Contacts of the helix formed by residues 90 - 122 (chain H) in PDB entry 3MQ6
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 90 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G ASP* 5.5 2.4 - - - +
91G SER* 4.1 11.5 + - - -
89H VAL* 1.3 76.2 - - - +
91H SER* 1.3 70.3 + - - +
92H ASN* 2.9 35.4 + - - +
93H ALA* 3.0 16.7 + - + +
94H LYS* 3.4 10.0 + - - +
11Q G 3.8 23.9 - - - +
12Q T 3.8 24.0 + - - +
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Residues in contact with SER 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G ASP* 4.1 10.9 + - - -
92G ASN* 4.0 12.0 + - - -
89H VAL 3.8 1.2 + - - -
90H ASP* 1.3 78.4 + - - +
92H ASN* 1.3 59.2 + - - +
94H LYS* 3.4 17.4 + - - +
95H ALA* 2.9 30.2 + - - +
10R G 4.2 8.4 - - - +
11R G 3.7 37.4 - - - -
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Residues in contact with ASN 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G SER* 4.0 10.5 + - - -
92G ASN* 3.4 21.2 + - - +
90H ASP* 2.9 14.5 + - - +
91H SER* 1.3 77.8 + - - +
93H ALA* 1.3 57.4 + - - +
95H ALA* 3.9 5.6 - - - +
96H LYS* 3.1 12.6 + - - +
10Q G 3.1 41.4 + - - -
11Q G 2.8 67.2 + - - +
12Q T 4.1 2.6 + - - +
9R C 4.8 0.5 - - - +
10R G 4.6 1.9 + - - +
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Residues in contact with ALA 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H THR* 6.3 0.7 - - + -
35H PHE 5.9 0.7 - - - +
37H LEU* 3.7 12.3 - - + -
89H VAL* 4.8 4.9 - - + -
90H ASP* 3.0 17.8 + - + +
92H ASN* 1.3 76.2 - - - +
94H LYS* 1.3 64.9 + - - +
95H ALA 3.1 0.9 - - - -
96H LYS* 3.7 2.8 - - - +
97H VAL* 3.0 29.6 + - - +
12Q T 3.4 37.3 + - - +
13Q G 4.2 7.0 - - - +
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Residues in contact with LYS 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 4.8 12.5 + - - -
37H LEU* 3.7 13.7 - - + -
72H VAL* 3.9 26.7 - - + +
76H VAL* 4.9 8.9 - - + +
89H VAL* 3.6 32.9 + - + +
90H ASP 3.4 3.1 + - - +
91H SER* 3.4 20.3 + - - +
93H ALA* 1.3 76.2 - - - +
95H ALA* 1.3 57.8 - - - +
97H VAL* 4.1 0.5 - - - +
98H ALA* 2.8 33.7 + - - +
10R G 5.2 2.2 - - - -
11R G 5.6 4.4 + - - -
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Residues in contact with ALA 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H SER 2.9 18.0 + - - +
92H ASN* 3.9 8.7 - - - +
94H LYS* 1.3 75.6 - - - +
96H LYS* 1.3 67.4 + - - +
98H ALA* 4.5 1.6 - - - +
99H GLY 3.2 15.4 + - - -
11Q G 5.1 1.1 - - - +
9R C 3.2 36.4 - - - +
10R G 3.4 32.9 - - - +
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Residues in contact with LYS 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 3.0 21.1 + - - +
92H ASN 3.1 17.2 + - - +
93H ALA 3.3 4.7 + - - +
95H ALA* 1.3 80.9 - - - +
97H VAL* 1.3 61.8 + - + +
99H GLY* 3.8 0.9 - - - -
100H ASP* 2.6 44.3 + - - +
152H ARG* 3.7 17.9 - - - +
12Q T 3.0 28.9 - - + +
13Q G 3.2 50.3 + - - +
14Q G 4.5 2.0 + - - -
7R A 4.6 0.9 - - + -
8R C 3.4 25.1 + - + +
