Contacts of the helix formed by residues 105 - 138 (chain R) in PDB entry 6VMS
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 ILE 105 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103R SER* 3.4 3.5 - - - -
104R ARG* 1.3 99.2 - - + +
106R HIS* 1.3 63.8 + - - +
107R CYS 3.3 0.2 - - - -
108R ASP* 3.0 18.7 + - - +
109R ILE* 3.2 23.6 + - + +
171R LEU 4.9 8.1 - - - +
172R PHE* 3.2 40.8 - - + -
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Residues in contact with HIS 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R TRP* 2.9 50.9 + + - -
100R TRP* 3.5 21.5 - + + -
102R PHE* 4.4 14.3 - + + -
103R SER* 3.8 26.7 + - - +
104R ARG 3.3 1.0 - - - -
105R ILE* 1.3 79.0 - - - +
107R CYS* 1.3 58.8 + - - +
109R ILE* 3.0 17.9 + - + +
110R PHE* 3.0 26.3 + - + +
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Residues in contact with CYS 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100R TRP* 3.8 15.6 - - + -
103R SER 4.2 6.9 + - - +
104R ARG 4.0 7.7 + - - +
105R ILE 3.3 1.0 - - - -
106R HIS* 1.3 78.1 - - - +
108R ASP* 1.3 58.8 + - - +
110R PHE* 3.6 1.4 - - - +
111R VAL* 3.0 33.1 + - - +
175R ASN* 4.1 12.6 - - - +
181R GLU 4.7 2.9 - - - +
182R CYS* 2.0 61.5 - - + -
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Residues in contact with ASP 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R ARG 4.0 12.1 - - - +
105R ILE* 3.0 14.9 + - - +
107R CYS* 1.3 75.6 - - - +
109R ILE* 1.3 59.1 + - - +
111R VAL* 3.9 4.7 - - - +
112R THR* 2.5 38.9 + - - -
170R LEU 3.3 23.0 - - - +
171R LEU 3.5 13.7 - - - +
172R PHE* 3.8 0.9 - - - -
173R GLY* 3.5 21.1 + - - -
175R ASN* 3.7 30.7 + - - +
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Residues in contact with ILE 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R ILE* 3.2 25.8 + - + +
106R HIS* 3.0 20.1 + - + +
108R ASP* 1.3 76.6 - - - +
110R PHE* 1.3 66.0 + - - +
112R THR* 3.7 4.3 - - - -
113R LEU* 2.9 42.4 + - + +
171R LEU* 4.3 25.1 - - + +
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Residues in contact with PHE 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R LEU 5.5 1.1 - - - -
87R VAL* 3.1 44.2 - - + -
90R TRP* 3.2 28.3 - + + -
91R VAL* 3.7 28.3 - - + -
94R LEU* 4.0 14.8 - - + -
100R TRP* 4.4 10.1 - + + -
106R HIS 3.0 12.3 + - - +
107R CYS* 3.6 8.3 - - - +
108R ASP 3.3 0.2 - - - -
109R ILE* 1.3 77.7 - - - +
111R VAL* 1.3 66.9 + - + +
113R LEU* 3.3 7.2 + - - +
114R ASP* 3.0 25.3 + - - +
182R CYS* 3.9 17.7 - - - -
601R 08Y 3.5 26.0 - - + -
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Residues in contact with VAL 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107R CYS* 3.0 29.7 + - - +
108R ASP* 4.1 4.9 - - - +
110R PHE* 1.3 80.2 - - + +
112R THR* 1.3 64.6 + - - +
114R ASP* 3.2 8.4 + - + +
115R VAL* 3.0 27.3 + - + +
170R LEU* 3.7 22.4 - - + -
175R ASN* 5.0 6.3 - - - +
182R CYS 4.8 0.7 - - - +
184R ILE* 3.6 32.5 - - + -
601R 08Y 3.5 28.3 - - + -
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Residues in contact with THR 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108R ASP 2.5 23.7 + - - -
109R ILE* 3.7 5.6 - - - -
111R VAL* 1.3 78.4 - - - +
113R LEU* 1.3 59.9 + - + +
115R VAL* 3.4 0.4 + - - -
116R MET* 2.9 36.8 + - + +
164R PHE* 6.1 2.5 - - + -
167R SER* 3.7 31.5 - - - +
170R LEU* 3.6 26.4 - - - +
171R LEU* 3.7 26.6 + - + -
