Contacts of the helix formed by residues 97 - 136 (chain C) in PDB entry 5TXV
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 97 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS* 4.4 16.5 - - - -
95C GLU* 3.2 8.3 - - + +
96C VAL* 1.3 82.2 - - - +
98C SER* 1.3 61.1 + - - +
99C ILE 3.1 1.7 + - - -
100C ILE* 3.3 14.7 + - - +
101C ARG* 3.4 25.0 + - - +
280C ASP 5.7 0.7 - - - +
283C PRO* 6.0 1.7 - - - +
284C LEU* 4.7 10.7 - - - +
290C VAL* 3.9 31.4 - - + +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LYS* 4.8 6.1 + - - -
86C PHE* 4.0 10.6 - - - -
94C LYS* 4.9 9.0 - - - +
95C GLU* 2.9 25.6 + - - +
96C VAL 3.1 0.2 - - - -
97C ASP* 1.3 74.9 - - - +
99C ILE* 1.3 57.7 + - - +
101C ARG* 3.6 16.7 - - - +
102C ASP* 2.7 50.2 + - - -
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.0 7.5 - - + +
81C VAL* 4.1 26.2 - - + -
85C LYS* 5.7 0.4 - - - +
86C PHE* 3.6 33.7 - - + -
96C VAL* 3.4 15.3 - - + +
97C ASP 3.1 1.0 - - - -
98C SER* 1.3 76.4 + - - +
100C ILE* 1.3 64.0 + - + +
102C ASP* 3.8 5.5 - - - +
103C LEU* 2.8 29.1 + - - +
253C VAL* 3.9 34.5 - - + -
255C ILE* 5.6 2.7 - - + -
281C LEU* 3.9 24.2 - - + -
284C LEU* 4.3 10.1 - - + -
304C PHE* 5.6 1.1 - - + -
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ASP 3.3 8.1 + - - +
99C ILE* 1.3 83.8 - - + +
101C ARG* 1.3 59.5 + - - +
103C LEU* 3.6 9.4 - - + +
104C THR* 2.8 36.6 + - - +
247C VAL* 4.8 5.6 - - + -
253C VAL* 5.1 1.1 - - + -
284C LEU* 4.1 24.2 - - + -
290C VAL* 4.3 18.4 - - + -
292C THR* 4.8 2.2 - - + -
297C VAL* 4.1 32.5 - - + -
299C THR* 3.9 27.1 - - + -
302C ILE* 4.2 12.8 - - + -
304C PHE* 5.0 9.0 - - + -
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASP* 3.4 23.6 + - - +
98C SER* 3.1 18.5 + - - +
100C ILE* 1.3 77.2 - - - +
102C ASP* 1.3 64.4 + - - +
104C THR* 3.3 3.8 + - - -
105C ASP* 3.1 32.6 + - - +
290C VAL* 4.8 6.8 - - + +
291C SER* 2.9 33.8 + - - +
292C THR* 3.8 29.8 - - + +
293C LYS 4.6 3.0 - - - +
294C HIS* 5.4 0.2 - - - -
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Residues in contact with ASP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 3.5 23.5 - - + +
81C VAL* 6.0 0.5 - - - +
85C LYS* 4.7 10.2 + - - -
98C SER* 2.7 35.2 + - - +
99C ILE* 5.0 0.7 - - - -
101C ARG* 1.3 73.3 - - - +
103C LEU* 1.3 64.6 + - - +
105C ASP* 3.4 13.4 + - - +
106C ALA* 3.2 21.7 + - - +
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PRO* 3.6 22.2 - - + -
78C PHE 3.7 17.3 - - - +
79C ILE* 3.8 23.5 - - + +
99C ILE 2.8 19.2 + - - +
100C ILE* 3.6 9.0 - - + +
102C ASP* 1.3 77.7 - - - +
104C THR* 1.3 57.1 + - - +
106C ALA* 3.3 3.4 + - - +
107C ALA* 2.9 23.9 + - - +
247C VAL* 3.7 28.7 - - + -
251C GLY* 4.6 8.1 - - - -
252C ILE 3.9 5.2 - - - +
253C VAL* 3.9 21.1 - - + -
302C ILE* 4.5 11.0 - - + -
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Residues in contact with THR 104 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ILE* 2.8 20.5 + - - +