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Residues in contact with VAL 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H LEU* 3.7 30.1 - - + +
39H GLN* 3.7 28.7 - - + +
42H MET* 3.8 28.0 - - + -
72H VAL* 4.3 5.2 - - + -
93H ALA 3.0 19.5 + - - +
94H LYS 4.2 0.9 - - - +
96H LYS* 1.3 72.8 - - - +
98H ALA* 1.3 68.4 + - - +
100H ASP* 3.3 1.8 + - - +
101H ILE* 2.9 30.5 + - + +
13Q G 3.7 21.1 - - - -
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Residues in contact with ALA 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H ILE* 4.2 7.5 - - + +
69H GLY* 6.6 0.2 - - - -
72H VAL* 4.6 11.6 - - + +
94H LYS 2.8 24.9 + - - +
95H ALA 4.1 3.1 - - - +
97H VAL* 1.3 74.7 - - - +
99H GLY* 1.3 57.8 + - - +
101H ILE* 3.5 6.3 + - - +
102H PHE* 3.0 26.9 + - - +
243H ARG* 4.1 23.3 - - - +
10R G 4.3 8.1 - - - +
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Residues in contact with GLY 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ALA 3.2 9.7 + - - -
96H LYS 3.8 1.1 - - - -
97H VAL 3.1 0.8 - - - -
98H ALA* 1.3 74.7 - - - +
100H ASP* 1.3 64.9 + - - +
102H PHE* 3.1 7.2 + - - +
103H GLU* 3.1 22.7 + - - +
241H PHE* 5.7 0.3 - - - +
243H ARG* 4.6 0.7 - - - -
8R C 3.3 26.7 - - - -
9R C 3.3 18.3 + - - -
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Residues in contact with ASP 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 2.8 27.0 + - - +
96H LYS* 2.6 42.9 + - - -
97H VAL 3.9 3.4 - - - +
99H GLY* 1.3 74.8 - - - +
101H ILE* 1.3 57.8 + - + +
103H GLU* 3.3 11.5 + - - +
104H ILE* 2.7 43.4 + - + +
152H ARG* 3.2 29.3 + - - -
8R C 3.5 13.4 - - - +
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Residues in contact with ILE 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 4.9 4.3 - - + +
42H MET* 4.1 6.7 - - + -
43H LEU* 4.1 26.9 - - + -
47H PHE* 4.6 0.7 - - + -
68H ILE* 3.8 23.1 - - + +
71H PRO* 3.3 37.7 - - + -
72H VAL* 5.1 2.9 - - + +
97H VAL* 2.9 40.1 + - + +
98H ALA* 3.8 5.2 - - - +
100H ASP* 1.3 74.6 - - + +
102H PHE* 1.3 66.5 + - - +
104H ILE* 4.5 1.3 - - - +
105H VAL* 2.8 40.0 + - + +
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Residues in contact with PHE 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H TYR* 4.1 5.4 - + - -
68H ILE* 3.9 26.2 - - + +
98H ALA 3.0 13.6 + - - +
99H GLY 3.1 7.4 + - - +
101H ILE* 1.3 74.0 - - - +
103H GLU* 1.3 57.1 + - - +
105H VAL* 4.2 0.7 - - - +
106H SER* 3.0 49.9 + - - -
241H PHE* 3.8 17.9 - + + -
242H LYS 3.6 13.0 - - - -
243H ARG* 3.6 28.0 - - + -
278H HIS* 3.6 42.0 - - + -
279H THR* 4.1 1.8 - - - -
280H LEU* 3.5 35.7 - - + -
316H PRO* 4.8 2.9 - - + -
9R C 4.6 1.6 - - - -
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Residues in contact with GLU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H GLY 3.1 12.5 + - - +
100H ASP* 3.6 16.4 - - - +
102H PHE* 1.3 75.7 - - - +
104H ILE* 1.3 74.6 + - - +
106H SER* 3.3 1.7 + - - -
107H SER* 2.9 28.8 + - - +