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Residues in contact with LEU 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R LEU* 3.9 42.0 - - + +
87R VAL* 3.3 14.5 - - + +
90R TRP* 5.6 2.7 - - + -
109R ILE* 2.9 36.7 + - + +
110R PHE* 3.8 2.9 - - - +
112R THR* 1.3 75.6 - - + +
114R ASP* 1.3 68.3 + - - +
116R MET* 4.4 10.1 - - - -
117R MET* 2.9 49.8 + - + +
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Residues in contact with ASP 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83R VAL* 6.0 0.7 - - - -
87R VAL* 3.3 17.5 - - + +
91R VAL* 5.9 0.5 - - - +
110R PHE* 3.0 22.3 + - + +
111R VAL* 3.3 12.8 - - - +
113R LEU* 1.3 78.6 - - - +
115R VAL* 1.3 62.7 + - + +
117R MET* 4.3 1.0 - - - +
118R CYS* 3.0 24.5 + - - -
412R THR* 5.0 0.3 - - - +
416R TYR* 2.3 28.7 + - - -
601R 08Y 2.8 51.0 + - + +
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Residues in contact with VAL 115 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111R VAL* 3.0 18.8 + - + +
112R THR 4.0 2.0 - - - +
114R ASP* 1.3 76.6 - - + +
116R MET* 1.3 64.5 + - - +
118R CYS* 4.2 0.3 - - - +
119R THR* 2.8 40.7 + - - +
166R ILE* 4.8 8.5 - - + +
167R SER* 4.4 17.7 - - - -
170R LEU* 4.0 20.6 - - + -
184R ILE* 5.5 0.4 - - + -
189R PHE* 5.2 1.8 - - + -
193R SER* 5.1 3.6 - - - +
601R 08Y 3.9 53.6 - - + +
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Residues in contact with MET 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112R THR* 2.9 22.9 + - - +
113R LEU* 4.0 11.4 - - - +
115R VAL* 1.3 77.8 - - - +
117R MET* 1.3 75.5 + - + +
119R THR* 4.5 0.2 - - - -
120R ALA* 2.9 24.6 + - - +
160R TRP* 4.3 24.0 - - + +
163R SER* 3.4 26.3 - - - +
164R PHE* 3.4 45.3 - - + +
167R SER* 3.6 19.5 - - - +
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Residues in contact with MET 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R ALA* 3.9 5.8 - - - +
82R LEU* 3.2 48.2 - - + +
83R VAL* 3.2 28.5 - - + +
86R LEU* 5.3 2.2 - - + -
87R VAL* 5.1 0.2 - - + -
113R LEU* 2.9 41.3 + - + +
116R MET* 1.3 90.2 - - + +
118R CYS* 1.3 59.2 + - - +
120R ALA* 3.2 4.1 + - - +
121R SER* 2.9 30.1 + - - -
160R TRP* 3.5 30.7 - - + -
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Residues in contact with CYS 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83R VAL* 4.4 9.0 - - - -
114R ASP* 3.0 33.8 + - - +
115R VAL 4.2 0.2 - - - +
117R MET* 1.3 76.0 - - - +
119R THR* 1.3 62.0 + - - +
121R SER* 3.2 7.7 + - - -
122R ILE* 3.0 27.5 + - - +
386R TRP* 3.4 31.3 - - + -
416R TYR* 3.8 15.7 - - - -
419R SER* 5.9 0.9 - - - -
601R 08Y 3.4 27.6 - - + -
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Residues in contact with THR 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115R VAL* 2.8 30.6 + - - +
116R MET 3.6 3.6 - - - -
118R CYS* 1.3 74.9 - - - +
120R ALA* 1.3 59.9 + - - +
122R ILE* 3.3 2.4 + - - +
123R LEU* 2.9 57.4 + - + +
162R LEU* 5.6 0.9 - - + -
163R SER* 3.7 19.7 - - - -
166R ILE* 4.1 5.0 - - + +
196R VAL* 6.4 0.4 - - + -
197R SER* 3.0 35.4 + - - +
601R 08Y 3.5 8.8 - - - +
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Residues in contact with ALA 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R ALA* 4.1 8.5 - - + -
116R MET 2.9 17.9 + - - +
117R MET 3.5 5.8 - - - +
119R THR* 1.3 77.0 - - - +
121R SER* 1.3 58.2 + - - +
124R ASN* 2.9 37.4 + - - +
159R VAL* 3.5 14.9 - - + +
160R TRP* 3.8 33.0 - - + -
163R SER* 3.9 6.0 - - - +
