Contacts of the helix formed by residues 90 - 122 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASP* 5.6 0.4 - - - +
91E SER* 3.9 11.0 + - - -
89F VAL* 1.3 76.9 - - - +
91F SER* 1.3 65.0 + - - +
92F ASN* 2.8 38.4 + - - +
93F ALA* 2.9 27.8 + - + +
94F LYS* 3.4 3.6 + - - +
11O G 3.6 26.5 - - - +
12O T 3.6 27.1 + - - +
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Residues in contact with SER 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ASP* 4.2 10.6 + - - -
91E SER* 5.6 0.2 + - - -
92E ASN* 3.8 19.6 + - - -
89F VAL 3.6 2.6 + - - -
90F ASP* 1.3 76.3 + - - +
92F ASN* 1.3 60.3 + - - +
94F LYS* 3.4 17.0 + - - +
95F ALA* 2.8 28.1 + - - +
10P G 4.2 8.9 - - - +
11P G 3.9 30.4 - - - -
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Residues in contact with ASN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E SER* 3.9 10.7 + - - -
92E ASN* 3.5 18.2 + - - +
90F ASP* 2.8 14.9 + - - +
91F SER* 1.3 79.9 + - - +
93F ALA* 1.3 57.8 + - - +
95F ALA* 3.5 6.2 - - - +
96F LYS* 2.9 24.9 + - - +
10O G 3.1 35.9 + - - -
11O G 2.7 62.2 + - - +
12O T 4.3 1.3 - - - +
9P C 4.8 0.2 - - - +
10P G 4.6 2.4 + - - +
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Residues in contact with ALA 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F THR* 6.4 0.4 - - + -
35F PHE 5.8 1.3 - - - +
37F LEU* 3.5 19.5 - - + -
89F VAL* 4.5 5.4 - - + -
90F ASP* 2.9 19.4 + - - +
92F ASN* 1.3 75.5 - - - +
94F LYS* 1.3 65.2 + - - +
96F LYS* 3.4 1.4 + - - +
97F VAL* 3.1 29.5 + - - +
12O T 3.7 37.6 - - - +
13O G 4.3 2.2 - - - +
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Residues in contact with LYS 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ASP* 3.0 38.3 + - - -
37F LEU* 3.8 12.8 - - + -
72F VAL* 4.6 20.1 - - + +
76F VAL* 4.5 15.4 - - - +
89F VAL* 3.6 28.5 - - + -
90F ASP 3.4 3.9 + - - +
91F SER* 3.6 14.6 - - - +
93F ALA* 1.3 78.5 - - - +
95F ALA* 1.3 57.5 + - - +
97F VAL* 4.2 0.4 - - - +
98F ALA* 2.9 36.2 + - + +
10P G 5.0 5.4 - - - -
11P G 6.1 0.9 - - - +
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F SER 2.8 17.7 + - - +
92F ASN* 3.5 12.6 - - - +
93F ALA 3.1 0.4 - - - -
94F LYS* 1.3 77.3 - - - +
96F LYS* 1.3 64.5 + - - +
98F ALA* 4.0 0.3 - - - +
99F GLY 3.1 17.7 + - - -
11O G 4.5 3.1 - - - +
9P C 3.2 45.3 - - - +
10P G 3.9 20.6 - - - +
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Residues in contact with LYS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLN* 2.9 27.2 + - - +
92F ASN 2.9 16.3 + - - +
93F ALA 3.4 3.6 + - - +
95F ALA* 1.3 77.2 - - - +
97F VAL* 1.3 61.5 + - + +
99F GLY* 3.4 1.2 + - - -
100F ASP* 2.9 45.9 + - - +
152F ARG* 3.7 14.3 - - - +
12O T 3.3 26.2 - - + +
13O G 2.9 51.0 + - + +
14O G 4.4 3.8 + - - -
7P A 4.6 1.3 - - + -
8P C 3.4 29.7 + - + +
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 3.8 18.6 - - + +