101C ARG* 3.3 5.8 + - - -
103C LEU* 1.3 73.4 - - - +
105C ASP* 1.3 55.3 + - - +
107C ALA 3.1 0.9 + - - -
108C VAL* 2.7 39.3 + - + +
243C ALA* 4.9 4.3 - - + -
244C ILE* 4.8 10.1 - - + -
247C VAL* 3.9 19.4 - - + +
292C THR* 4.4 9.0 - - - +
294C HIS* 4.1 28.9 - - + -
297C VAL* 4.0 22.0 - - + +
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.1 22.4 + - - +
102C ASP* 3.7 14.8 - - - +
103C LEU 3.3 0.4 - - - -
104C THR* 1.3 75.7 - - - +
106C ALA* 1.3 60.6 + - - +
108C VAL* 3.6 7.2 + - - +
109C LYS* 3.3 21.0 + - - +
293C LYS* 4.2 6.4 - - - -
294C HIS* 2.7 37.5 + - - -
289D THR* 5.1 5.4 - - + +
291D SER* 4.0 23.2 + - - +
296D MET* 4.5 13.5 - - + +
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PRO* 5.5 0.4 - - - -
78C PHE 4.3 19.7 - - - +
79C ILE* 5.8 1.3 - - + -
102C ASP 3.2 13.5 + - - +
103C LEU* 3.6 9.2 - - + +
105C ASP* 1.3 76.5 - - - +
107C ALA* 1.3 59.4 + - - +
109C LYS* 3.5 5.3 + - - +
110C MET* 2.9 30.4 + - - +
289D THR* 5.2 15.2 - - - +
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PRO* 3.7 21.0 - - + +
103C LEU 2.9 8.8 + - - +
104C THR 3.1 5.1 + - - +
106C ALA* 1.3 73.8 - - - +
108C VAL* 1.3 59.9 + - - +
110C MET* 4.1 6.1 - - - -
111C VAL* 2.9 34.3 + - - +
243C ALA* 3.6 13.9 - - + +
246C ALA* 4.8 1.6 - - + -
247C VAL* 3.5 32.1 - - + -
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Residues in contact with VAL 108 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C THR* 2.7 25.4 + - + +
105C ASP* 3.8 7.6 - - - +
106C ALA 3.2 0.2 - - - -
107C ALA* 1.3 72.8 - - - +
109C LYS* 1.3 61.5 + - - +
111C VAL* 3.3 6.0 - - + +
112C ARG* 2.9 39.8 + - + +
239C LEU* 5.4 6.1 - - + -
240C LYS* 5.4 8.3 - - + -
243C ALA* 3.8 17.5 - - + -
294C HIS* 3.6 41.1 - - + +
296D MET* 5.0 9.9 - - + -
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASP 3.3 13.7 + - - +
106C ALA* 4.0 4.0 - - - +
108C VAL* 1.3 81.9 - - + +
110C MET* 1.3 61.1 + - - +
112C ARG* 4.3 8.1 - - + +
113C VAL* 3.1 42.1 + - + +
248D GLU* 4.8 6.4 + - - -
289D THR* 3.7 26.9 - - + +
296D MET* 3.9 32.1 + - + +
298D LYS* 4.5 26.0 - - - -
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Residues in contact with MET 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ASN* 3.3 29.6 - - - +
76C ALA 3.7 14.4 - - - +
77C PRO* 3.5 33.9 - - + -
78C PHE 5.5 0.4 - - - -
106C ALA 2.9 19.7 + - - +
107C ALA* 3.7 6.1 - - - +
109C LYS* 1.3 76.3 - - - +
111C VAL* 1.3 73.5 + - + +
113C VAL* 4.1 1.7 - - - +
114C GLN* 3.1 46.7 + - - +
246C ALA* 5.0 2.7 - - + -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ALA 2.9 23.8 + - - +
108C VAL* 3.3 7.9 - - - +
110C MET* 1.3 83.0 - - + +
112C ARG* 1.3 60.3 + - - +
114C GLN* 3.9 10.8 - - - +
115C ALA* 2.9 30.0 + - - +
239C LEU* 3.9 27.6 - - + +
242C ASP* 3.3 26.2 - - - +
243C ALA* 3.7 27.1 - - + -