149H ASN* 3.3 10.8 - - - +
188H ASP* 3.3 28.9 - - + +
241H PHE* 3.4 39.0 - - + -
341H CA 2.6 29.6 - - - -
8R C 5.8 5.5 - - - +
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Residues in contact with ILE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 4.5 9.0 - - - +
40H GLN* 6.2 2.0 - - + -
43H LEU* 3.7 34.5 - - + -
100H ASP* 2.7 37.5 + - + +
101H ILE 4.3 0.9 - - - +
103H GLU* 1.3 81.3 - - - +
105H VAL* 1.3 64.4 + - - +
107H SER* 3.4 2.4 + - - -
108H ALA* 3.1 20.8 + - - +
149H ASN* 4.1 19.7 + - - +
211H LEU* 4.2 21.5 - - + -
216H GLN* 5.4 5.2 - - + +
219H LEU* 5.3 3.3 - - + +
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Residues in contact with VAL 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LEU* 3.8 16.8 - - + -
47H PHE* 3.8 31.6 - - + -
52H PRO* 4.0 31.0 - - + -
64H TYR* 3.8 13.0 - - - +
67H VAL* 5.2 0.2 - - + -
68H ILE* 3.9 12.1 - - + -
101H ILE* 2.8 26.0 + - + +
104H ILE* 1.3 75.6 - - - +
106H SER* 1.3 63.3 + - - +
108H ALA* 3.0 9.5 + - + +
109H VAL* 3.0 20.8 + - + +
211H LEU* 4.0 7.2 - - + -
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Residues in contact with SER 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H TYR* 2.9 24.4 + - - -
102H PHE* 3.0 33.1 + - - -
103H GLU 3.9 0.2 - - - -
105H VAL* 1.3 76.2 - - - +
107H SER* 1.3 61.7 + - - +
109H VAL* 3.3 3.7 + - - +
110H MET* 3.0 27.4 + - - +
241H PHE* 3.2 30.6 - - - -
278H HIS* 5.3 0.3 + - - -
316H PRO* 5.8 0.2 - - - +
322H LEU* 4.0 13.1 - - - +
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Residues in contact with SER 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H GLU* 2.9 20.9 + - - +
104H ILE 3.7 4.7 - - - -
106H SER* 1.3 77.8 - - - +
108H ALA* 1.3 57.4 + - - +
110H MET* 3.6 3.6 + - - +
111H TRP* 2.9 26.0 + - - +
147H VAL* 3.8 6.2 - - - +
149H ASN* 4.1 25.5 + - - -
189H LEU* 3.1 32.9 - - - +
219H LEU* 4.9 3.9 - - - +
241H PHE* 3.6 9.6 - - - -
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Residues in contact with ALA 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H ILE* 4.0 25.1 - - + +
52H PRO* 6.2 0.2 - - + -
104H ILE 3.1 11.7 + - - +
105H VAL* 3.0 14.2 + - + +
107H SER* 1.3 75.2 - - - +
109H VAL* 1.3 66.4 + - - +
110H MET 3.2 0.2 - - - -
111H TRP* 3.1 2.3 + - - +
112H ASN* 3.0 24.3 + - - +
208H ILE* 4.6 0.7 - - + +
211H LEU* 4.4 9.6 - - + -
219H LEU* 3.7 26.2 - - + +
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Residues in contact with VAL 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H ILE* 4.1 8.2 - - - +
52H PRO* 2.9 41.7 - - + +
54H PHE* 3.4 16.2 - - + -
64H TYR* 4.3 14.1 - - - +
105H VAL 3.0 17.7 + - - +
106H SER 3.6 7.0 - - - +
108H ALA* 1.3 75.1 - - - +
110H MET* 1.3 58.9 + - + +
112H ASN 3.4 0.7 + - - -
113H CYS* 3.0 25.5 + - - -
319H ALA* 4.3 6.3 - - + +
322H LEU* 4.1 20.6 - - + -
323H ALA* 4.3 17.9 - - + -