39F GLN* 3.6 31.6 - - + +
42F MET* 4.0 17.0 - - + -
72F VAL* 4.3 3.4 - - + -
93F ALA 3.1 17.4 + - - +
94F LYS 4.2 1.3 - - - +
96F LYS* 1.3 73.3 - - + +
98F ALA* 1.3 67.3 + - - +
99F GLY 3.1 1.6 - - - -
100F ASP* 3.1 1.7 + - - +
101F ILE* 2.8 45.8 + - + +
13O G 3.7 26.5 - - - -
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ILE* 4.4 7.8 - - + +
72F VAL* 4.7 12.0 - - + +
94F LYS* 2.9 20.8 + - + +
95F ALA 4.0 2.5 - - - +
97F VAL* 1.3 76.8 - - - +
99F GLY* 1.3 57.7 + - - +
101F ILE* 3.5 6.0 + - - +
102F PHE* 3.0 29.8 + - - +
243F ARG* 4.0 23.2 - - - +
10P G 4.2 8.3 - - - +
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Residues in contact with GLY 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ALA 3.1 10.5 + - - -
96F LYS 3.7 1.6 - - - -
97F VAL 3.1 0.8 - - - -
98F ALA* 1.3 77.8 - - - +
100F ASP* 1.3 63.8 + - - +
102F PHE* 3.3 6.6 + - - +
103F GLU* 3.1 22.7 + - - +
243F ARG* 4.7 0.9 - - - -
8P C 3.3 27.0 - - - +
9P C 3.5 17.9 + - - -
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Residues in contact with ASP 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLN* 2.9 38.4 + - - +
96F LYS* 2.9 23.6 + - - +
97F VAL 3.1 0.9 + - - +
99F GLY* 1.3 75.7 - - - +
101F ILE* 1.3 52.8 + - - +
103F GLU* 3.3 12.1 + - - +
104F ILE* 2.8 44.7 + - + +
152F ARG* 2.9 44.7 + - - -
8P C 3.6 12.5 - - - +
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Residues in contact with ILE 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLN* 4.8 7.6 - - + -
42F MET* 4.3 7.0 - - + -
43F LEU* 3.9 22.0 - - + -
47F PHE* 4.7 0.9 - - + -
68F ILE* 3.9 24.5 - - + +
71F PRO* 3.6 33.4 - - + -
72F VAL* 5.0 3.8 - - + -
97F VAL* 2.8 42.0 + - + +
98F ALA* 3.8 3.8 - - - +
100F ASP* 1.3 73.8 - - + +
102F PHE* 1.3 66.6 + - - +
103F GLU 3.1 1.1 - - - -
104F ILE* 4.4 4.3 - - - +
105F VAL* 2.9 45.5 + - + +
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Residues in contact with PHE 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F TYR* 4.0 7.6 - + - -
68F ILE* 3.8 25.1 - - + +
98F ALA 3.0 17.8 + - - +
99F GLY 3.5 4.5 - - - +
101F ILE* 1.3 74.8 - - - +
103F GLU* 1.3 62.3 + - - +
105F VAL* 4.3 0.7 - - - +
106F SER* 2.9 43.1 + - - -
241F PHE* 3.8 19.1 - + + -
242F LYS 3.6 11.9 - - - -
243F ARG* 3.6 26.7 - - + -
278F HIS* 3.4 41.1 - - + -
279F THR* 4.2 3.4 - - - -
280F LEU* 3.6 35.0 - - + -
316F PRO* 4.8 2.2 - - + -
9P C 4.6 1.8 - - - -
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Residues in contact with GLU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F GLY 3.1 10.8 + - - +
100F ASP* 3.6 21.6 - - - +
102F PHE* 1.3 79.2 - - - +
104F ILE* 1.3 69.1 + - - +
106F SER* 3.4 1.4 + - - -
107F SER* 2.9 31.3 + - - +
149F ASN* 3.8 7.9 - - - +
188F ASP* 3.0 32.2 - - + +
241F PHE* 3.4 37.6 - - + +
341F CA 2.7 29.4 - - - -
8P C 5.6 5.9 - - - +