246C ALA* 4.4 10.8 - - + -
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Residues in contact with ARG 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C VAL* 2.9 25.4 + - + +
109C LYS* 4.0 7.9 - - - +
111C VAL* 1.3 74.7 - - - +
113C VAL* 1.3 64.8 + - + +
115C ALA* 3.1 3.8 + - - +
116C ILE* 2.9 53.8 + - + +
234C VAL* 5.8 6.3 - - - +
239C LEU* 4.2 24.5 - - + +
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Residues in contact with VAL 113 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LYS* 3.1 44.0 + - + +
110C MET* 4.3 2.0 - - - +
112C ARG* 1.3 78.5 - - + +
114C GLN* 1.3 63.6 + - + +
116C ILE* 3.2 19.7 + - + +
117C GLU* 3.2 32.4 + - + +
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Residues in contact with GLN 114 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ASN* 2.5 46.2 + - - +
110C MET* 3.1 37.3 + - - +
111C VAL* 3.9 11.7 - - - +
113C VAL* 1.3 78.6 - - + +
115C ALA* 1.3 60.7 + - - +
117C GLU* 3.2 24.7 + - + +
118C LYS* 3.6 11.0 + - - +
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C VAL 2.9 19.4 + - - +
112C ARG 3.1 4.7 + - - +
114C GLN* 1.3 73.8 - - - +
116C ILE* 1.3 65.5 + - - +
118C LYS* 3.2 15.9 + - + +
119C ASN* 3.1 32.2 + - - +
234C VAL* 5.0 3.1 - - + -
239C LEU* 3.7 22.7 - - + -
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Residues in contact with ILE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ARG* 2.9 49.7 + - + +
113C VAL* 3.2 22.4 + - + +
115C ALA* 1.3 75.7 - - + +
117C GLU* 1.3 55.3 + - - +
119C ASN* 3.6 13.6 - - + +
120C ARG* 2.7 38.7 + - + +
230C ALA* 6.5 0.7 - - + -
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Residues in contact with GLU 117 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 3.2 24.9 + - + +
114C GLN* 3.3 16.2 - - + +
115C ALA 3.2 0.2 - - - -
116C ILE* 1.3 82.7 - - - +
118C LYS* 1.3 61.9 + - + +
120C ARG* 3.8 31.6 + - - +
121C TYR* 4.2 5.2 + - - +
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLN 3.9 12.1 - - - +
115C ALA* 3.2 13.5 + - + +
117C GLU* 1.3 79.0 - - + +
119C ASN* 1.3 66.2 + - - +
120C ARG 3.2 0.9 + - - -
121C TYR* 3.3 13.9 + - - +
122C ARG* 3.8 14.4 + - - +
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Residues in contact with ASN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ALA* 3.1 21.6 + - - +
116C ILE* 3.9 14.7 - - + +
118C LYS* 1.3 76.0 - - - +
120C ARG* 1.3 64.5 + - - +
122C ARG* 4.8 1.3 - - - +
123C ALA* 3.1 28.2 + - - +
226C ILE* 6.2 0.4 - - - -
230C ALA* 3.8 42.3 + - + +
233C LEU* 3.9 22.5 - - + +
234C VAL* 4.0 19.6 + - - +
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Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ILE* 2.7 25.9 + - + +
117C GLU* 3.8 28.3 + - - +
118C LYS 3.2 0.6 - - - -
119C ASN* 1.3 73.5 - - - +
121C TYR* 1.3 56.2 + - - +
123C ALA* 4.7 1.9 - - - +
124C GLU* 3.1 40.7 + - - +
226C ILE* 5.9 5.1 - - - +