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Residues in contact with MET 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H SER 3.0 20.3 + - - +
107H SER 3.8 4.9 - - - +
108H ALA 3.2 0.2 - - - -
109H VAL* 1.3 73.5 - - + +
111H TRP* 1.3 59.1 + - - +
113H CYS* 3.1 9.4 + - - +
114H ALA* 2.8 30.5 + - - +
147H VAL* 3.5 11.3 - - + +
189H LEU* 3.7 35.2 - - + -
191H VAL* 3.8 4.5 - - + -
237H LEU* 4.3 9.4 - - + -
239H VAL* 4.6 2.7 - - + -
241H PHE* 4.5 12.3 - - - -
276H GLU* 5.9 0.4 - - - +
278H HIS* 4.8 13.5 - - + -
322H LEU* 4.8 13.7 - - + -
326H PHE* 3.6 48.1 - - + -
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Residues in contact with TRP 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H SER 2.9 16.5 + - - +
108H ALA* 3.1 12.8 + - - +
110H MET* 1.3 74.2 - - - +
112H ASN* 1.3 72.7 + - - +
114H ALA* 3.0 7.1 + - + +
115H ALA* 2.8 24.6 + - + +
147H VAL* 3.3 38.5 - - + +
203H MET* 3.9 30.2 + - + -
204H TRP* 3.8 28.7 - + - -
206H GLU 3.8 17.6 + - - -
208H ILE* 4.0 12.0 - - + +
218H LEU* 4.4 17.2 - - + +
219H LEU* 3.6 39.3 - - + +
222H ALA* 3.7 18.6 - - + -
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Residues in contact with ASN 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H ILE* 3.6 21.0 - - - +
54H PHE* 3.4 36.2 - - + +
108H ALA 3.0 11.0 + - - +
109H VAL 3.7 2.0 - - - +
111H TRP* 1.3 78.0 - - - +
113H CYS* 1.3 63.7 + - - +
115H ALA* 3.0 7.3 + - - +
116H ARG* 2.9 23.7 + - - +
207H GLU* 3.3 14.8 + - + +
208H ILE* 2.8 54.5 + - - +
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Residues in contact with CYS 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PHE* 3.5 4.9 - - - -
109H VAL* 3.0 22.3 + - - +
110H MET* 3.4 8.3 - - - +
112H ASN* 1.3 75.3 - - - +
114H ALA* 1.3 64.8 + - - +
116H ARG 3.3 0.3 + - - -
117H TRP* 2.9 25.6 + - - +
323H ALA* 3.6 42.6 - - - -
326H PHE* 3.5 22.4 - - + -
327H PHE* 3.4 30.9 - - + -
330H LEU* 5.2 0.4 - - - -
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Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H MET 2.8 6.3 + - - -
111H TRP* 3.4 9.4 - - + +
113H CYS* 1.3 75.5 - - - +
115H ALA* 1.3 57.0 + - - +
117H TRP* 3.6 6.0 - - - +
118H ASN* 2.8 39.9 + - - +
145H VAL* 4.0 25.8 - - + +
147H VAL* 3.5 31.6 - - + +
204H TRP 5.4 0.2 - - - +
326H PHE* 4.3 4.4 - - + -
330H LEU* 5.0 0.4 - - - -
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Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H TRP* 2.8 13.6 + - + +
112H ASN 3.2 9.0 - - - +
114H ALA* 1.3 77.4 - - - +
116H ARG* 1.3 63.7 + - - +
118H ASN* 3.1 2.8 + - - +
119H SER* 2.9 25.3 + - - -
127H ARG* 3.5 3.5 + - - -
204H TRP 3.5 13.2 + - - +
205H ARG* 3.8 6.4 - - - +
206H GLU 3.6 25.6 - - - +
207H GLU* 3.6 19.1 - - + -
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Residues in contact with ARG 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PHE* 3.4 20.7 - - + +
112H ASN 2.9 15.8 + - - +
113H CYS 3.8 3.8 - - - +
115H ALA* 1.3 72.3 - - - +
117H TRP* 1.3 62.5 + - - +