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Residues in contact with ILE 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F GLN* 4.2 19.5 - - - +
40F GLN* 6.4 1.3 - - + -
43F LEU* 3.8 33.2 - - + -
100F ASP* 2.8 27.1 + - + +
101F ILE 4.2 1.6 - - - +
103F GLU* 1.3 82.5 - - - +
105F VAL* 1.3 58.4 + - - +
107F SER* 3.3 2.9 + - - -
108F ALA* 2.9 26.9 + - - +
149F ASN* 4.2 19.2 + - - +
211F LEU* 4.4 17.7 - - + -
216F GLN* 5.5 4.9 - - + +
219F LEU* 5.5 1.8 - - + +
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Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LEU* 3.8 17.9 - - + -
47F PHE* 3.8 28.0 - - + -
52F PRO* 3.8 33.0 - - + -
64F TYR* 3.9 5.6 - - - +
68F ILE* 3.9 18.4 - - + -
101F ILE* 2.9 24.6 + - + +
104F ILE* 1.3 73.2 - - - +
106F SER* 1.3 66.5 + - - +
108F ALA* 3.1 8.1 + - + +
109F VAL* 2.9 22.8 + - + +
211F LEU* 4.1 6.3 - - + -
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Residues in contact with SER 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F TYR* 2.9 32.5 + - - -
102F PHE* 2.9 29.7 + - - -
103F GLU 3.9 0.2 - - - -
105F VAL* 1.3 77.8 - - - +
107F SER* 1.3 62.7 + - - +
109F VAL* 3.3 5.0 + - - +
110F MET* 3.1 25.1 + - - +
241F PHE* 3.3 29.7 - - - -
278F HIS* 5.5 0.6 + - - -
322F LEU* 4.0 10.7 - - - +
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Residues in contact with SER 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLU* 2.9 22.0 + - - +
104F ILE 3.6 4.9 - - - -
106F SER* 1.3 77.0 - - - +
108F ALA* 1.3 57.3 + - - +
110F MET* 3.3 3.6 + - - +
111F TRP* 2.8 26.5 + - - +
147F VAL* 3.9 5.6 - - - +
149F ASN* 4.0 27.2 + - - +
189F LEU* 3.1 32.9 - - - +
219F LEU* 5.0 3.1 - - - +
241F PHE* 3.6 7.1 - - - -
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Residues in contact with ALA 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ILE* 4.0 16.7 - - + +
52F PRO* 6.3 0.2 - - + -
104F ILE 2.9 17.0 + - - +
105F VAL* 3.1 6.3 + - + +
107F SER* 1.3 73.6 - - - +
109F VAL* 1.3 66.6 + - - +
111F TRP* 3.2 2.8 + - - +
112F ASN* 3.1 24.1 + - - +
208F ILE* 4.5 1.7 - - + +
211F LEU* 3.8 22.9 - - + -
219F LEU* 3.8 27.1 - - + +
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Residues in contact with VAL 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ILE* 4.1 10.9 - - + +
52F PRO* 3.3 35.4 - - + +
53F GLY* 5.3 0.2 - - - -
54F PHE* 3.5 14.9 - - + -
64F TYR* 4.2 14.8 - - - +
105F VAL 2.9 20.5 + - - +
106F SER 3.4 7.4 - - - +
108F ALA* 1.3 79.6 - - - +
110F MET* 1.3 62.4 + - + +
112F ASN 3.3 0.9 + - - -
113F CYS* 3.1 26.9 + - - -
319F ALA* 4.3 12.6 - - + +
322F LEU* 4.0 22.7 - - + -
323F ALA* 4.6 2.9 - - + +
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Residues in contact with MET 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F SER 3.1 14.7 + - - +
107F SER* 3.8 6.5 - - - +
108F ALA 3.3 0.4 - - - -
109F VAL* 1.3 74.2 - - + +
111F TRP* 1.3 66.2 + - - +
