Contacts of the helix formed by residues 52 - 79 (chain B) in PDB entry 1ZHH
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 THR 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 1.3 76.6 - - - +
53B LYS* 1.3 68.1 + - + +
54B GLN 3.2 2.6 + - - -
55B GLN* 2.7 39.6 + - - +
56B THR* 3.6 17.7 + - - +
251B ILE* 4.8 2.3 - - + +
270B GLN* 5.6 7.7 + - - +
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Residues in contact with LYS 53 (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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51B ARG 3.1 28.4 - - - +
52B THR* 1.3 83.2 - - + +
54B GLN* 1.3 62.2 + - + +
56B THR* 3.9 0.7 + - - -
57B SER* 3.3 26.3 + - - -
251B ILE* 4.1 36.9 - - + +
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 3.6 22.4 + - - +
52B THR 3.2 1.0 - - - -
53B LYS* 1.3 79.0 - - + +
55B GLN* 1.3 59.9 + - - +
57B SER* 3.3 6.2 + - - -
58B ALA* 3.1 28.1 + - - +
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG 4.9 0.4 + - - -
52B THR* 2.7 36.8 + - - +
54B GLN* 1.3 79.0 - - - +
56B THR* 1.3 66.5 + - - +
58B ALA* 3.7 6.4 + - - +
59B LEU* 3.2 23.7 + - - +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR* 3.6 16.4 + - - -
53B LYS 4.2 0.4 - - - -
54B GLN 3.3 0.4 - - - -
55B GLN* 1.3 81.1 - - - +
57B SER* 1.3 64.6 + - - +
59B LEU* 3.3 7.2 + - + +
60B ILE* 3.2 28.8 + - + +
208B VAL* 4.4 13.0 - - + -
251B ILE* 4.0 10.3 - - + -
268B THR* 3.9 20.6 - - + +
270B GLN* 3.4 38.9 + - - +
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS 3.3 18.5 + - - -
54B GLN* 3.3 6.0 + - - -
56B THR* 1.3 79.2 - - - +
58B ALA* 1.3 60.0 + - - +
60B ILE* 3.4 4.8 - - - +
61B HIS* 3.2 25.5 + - - +
251B ILE* 3.7 9.6 - - - +
252B GLU 3.9 4.7 + - - -
253B THR* 2.6 35.2 + - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN 3.1 16.6 + - - +
55B GLN* 4.0 7.6 - - - +
56B THR 3.3 0.2 - - - -
57B SER* 1.3 75.7 - - - +
59B LEU* 1.3 57.7 + - - +
61B HIS* 4.0 5.0 - - - +
62B ASN* 3.0 40.8 + - - +
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Residues in contact with LEU 59 (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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55B GLN 3.2 18.3 + - - +
56B THR* 3.7 8.5 - - + +
57B SER 3.3 0.4 - - - -
58B ALA* 1.3 76.4 - - - +
60B ILE* 1.3 61.3 + - + +
62B ASN* 3.1 13.9 + - + +
63B ILE* 3.0 45.2 + - + +
205B GLU 4.4 4.9 - - - +
206B SER* 3.8 31.6 - - - +
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 3.2 16.8 + - + +
57B SER* 3.4 11.2 - - - +
59B LEU* 1.3 76.3 - - + +
61B HIS* 1.3 61.1 + - - +
63B ILE* 4.2 7.6 - - - -
64B PHE* 2.9 27.2 + - - +
202B LEU* 3.7 13.4 - - + +
206B SER* 3.5 28.5 - - - +
208B VAL* 5.0 0.4 - - + -
211B VAL* 5.8 0.9 - - + -
253B THR* 3.5 31.2 - - + +
266B LEU* 3.9 23.1 - - + +
268B THR* 3.5 35.0 - - + +
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER 3.2 15.0 + - - +
58B ALA* 4.0 5.4 - - - +
60B ILE* 1.3 81.3 - - - +
62B ASN* 1.3 60.5 + - - +
64B PHE* 4.1 14.5 - + - +
65B ASP* 3.0 45.4 + - - +
253B THR* 4.2 10.5 - - + -
254B PRO 3.5 16.7 + - - -