119H SER* 3.5 2.9 + - - -
120H LEU* 3.2 21.5 + - - +
125H GLY 4.7 0.9 - - - +
126H TRP* 3.5 34.4 - - + -
127H ARG* 3.3 49.7 + - + +
129H GLN 2.9 23.0 + - - -
130H PRO* 3.0 29.5 + - - +
132H TYR* 4.2 6.9 - - - +
207H GLU* 2.6 39.0 + - - +
327H PHE* 4.2 12.3 - - + -
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Residues in contact with TRP 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H CYS 2.9 17.1 + - - +
114H ALA 3.6 3.4 - - - +
116H ARG* 1.3 76.0 - - - +
118H ASN* 1.3 75.8 + - - +
120H LEU* 3.3 5.5 + - + +
121H MET* 2.9 52.4 + - + +
126H TRP* 4.2 7.7 - - - -
135H PRO* 3.7 36.8 - - + -
137H LEU* 3.6 35.2 - - + -
143H ARG 2.9 20.7 + - - -
145H VAL* 4.3 13.0 - - + +
327H PHE* 4.5 9.9 - + + -
330H LEU* 3.9 25.4 - - + -
331H ASN* 3.7 27.1 - - - -
334H MET* 3.8 17.5 - - + +
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Residues in contact with ASN 118 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H ALA* 2.8 27.4 + - - +
115H ALA 3.1 1.3 + - - +
117H TRP* 1.3 74.8 - - - +
119H SER* 1.3 66.3 + - - +
121H MET* 3.0 12.4 + - - +
122H VAL* 3.1 18.4 + - - +
144H GLN* 3.2 30.6 - - - +
145H VAL* 3.0 43.4 + - - +
204H TRP* 2.6 37.6 + - - +
205H ARG* 3.8 4.3 - - + -
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Residues in contact with SER 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H ALA 2.9 14.3 + - - -
116H ARG 3.6 5.6 - - - -
118H ASN* 1.3 79.2 - - - +
120H LEU* 1.3 63.4 + - - +
122H VAL* 3.2 11.2 + - - +
124H GLU* 3.0 47.0 + - - +
125H GLY 3.7 8.0 + - - -
127H ARG* 2.8 33.9 + - - +
205H ARG* 4.2 8.4 - - - +
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H ARG 3.2 10.7 + - - +
117H TRP* 3.4 8.1 - - + +
119H SER* 1.3 77.1 - - - +
121H MET* 1.3 84.7 + - + +
123H GLY* 3.2 11.8 + - - -
125H GLY* 3.4 29.4 + - - +
126H TRP* 3.9 15.5 - - + +
134H ARG* 3.5 33.9 - - + +
135H PRO* 3.8 39.0 - - + +
137H LEU 5.2 1.3 - - - +
139H PRO* 3.4 18.9 - - + +
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Residues in contact with MET 121 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H TRP* 2.9 57.1 + - + +
118H ASN* 3.0 8.9 + - - +
120H LEU* 1.3 99.8 - - + +
122H VAL* 1.3 59.9 + - - +
123H GLY 3.7 0.3 + - - -
135H PRO* 5.6 0.2 - - + -
137H LEU* 4.4 7.0 - - + +
138H SER 4.7 0.2 - - - -
139H PRO* 3.5 21.8 - - + +
140H SER* 3.1 57.6 + - - +
141H PRO* 3.2 2.9 - - - +
143H ARG* 3.7 22.7 - - - +
144H GLN* 3.9 10.1 - - + +
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Residues in contact with VAL 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H ASN 3.1 4.9 + - - +
119H SER 3.3 13.5 - - - +
121H MET* 1.3 78.0 - - - +
123H GLY* 1.3 57.8 + - - +
124H GLU* 3.8 19.2 - - + +
141H PRO* 4.2 17.3 - - + +
144H GLN* 3.5 38.4 - - - +
199H GLN 4.2 7.2 - - - +
200H ASN* 5.8 1.6 - - - +
205H ARG* 3.6 25.6 - - - +
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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