113F CYS* 3.2 1.6 + - - -
114F ALA 3.0 18.9 + - - -
147F VAL* 3.5 11.6 - - + +
189F LEU* 3.7 27.6 - - + -
191F VAL* 3.9 17.0 - - + -
237F LEU* 4.5 3.6 - - + -
239F VAL* 4.2 11.9 - - + -
241F PHE* 4.3 20.4 - - - -
276F GLU* 5.8 0.4 - - - +
278F HIS* 4.8 11.0 - - + -
322F LEU* 4.9 13.0 - - + -
326F PHE* 3.5 46.0 - - + -
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Residues in contact with TRP 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F SER 2.8 14.9 + - - +
108F ALA* 3.2 13.4 + - - +
110F MET* 1.3 76.5 - - - +
112F ASN* 1.3 79.6 + - - +
114F ALA* 3.2 5.3 + - + +
115F ALA* 3.0 20.6 + - + +
147F VAL* 3.5 34.0 - - + +
203F MET* 3.9 26.7 + - + -
204F TRP* 3.7 28.7 - + - -
206F GLU 3.6 17.4 + - - -
208F ILE* 4.0 12.0 - - + +
218F LEU* 3.9 21.5 - - + +
219F LEU* 3.5 37.3 - - + +
222F ALA* 3.6 26.2 - - + -
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Residues in contact with ASN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ILE* 3.7 21.4 - - - +
54F PHE* 3.6 34.8 - - + +
108F ALA 3.1 12.0 + - - +
109F VAL 3.7 2.0 - - - +
110F MET 3.2 0.2 - - - -
111F TRP* 1.3 83.3 - - - +
113F CYS* 1.3 65.3 + - - +
115F ALA* 3.2 2.6 + - - +
116F ARG* 3.0 24.3 + - - +
207F GLU* 3.2 21.6 + - + +
208F ILE* 2.8 44.5 + - - +
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Residues in contact with CYS 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE* 3.7 14.4 - - - -
109F VAL* 3.1 22.5 + - - -
110F MET* 3.2 1.8 + - - +
112F ASN* 1.3 76.2 - - - +
114F ALA* 1.3 59.4 + - - +
116F ARG 3.3 0.2 + - - -
117F TRP* 2.8 31.5 + - - +
323F ALA* 3.8 31.0 - - - -
326F PHE* 3.4 29.4 - - + -
327F PHE* 3.3 28.3 - - + -
330F LEU* 5.2 0.2 - - - -
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Residues in contact with ALA 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F MET 3.0 5.1 + - - -
111F TRP* 3.5 9.0 - - + +
113F CYS* 1.3 79.1 - - - +
115F ALA* 1.3 53.1 + - - +
117F TRP* 3.6 5.8 - - - +
118F ASN* 2.7 42.8 + - - +
145F VAL* 4.1 25.8 - - + +
146F ALA* 5.3 0.2 - - - -
147F VAL* 3.5 31.6 - - + +
204F TRP 5.4 0.4 - - - +
326F PHE* 4.3 3.7 - - + -
330F LEU* 5.1 0.2 - - - -
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F TRP* 3.0 15.6 + - - +
112F ASN 3.8 6.7 - - - +
113F CYS 3.2 0.4 - - - -
114F ALA* 1.3 77.9 - - - +
116F ARG* 1.3 57.3 + - - +
118F ASN* 3.6 1.4 - - - +
119F SER* 2.9 30.8 + - - -
127F ARG* 3.8 2.5 - - - -
204F TRP 3.3 15.0 + - - +
205F ARG 3.4 26.2 - - - +
206F GLU 3.6 20.0 - - - +
207F GLU* 3.8 6.5 - - + +
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Residues in contact with ARG 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE* 3.6 16.9 - - - -
112F ASN 3.0 13.1 + - - +
113F CYS 3.7 2.9 - - - +
115F ALA* 1.3 76.4 - - - +
117F TRP* 1.3 61.4 + - - +
119F SER* 3.3 4.7 + - - -
120F LEU* 3.1 20.6 + - - +
125F GLY 4.6 0.9 - - - +