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Residues in contact with TYR 121 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C GLU 4.2 4.4 + - - +
118C LYS* 3.3 9.9 + - - +
119C ASN 3.1 0.8 - - - -
120C ARG* 1.3 76.6 - - - +
122C ARG* 1.3 76.1 + - + +
123C ALA 3.2 1.1 - - - -
124C GLU* 3.1 22.5 + - - +
125C GLU* 3.4 37.1 + - + +
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Residues in contact with ARG 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LYS 3.8 11.1 + - - +
119C ASN* 3.7 1.7 + - - +
121C TYR* 1.3 87.8 - - + +
123C ALA* 1.3 63.1 + - - +
125C GLU* 3.1 18.9 + - - +
126C LEU* 3.0 38.0 + - + +
233C LEU* 3.6 32.4 - - + +
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Residues in contact with ALA 123 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ASN 3.1 20.5 + - - +
120C ARG 4.7 1.3 - - - +
122C ARG* 1.3 77.9 - - - +
124C GLU* 1.3 53.8 + - + +
126C LEU* 4.2 0.3 - - - +
127C ALA* 2.7 38.4 + - - +
226C ILE* 4.3 28.0 - - + +
229C GLU* 3.8 29.4 - - + +
230C ALA* 4.4 5.4 - - + +
233C LEU* 4.0 2.2 - - + +
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Residues in contact with GLU 124 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ARG* 3.1 39.2 + - - +
121C TYR* 3.1 13.8 + - - +
123C ALA* 1.3 77.2 - - + +
125C GLU* 1.3 59.4 + - + +
127C ALA* 4.0 5.2 - - - +
128C GLU* 3.0 38.3 + - + +
222C MET* 5.2 4.2 - - - +
226C ILE* 5.1 15.9 - - + +
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Residues in contact with GLU 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TYR* 3.4 46.1 + - + +
122C ARG* 3.1 19.4 + - - +
124C GLU* 1.3 77.6 - - + +
126C LEU* 1.3 70.4 + - + +
128C GLU* 3.2 12.0 + - - +
129C GLU* 3.1 34.5 + - - +
164C ARG* 6.3 0.9 - - - +
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Residues in contact with LEU 126 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 3.0 42.0 + - + +
125C GLU* 1.3 85.1 - - + +
127C ALA* 1.3 61.5 + - - +
129C GLU* 3.5 25.9 + - + +
130C ARG* 3.1 31.2 + - - +
229C GLU* 3.3 41.5 - - + +
233C LEU* 5.3 4.9 - - + -
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Residues in contact with ALA 127 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ALA 2.7 23.9 + - - +
124C GLU* 4.0 3.1 - - - +
126C LEU* 1.3 72.2 - - - +
128C GLU* 1.3 64.5 + - - +
130C ARG* 3.3 3.3 + - - +
131C ILE* 3.1 24.9 + - - +
222C MET* 3.5 26.4 - - - +
225C LEU* 3.7 35.6 - - + +
226C ILE* 4.8 2.9 - - + +
229C GLU* 5.0 1.5 - - - +
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Residues in contact with GLU 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLU* 3.0 28.7 + - + +
125C GLU* 3.2 10.7 + - - +
127C ALA* 1.3 74.6 - - - +
129C GLU* 1.3 64.5 + - + +
131C ILE* 3.2 7.6 - - - +
132C LEU* 3.0 37.9 + - + +
160C ARG* 4.6 7.6 + - - +
163C LEU* 3.8 21.5 - - + +
164C ARG* 2.6 60.3 + - - +
