4.1 13.1 + - - -
19B ILE* 3.8 16.4 - - - +
53B VAL* 3.4 8.2 + - - +
54B LEU* 3.5 26.7 - - + +
56B ASP 2.7 20.9 + - - +
57B PRO* 3.7 8.7 - - - +
59B LYS* 1.3 73.4 - - - +
61B GLU* 1.3 51.3 + - - +
63B PHE* 3.2 6.4 + - - +
64B ASP* 2.8 43.1 + - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO 2.9 16.6 + - - +
58B ARG* 3.4 15.0 - - - +
60B ARG* 1.3 73.8 - - - +
62B ILE* 1.3 65.0 + - + +
64B ASP* 3.1 8.2 + - - +
65B ARG* 2.5 75.8 + - + +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG* 3.1 28.9 + - + +
59B LYS* 3.7 10.3 - - + +
61B GLU* 1.3 82.9 - - + +
63B PHE* 1.3 63.8 + - - +
65B ARG* 3.5 17.3 + - - +
66B TYR* 3.3 19.8 + - - +
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS 4.3 8.5 - - - -
3B ASP* 4.0 14.4 - - - -
4B TYR* 3.5 52.0 - + + -
5B TYR* 3.6 38.8 - + - -
12B ARG* 3.9 14.3 + - - -
53B VAL* 4.4 9.0 - - + -
54B LEU* 4.4 6.3 - - + -
59B LYS 3.1 17.4 + - - +
60B ARG* 3.6 3.4 - - - +
62B ILE* 1.3 76.5 - - - +
64B ASP* 1.3 66.8 + - - +
66B TYR* 3.5 21.3 + + + +
67B GLY 3.3 14.9 + - - -
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 2.9 38.1 + - - -
12B ARG* 4.4 16.7 + - - +
60B ARG* 2.8 32.9 + - - +
61B GLU* 3.7 7.4 - - - +
63B PHE* 1.3 74.9 - - - +
65B ARG* 1.3 60.3 + - + +
67B GLY* 3.1 3.2 + - - +
68B GLU* 3.0 32.5 + - + +
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 2.5 53.7 + - + +
62B ILE* 3.8 16.0 - - - +
63B PHE 3.4 0.2 - - - -
64B ASP* 1.3 74.0 - - + +
66B TYR* 1.3 65.1 + - - +
68B GLU* 3.4 9.3 + - + +
69B GLU* 3.2 35.5 + - - +
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B GLY* 5.8 4.2 - - - -
12B ARG* 5.7 0.4 - - - -
62B ILE 3.3 11.8 + - - +
63B PHE* 3.6 28.3 - + + +
64B ASP 3.2 0.6 - - - -
65B ARG* 1.3 79.7 - - - +
67B GLY* 1.3 65.9 + - - +
69B GLU* 3.2 17.4 + - + +
70B VAL* 3.1 46.6 + - + +
358B ILE* 5.6 5.2 - - - +
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 3.5 27.4 - - - -
63B PHE 3.3 4.6 + - - -
64B ASP 3.1 5.3 + - - -
66B TYR* 1.3 86.6 - - - +
68B GLU* 1.3 57.4 + - - +
70B VAL* 3.1 8.3 + - - +
71B LYS* 3.0 27.6 + - - +
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 5.5 6.4 + - - -
64B ASP* 3.0 18.7 + - + +
65B ARG* 3.7 13.0 - - + +
66B TYR 3.2 0.2 - - - -
67B GLY* 1.3 76.9 - - - +
69B GLU* 1.3 58.7 + - + +
71B LYS* 3.3 40.6 + - - +
72B GLU* 3.0 27.9 + - - +
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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 ARG* 3.2 22.6 + - - +
66B TYR* 3.2 16.5 + - + +
68B GLU* 1.3 73.9 - - + +
70B VAL* 1.3 67.4 + - + +
72B GLU* 3.4 17.7 + - - +
73B PHE* 3.0 24.3 + - - +
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 3.1 48.9 + - + +
67B GLY* 3.1 7.8 + - - +
69B GLU* 1.3 76.5 - - + +
71B LYS* 1.3 58.4 + - - +
73B PHE* 3.4 7.4 + - + +
74B LEU* 3.0 29.5 + - + +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY 3.0 12.4 + - - +
68B GLU* 3.3 42.4 + - - +
70B VAL* 1.3 78.2 - - - +
72B GLU* 1.3 56.5 + - - +
74B LEU* 3.4 10.8 + - + +
75B ALA* 2.9 28.7 + - + +
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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
----------------------------------------------------------
68B GLU 3.0 15.8 + - - +
69B GLU* 3.6 20.3 - - - +
70B VAL 3.3 0.2 - - - -
71B LYS* 1.3 74.5 - - - +
73B PHE* 1.3 65.8 + - - +
75B ALA* 3.2 9.9 + - - +
76B LYS* 3.0 51.5 + - - +
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU 3.0 16.8 + - - +
70B VAL* 3.7 6.7 - - + +
72B GLU* 1.3 78.3 - - - +
74B LEU* 1.3 64.0 + - - +
76B LYS* 3.4 15.7 + - + +
77B ALA* 3.1 26.3 + - + +
155B PHE* 6.1 2.9 - + - -
361B TYR* 3.5 32.5 - + - -
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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
----------------------------------------------------------
70B VAL* 3.0 19.0 + - + +
71B LYS* 3.5 10.5 - - + +
72B GLU 3.3 0.2 - - - -