126F TRP* 3.5 31.7 - - + -
127F ARG* 3.5 46.8 + - + +
129F GLN 3.0 28.7 + - - +
130F PRO* 3.0 28.3 + - - +
132F TYR* 4.1 9.5 - - - +
207F GLU* 2.6 41.0 + - - +
327F PHE* 4.3 12.6 - - + -
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Residues in contact with TRP 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F CYS 2.8 21.1 + - - +
114F ALA 3.6 2.7 - - - +
116F ARG* 1.3 73.3 - - - +
118F ASN* 1.3 79.2 + - - +
120F LEU* 3.2 6.3 + - + +
121F MET* 2.9 56.2 + - + +
126F TRP* 4.1 8.4 - - - -
135F PRO* 3.7 35.9 - - + -
137F LEU* 3.7 14.8 - - + -
143F ARG 2.9 20.5 + - - -
145F VAL* 4.2 11.7 - - + +
327F PHE* 4.5 10.3 - + + -
330F LEU* 3.5 42.2 - - + -
331F ASN* 3.8 15.9 - - - -
334F MET* 3.7 25.7 - - + +
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Residues in contact with ASN 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F ALA* 2.7 26.7 + - - +
115F ALA 3.6 4.0 - - - +
117F TRP* 1.3 79.2 - - - +
119F SER* 1.3 63.8 + - - +
121F MET* 3.1 3.2 + - - +
122F VAL* 3.1 27.7 + - - +
144F GLN* 3.1 29.1 - - + +
145F VAL* 2.9 42.2 + - - +
194F LEU* 5.2 0.2 - - - +
204F TRP* 2.8 36.5 + - - +
205F ARG* 4.1 6.5 - - + -
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Residues in contact with SER 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F ALA 2.9 17.9 + - - -
116F ARG* 3.4 6.3 - - - -
117F TRP 3.2 0.2 - - - -
118F ASN* 1.3 78.3 - - - +
120F LEU* 1.3 58.2 + - - +
122F VAL* 3.5 9.6 - - - +
124F GLU* 2.9 54.7 + - - +
125F GLY 3.9 8.9 + - - -
127F ARG* 3.4 28.4 + - - +
205F ARG* 4.1 8.0 - - - +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ARG 3.1 12.0 + - - +
117F TRP* 3.4 8.5 - - + +
119F SER* 1.3 76.1 - - - +
121F MET* 1.3 73.1 + - + +
123F GLY* 2.8 23.3 + - - -
125F GLY* 3.7 12.9 + - - +
126F TRP* 4.0 23.8 - - + +
134F ARG* 3.8 29.6 - - + +
135F PRO* 3.5 49.4 - - + +
137F LEU 5.4 0.9 - - - +
139F PRO* 4.0 17.6 - - + +
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Residues in contact with MET 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F TRP* 2.9 60.8 + - + +
118F ASN 3.1 7.3 + - - +
120F LEU* 1.3 93.0 - - + +
122F VAL* 1.3 58.3 + - - +
123F GLY 3.3 1.0 + - - -
135F PRO* 5.3 0.2 - - + -
137F LEU* 4.2 14.8 - - + +
138F SER 4.4 1.1 - - - +
139F PRO* 3.9 20.7 - - + +
140F SER* 3.0 49.4 + - - +
141F PRO* 3.3 1.7 - - - +
143F ARG* 3.6 28.9 - - - +
144F GLN* 4.2 11.7 - - + -
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Residues in contact with VAL 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASN 3.1 7.0 + - - +
119F SER 3.5 13.9 - - - +
121F MET* 1.3 75.7 - - - +
123F GLY* 1.3 57.3 + - - +
124F GLU* 3.9 10.5 - - + +
141F PRO* 4.0 16.7 - - + +
144F GLN* 3.3 40.6 - - - +
199F GLN 4.1 7.0 - - - +
205F ARG* 3.7 36.1 - - - +
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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