255B ILE* 3.7 9.8 - - + -
256B VAL* 3.1 48.4 + - + +
257B VAL* 5.4 0.4 - - + -
266B LEU* 5.4 1.8 - - - -
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 3.0 31.8 + - - +
59B LEU* 3.1 13.3 + - + +
61B HIS* 1.3 78.0 - - - +
63B ILE* 1.3 60.0 + - + +
65B ASP* 3.9 9.4 - - - +
66B SER* 3.0 28.9 + - - -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.0 23.6 + - + +
60B ILE* 3.8 7.9 - - - +
61B HIS 3.3 0.2 - - - -
62B ASN* 1.3 75.0 - - + +
64B PHE* 1.3 65.4 + - - +
66B SER* 2.8 21.1 + - - +
67B HIS* 3.2 11.4 + - - +
198B LEU* 5.9 0.8 - - + +
201B LYS* 4.0 24.9 - - + +
202B LEU* 4.0 15.7 - - + +
205B GLU* 3.5 58.3 - - + +
206B SER* 3.5 17.7 - - - +
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE 2.9 18.1 + - - +
61B HIS* 3.6 10.1 - + - +
63B ILE* 1.3 78.2 - - - +
65B ASP* 1.3 75.0 + - - +
67B HIS* 3.2 9.9 + - - +
68B PHE* 3.2 56.6 - + - -
168B LEU* 5.1 6.3 - - + -
192B LEU* 4.7 12.8 - - + -
198B LEU* 4.9 8.5 - - + -
202B LEU* 3.9 16.1 - - + +
213B LEU* 5.1 5.6 - - + -
255B ILE* 3.6 49.1 - - + -
257B VAL* 4.9 7.9 - - + -
264B LEU* 5.0 6.5 - - + -
266B LEU* 4.2 16.6 - - + -
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Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B HIS* 3.0 46.9 + - - +
62B ASN* 3.9 10.7 - - - +
63B ILE 3.3 0.2 - - - -
64B PHE* 1.3 82.6 - - - +
66B SER* 1.3 56.1 + - - +
68B PHE* 3.3 6.2 + - - +
69B ALA* 2.9 31.4 + - + +
256B VAL 4.8 2.4 - - - +
257B VAL* 5.5 3.6 - - - +
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN 3.0 15.9 + - - -
63B ILE* 2.8 26.0 + - - +
65B ASP* 1.3 74.4 - - - +
67B HIS* 1.3 64.5 + - - +
69B ALA* 4.0 6.2 - - - +
70B ALA* 3.1 26.2 + - - +
110B HIS* 4.2 4.6 + - - -
201B LYS* 6.0 0.7 - - - -
205B GLU* 4.8 4.3 + - - -
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE 3.2 7.5 + - - +
64B PHE 3.3 11.7 - - - +
66B SER* 1.3 82.2 + - - +
68B PHE* 1.3 80.7 + + + +
70B ALA* 3.7 2.6 + - - +
71B ILE* 3.3 45.7 + - + +
109B SER 3.2 24.5 - - - -
110B HIS* 3.8 9.9 - + - -
111B THR 5.0 2.9 + - - -
113B GLU* 5.7 2.0 + - - -
190B VAL* 4.7 6.8 - - + +
195B ASN* 5.5 2.6 + - - -
197B ALA* 6.3 0.7 - - + -
198B LEU* 3.9 33.4 - - + +
201B LYS* 2.8 31.6 + - - +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.2 65.3 - + - -
65B ASP* 3.3 7.8 + - - +
67B HIS* 1.3 87.4 - + + +
69B ALA* 1.3 60.4 + - - +
71B ILE* 3.4 2.4 + - - +
72B GLN* 2.8 30.4 + - - +
153B TRP* 3.5 34.2 - + + +
168B LEU* 3.6 28.3 - - + -
190B VAL* 3.6 42.0 - - + -
192B LEU* 4.0 11.0 - - + -
198B LEU* 4.7 2.5 - - + -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 2.9 19.0 + - + +
66B SER* 4.0 7.6 - - - +
68B PHE* 1.3 76.5 - - - +
70B ALA* 1.3 57.2 + - - +
72B GLN* 3.4 13.2 + - - +
73B ILE* 3.0 42.4 + - + +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER 3.1 19.1 + - - +
67B HIS 3.8 0.2 - - - +
69B ALA* 1.3 75.3 - - - +
71B ILE* 1.3 63.9 + - - +
73B ILE* 3.3 9.3 + - - +
74B HIS* 3.1 33.4 + - + +
107B ASP* 5.0 0.4 - - - +
110B HIS* 3.4 35.9 - - + +
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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