73B PHE* 1.3 77.0 - - - +
75B ALA* 1.3 60.2 + - - +
77B ALA* 3.1 9.4 + - + +
78B LYS* 2.9 59.4 + - + +
214B SER* 3.5 35.2 - - - +
215B LEU* 5.0 0.7 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS 2.9 15.4 + - - +
72B GLU* 3.2 14.1 + - + +
74B LEU* 1.3 77.0 - - - +
76B LYS* 1.3 57.0 + - + +
78B LYS* 3.4 9.5 + - - +
79B GLU* 3.0 27.5 + - - +
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Residues in contact with LYS 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 47.1 + - + +
73B PHE* 3.7 17.7 - - + +
74B LEU 3.2 0.2 - - - -
75B ALA* 1.3 73.0 - - + +
77B ALA* 1.3 66.4 + - - +
79B GLU* 3.2 9.7 + - - +
80B ASP* 3.0 24.3 + - - +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 3.1 20.6 + - + +
74B LEU* 3.1 15.5 + - + +
76B LYS* 1.3 77.4 - - - +
78B LYS* 1.3 62.2 + - - +
80B ASP* 3.5 5.8 + - - +
81B PHE* 3.1 23.7 + - - +
211B TYR* 4.3 26.8 + - + -
215B LEU* 4.2 5.7 - - + +
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 2.9 42.1 + - + +
75B ALA* 3.7 7.2 - - - +
76B LYS 3.2 0.2 - - - -
77B ALA* 1.3 74.3 - - - +
79B GLU* 1.3 60.2 + - - +
81B PHE* 3.4 1.4 + - - +
82B LEU* 2.9 46.2 + - + +
214B SER 3.6 20.5 + - - -
215B LEU* 3.6 23.6 - - + +
216B ASP* 5.7 3.2 + - - -
245B ARG* 6.2 1.8 - - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 3.0 14.8 + - - +
76B LYS* 3.2 12.4 + - - +
78B LYS* 1.3 73.1 - - - +
80B ASP* 1.3 77.7 + - - +
82B LEU* 3.3 5.1 + - - +
83B LYS* 2.4 70.6 + - + +
504B ZN 2.2 34.4 - - - -
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS 3.0 16.6 + - - +
77B ALA* 3.8 6.3 - - - +
79B GLU* 1.3 83.7 + - - +
81B PHE* 1.3 63.1 + - - +
83B LYS* 3.9 1.4 - - - +
84B LYS* 2.7 64.5 + - - +
152B ALA 4.7 1.6 - - - +
154B ASN* 4.4 14.6 + - - +
504B ZN 3.1 19.6 - - - -
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA 3.1 18.1 + - - +
78B LYS 3.7 3.1 - - - +
80B ASP* 1.3 77.8 - - - +
82B LEU* 1.3 69.1 + - + +
84B LYS* 3.2 3.3 + - - +
85B TRP* 2.8 64.0 + + + +
149B ILE* 4.5 4.3 - - + -
152B ALA* 3.6 38.6 - - + +
153B VAL* 4.0 12.8 - - + -
211B TYR* 5.1 1.3 - - - +
215B LEU* 3.9 24.7 - - + -
217B LEU* 4.0 31.9 - - + -
245B ARG* 3.6 29.6 - - - -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LYS* 2.9 31.5 + - + +
79B GLU* 3.9 5.2 - - - +
81B PHE* 1.3 89.9 - - + +
83B LYS* 1.3 67.3 + - + +
85B TRP* 4.2 9.4 - - + -
86B GLU* 2.9 51.7 + - - +
245B ARG* 4.3 24.5 - - - +
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 2.4 64.6 + - + +
80B ASP* 3.9 4.9 - - - +
82B LEU* 1.3 77.4 - - + +
84B LYS* 1.3 65.0 + - + +
86B GLU* 4.2 8.2 - - - +
87B SER* 3.4 23.0 + - - +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 2.7 42.7 + - - +
81B PHE 3.2 1.4 + - - -
83B LYS* 1.3 80.5 - - + +
85B TRP* 1.3 61.3 + - - +
87B SER 4.2 3.4 - - - -
88B PRO* 3.4 26.2 - - - +
89B ALA 4.7 0.2 + - - -
148B ARG 5.0 0.9 - - - +
151B GLN* 3.8 17.9 + - + +
152B ALA* 3.6 32.3 + - + +
153B VAL 4.9 2.0 + - - -
154B ASN* 4.5 15.4 - - - +
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Residues in contact with TRP 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 2.8 45.5 + + + +
82B LEU* 3.9 13.0 - - + +
84B LYS* 1.3 78.2 - - - +
86B GLU* 1.3 77.5 + - + +
88B PRO* 3.4 5.9 - - - +
145B ASN* 4.9 10.3 - - - -
148B ARG* 2.9 91.8 + - + +
149B ILE* 3.5 31.0 - - + -
152B ALA* 3.9 4.9 - - + +
245B ARG* 4.5 28.6 - - + +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 2.9 42.4 + - - +
83B LYS* 4.3 8.8 - - - +
85B TRP* 1.3 92.2 - - + +
87B SER* 1.3 62.9 + - - +
88B PRO* 3.7 5.4 - - - +
148B ARG* 4.2 6.9 + - - +
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS 3.4 14.0 + - - +
84B LYS* 3.7 7.2 - - - +
86B GLU* 1.3 81.6 + - - +
88B PRO* 1.3 68.1 - - - +
89B ALA* 3.5 1.6 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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