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Residues in contact with SER 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R LEU* 3.6 19.4 - - - +
79R ALA* 3.8 11.6 - - - +
80R ASP* 3.1 24.1 + - - -
83R VAL* 5.0 1.6 - - - +
117R MET 2.9 16.2 + - - -
118R CYS* 3.2 11.0 + - - -
120R ALA* 1.3 77.7 - - - +
122R ILE* 1.3 64.6 + - - +
124R ASN* 4.6 0.2 - - - -
125R LEU* 3.0 28.4 + - - +
386R TRP* 5.8 6.1 - - - -
418R ASN* 5.5 6.5 - - - -
419R SER* 4.7 1.5 + - - -
422R ASN* 5.6 1.3 - - - -
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Residues in contact with ILE 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R CYS 3.0 10.0 + - - +
119R THR 3.9 2.7 - - - +
121R SER* 1.3 76.6 - - - +
123R LEU* 1.3 58.5 + - - +
125R LEU* 3.1 12.0 + - + +
126R CYS* 3.0 24.4 + - - +
197R SER 3.2 25.1 - - - +
198R PHE* 4.3 18.8 - - + -
201R PRO* 3.7 19.5 - - + -
205R ILE* 4.4 0.7 - - + +
382R PHE* 4.0 28.5 - - + -
386R TRP* 4.6 21.3 - - + +
390R PHE* 4.9 0.9 - - + -
601R 08Y 3.4 29.4 - - + -
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Residues in contact with LEU 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119R THR* 2.9 41.5 + - + +
122R ILE* 1.3 77.2 - - + +
124R ASN* 1.3 57.1 + - - +
126R CYS* 3.3 9.8 + - + +
127R ALA* 2.9 22.7 + - - +
159R VAL* 3.5 42.7 - - + +
162R LEU* 3.8 31.2 - - + -
196R VAL* 4.2 11.0 - - + +
197R SER 5.0 1.1 - - - +
201R PRO* 4.1 27.1 - - + -
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Residues in contact with ASN 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R LEU* 4.5 14.6 - - + +
75R SER* 3.5 43.8 + - - -
76R LEU* 3.6 16.2 - - + +
79R ALA* 4.9 0.2 - - - +
120R ALA* 2.9 26.2 + - - +
121R SER 3.8 3.8 - - - +
123R LEU* 1.3 75.0 - - - +
125R LEU* 1.3 59.9 + - - +
127R ALA* 3.2 4.6 + - - +
128R ILE* 2.9 36.5 + - + +
156R ILE* 4.9 3.1 - - - -
159R VAL* 3.1 26.4 - - - +
160R TRP* 4.8 5.3 + - - +
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Residues in contact with LEU 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R LEU* 3.9 17.9 - - + -
121R SER* 3.0 21.1 + - - +
122R ILE* 3.4 9.6 - - + +
124R ASN* 1.3 76.5 - - - +
126R CYS* 1.3 62.8 + - - +
128R ILE* 3.3 7.5 + - + +
129R SER* 3.0 27.4 + - - -
205R ILE* 3.9 11.0 - - + -
209R TYR* 4.9 0.3 + - - -
382R PHE* 3.6 37.0 - - + -
418R ASN* 4.1 4.3 - - - +
422R ASN* 3.8 19.3 - - - +
426R TYR* 3.3 42.2 + - + +
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Residues in contact with CYS 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ILE 3.0 11.9 + - - +
123R LEU* 3.4 14.1 - - + +
124R ASN 3.2 0.2 - - - -
125R LEU* 1.3 78.0 - - - +
127R ALA* 1.3 57.8 + - - +
129R SER* 3.3 3.3 + - - -
130R ILE* 2.9 41.7 + - - +
201R PRO* 4.0 21.1 - - + -
204R VAL* 3.4 37.9 - - - +
205R ILE* 3.7 13.1 - - + +
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Residues in contact with ALA 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R LEU* 4.0 13.5 - - + -
123R LEU 2.9 17.1 + - - +
124R ASN* 3.2 9.6 + - - +
126R CYS* 1.3 75.4 - - - +
128R ILE* 1.3 58.6 + - - +
130R ILE* 3.2 8.6 + - - +
131R ASP* 2.9 26.0 + - - +
155R MET* 3.5 39.4 - - + +
159R VAL* 4.5 6.7 - - + -
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Residues in contact with ILE 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R THR* 4.8 12.5 - - + +
72R LEU* 3.6 32.5 - - + +
73R ILE* 4.0 25.8 - - + +
76R LEU* 4.5 15.3 - - + -
124R ASN 2.9 23.9 + - - +
125R LEU* 3.6 11.0 - - + +
126R CYS 3.2 0.2 - - - -