----------------------------------------------------------
67B HIS* 3.3 48.2 + - + +
68B PHE* 3.8 5.6 - - - +
70B ALA* 1.3 76.6 - - - +
72B GLN* 1.3 56.6 + - - +
74B HIS* 3.4 3.0 + - - +
75B HIS* 2.9 28.5 + - + +
110B HIS* 3.5 27.6 - - - +
111B THR 3.8 16.6 - - - +
112B PRO* 4.7 10.3 - - + -
153B TRP* 3.9 18.8 - - + -
188B ASN* 3.7 21.3 + - - +
190B VAL* 4.0 15.0 - - + -
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE 2.8 18.4 + - - +
69B ALA* 3.5 13.0 - - - +
71B ILE* 1.3 76.7 - - - +
73B ILE* 1.3 69.5 + - - +
75B HIS* 3.4 1.5 + - - +
76B ASP* 2.9 56.3 + - - +
153B TRP* 4.3 12.4 + - + +
170B ARG* 3.3 38.6 - - - +
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Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA* 3.0 30.7 + - + +
70B ALA* 3.7 8.3 - - - +
71B ILE 3.3 0.2 - - - -
72B GLN* 1.3 88.7 - - - +
74B HIS* 1.3 70.1 + - + +
76B ASP* 3.5 4.6 + - - +
77B SER* 3.2 24.5 + - - -
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.1 25.7 + - - +
71B ILE* 3.8 5.2 - - - +
73B ILE* 1.3 79.3 - - + +
75B HIS* 1.3 55.8 + - - +
77B SER* 3.2 3.9 + - - -
78B ASN* 2.7 53.2 + - - +
103B ILE* 5.0 12.7 - - + +
106B SER* 5.8 1.8 - - - -
107B ASP* 2.7 38.9 + - + -
110B HIS* 3.7 20.8 + - + +
115B ARG* 6.1 0.9 - - - +
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Residues in contact with HIS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE 2.9 18.2 + - - +
72B GLN* 3.6 5.8 - - - +
74B HIS* 1.3 75.3 - - - +
76B ASP* 1.3 57.6 + - - +
78B ASN* 4.0 7.2 - - + +
79B SER* 2.5 43.2 + - - -
170B ARG* 3.1 46.2 + - + +
172B VAL* 3.7 14.3 - - + +
186B SER* 3.0 42.3 + - - -
188B ASN* 3.5 33.7 + - - +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 2.9 42.0 + - - +
73B ILE* 3.8 5.6 - - - +
75B HIS* 1.3 78.2 - - - +
77B SER* 1.3 61.6 + - - +
79B SER* 3.5 10.0 + - - -
80B LYS* 3.3 31.3 + - - +
151B ASN* 4.6 2.8 - - - +
170B ARG* 3.1 25.6 + - - -
172B VAL* 3.4 18.4 - - + +
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.2 16.9 + - - -
74B HIS* 3.8 5.6 - - - -
76B ASP* 1.3 76.0 - - - +
78B ASN* 1.3 69.4 + - - +
79B SER 3.1 1.6 - - - -
80B LYS* 3.1 23.4 + - - +
81B SER* 3.7 3.8 + - - -
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Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B HIS* 2.7 37.9 + - - +
75B HIS* 4.1 7.6 - - + +
77B SER* 1.3 76.6 + - - +
79B SER* 1.3 57.6 + - - +
81B SER* 3.0 28.5 - - - -
84B ILE* 3.1 13.5 - - + +
99B PHE* 4.7 2.9 - - + -
100B PHE* 4.6 13.7 - - + -
103B ILE* 3.5 47.0 - - + +
115B ARG* 4.0 18.2 - - - +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 2.5 39.6 + - - -
76B ASP 3.6 6.5 - - - -
77B SER 3.1 0.6 - - - -
78B ASN* 1.3 77.0 - - - +
80B LYS* 1.3 59.0 + - - +
81B SER 3.2 4.5 + - - +
84B ILE* 4.2 4.9 - - - +
172B VAL* 4.1 18.4 - - - +
173B PRO 4.6 2.5 - - - +
174B ILE* 3.6 39.8 - - - +
175B LEU 4.9 2.8 + - - +
186B SER* 3.9 9.5 + - - -
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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