222C MET* 4.5 6.5 - - + -
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Residues in contact with GLU 129 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 3.1 25.1 + - - +
126C LEU* 3.9 26.2 - - + +
127C ALA 3.3 0.2 - - - -
128C GLU* 1.3 78.1 - - + +
130C ARG* 1.3 59.7 + - + +
132C LEU* 4.0 2.2 - - + -
133C ASP* 3.0 30.0 + - - +
156C ARG* 3.3 19.3 + - - +
160C ARG* 5.4 7.9 - - - +
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Residues in contact with ARG 130 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LEU* 3.1 20.8 + - - +
127C ALA* 3.7 5.6 - - - +
128C GLU 3.2 0.4 - - - -
129C GLU* 1.3 75.9 - - + +
131C ILE* 1.3 63.2 + - - +
133C ASP* 3.2 29.1 + - - +
134C VAL* 4.0 4.0 + - - +
225C LEU* 3.7 28.7 - - + -
229C GLU* 4.7 14.9 + - - +
232C LYS* 5.1 13.1 - - - +
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Residues in contact with ILE 131 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ALA 3.1 14.6 + - - +
128C GLU* 3.2 15.5 - - - +
130C ARG* 1.3 77.2 - - - +
132C LEU* 1.3 59.1 + - + +
134C VAL* 3.1 30.6 - - + +
135C LEU* 3.6 17.0 - - + +
163C LEU* 3.7 41.1 - - + -
218C ILE* 4.7 26.0 - - + +
221C ALA* 5.2 9.9 - - + -
222C MET* 3.7 16.2 - - + +
225C LEU* 4.5 6.5 - - + +
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Residues in contact with LEU 132 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU* 3.0 28.3 + - + +
129C GLU* 4.5 2.0 - - + -
130C ARG 3.2 0.2 - - - -
131C ILE* 1.3 78.1 - - + +
133C ASP* 1.3 58.6 + - - +
134C VAL 3.2 1.1 - - - -
135C LEU* 3.8 10.3 - - + +
136C ILE* 2.9 27.1 + - + +
156C ARG* 3.2 51.5 + - - +
159C PHE* 3.9 15.5 - - + -
160C ARG* 3.4 60.1 - - + +
163C LEU* 5.2 5.4 - - + -
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Residues in contact with ASP 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLU 3.0 17.9 - - - +
130C ARG* 3.2 24.6 + - - +
132C LEU* 1.3 77.5 - - - +
134C VAL* 1.3 58.4 + - - +
136C ILE 4.0 3.1 - - - -
137C PRO* 3.1 29.0 - - - +
138C PRO* 4.0 18.5 - - + +
156C ARG* 3.0 25.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG 4.0 2.9 + - - +
131C ILE* 3.1 30.5 + - + +
133C ASP* 1.3 79.1 - - - +
135C LEU* 1.3 72.3 + - + +
137C PRO* 3.8 10.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ILE* 3.6 25.4 - - + +
132C LEU* 3.5 14.5 + - + +
133C ASP 3.4 0.2 - - - -
134C VAL* 1.3 88.1 - - + +
136C ILE* 1.3 70.2 + - + +
137C PRO* 3.6 4.9 - - - +
159C PHE* 3.8 56.3 - - + +
163C LEU* 6.1 4.7 - - + -
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 2.9 20.6 + - + +
133C ASP 3.7 0.2 - - - -
135C LEU* 1.3 85.4 - - + +
137C PRO* 1.3 70.4 - - + +
138C PRO* 3.3 7.9 - - + +
153C SER* 5.2 9.9 - - - +
155C ALA* 3.7 26.9 - - + +
156C ARG* 3.6 20.9 + - - +
159C PHE* 3.6 33.7 - - + -
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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