127R ALA* 1.3 76.6 - - - +
129R SER* 1.3 63.7 + - - +
131R ASP* 3.1 4.8 + - - +
132R ARG* 2.9 54.4 + - + +
209R TYR* 4.9 1.8 - - - +
426R TYR* 4.5 9.4 - - + -
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Residues in contact with SER 129 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R LEU 3.0 13.9 + - - -
126R CYS 3.3 7.6 + - - -
128R ILE* 1.3 76.1 - - - +
130R ILE* 1.3 62.8 + - - +
132R ARG* 3.3 6.2 + - - +
133R TYR 2.9 19.1 + - - -
204R VAL* 6.0 0.4 - - - -
205R ILE* 3.9 13.6 - - - +
208R VAL* 3.1 30.9 - - - +
209R TYR* 2.9 40.4 + - - -
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Residues in contact with ILE 130 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R CYS* 2.9 35.3 + - - +
127R ALA* 3.2 11.9 + - - +
129R SER* 1.3 78.8 - - - +
131R ASP* 1.3 57.1 + - - +
133R TYR* 3.3 10.2 + - + +
134R THR* 2.9 35.5 + - - +
151R ARG* 6.2 0.9 - - - -
155R MET* 3.9 19.5 - - + -
204R VAL* 4.5 14.6 - - + -
208R VAL* 4.8 5.8 - - + -
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Residues in contact with ASP 131 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R THR* 3.1 27.5 - - - +
69R THR* 2.8 30.9 - - + +
72R LEU* 4.4 3.8 - - + -
127R ALA 2.9 12.9 + - - +
128R ILE 3.1 8.5 + - - +
130R ILE* 1.3 77.6 - - - +
132R ARG* 1.3 58.3 + - - +
134R THR* 3.2 8.8 + - - -
135R ALA* 2.9 26.3 + - - +
142R TYR* 3.1 19.1 - - - -
151R ARG* 3.2 22.5 + - - -
155R MET* 4.1 7.3 - - + +
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Residues in contact with ARG 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A CYS* 2.3 51.7 + - + -
352A GLY* 3.8 3.2 + - - -
353A LEU* 3.5 31.5 - - + +
69R THR* 5.1 1.1 - - + -
73R ILE* 5.5 2.4 - - - +
128R ILE* 2.9 30.9 + - + +
129R SER* 3.3 6.0 + - - +
131R ASP* 1.3 73.5 - - - +
133R TYR* 1.3 66.9 + - - +
135R ALA* 3.0 18.9 + - - +
136R VAL* 3.0 18.2 + - - +
209R TYR* 3.6 31.2 + - - -
212R ILE* 3.7 12.3 - - + -
378R TYR* 3.5 14.9 + - - -
426R TYR* 3.3 36.4 - - - -
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Residues in contact with TYR 133 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129R SER 2.9 13.5 + - - +
130R ILE* 3.3 13.2 + - + +
132R ARG* 1.3 75.4 - - - +
134R THR* 1.3 62.7 + - - +
136R VAL* 4.2 3.8 - - + -
137R ALA* 2.8 60.9 + - + +
138R MET* 5.0 12.6 - - + -
208R VAL* 3.8 20.4 - - + -
211R LYS* 3.7 48.9 + - + +
212R ILE* 3.8 10.6 - - + +
215R VAL* 6.2 2.2 - - + -
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Residues in contact with THR 134 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130R ILE* 2.9 21.4 + - - +
131R ASP* 3.3 14.9 - - - +
133R TYR* 1.3 80.4 - - - +
135R ALA* 1.3 64.7 + - - +
138R MET* 3.0 53.0 + - + +
141R LEU* 4.5 19.5 - - + -
142R TYR* 4.7 6.9 - - + +
151R ARG* 4.5 26.4 - - - +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 4.8 2.3 - - - +
347A ASN* 3.5 33.9 + - + +
351A CYS* 4.7 5.2 - - - -
131R ASP 2.9 13.1 + - - +
132R ARG* 3.0 14.3 + - - +
134R THR* 1.3 76.8 - - - +
136R VAL* 1.3 63.6 + - + +
139R PRO* 3.1 23.4 - - - +
142R TYR* 4.0 25.4 - - + -
----------------------------------------------------------
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Residues in contact with VAL 136 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 4.6 16.2 - - + +
348A LEU* 3.3 40.2 - - + -
353A LEU* 5.2 0.7 - - + -
132R ARG 3.0 15.7 + - - +
133R TYR* 3.8 5.2 - - + +
135R ALA* 1.3 82.2 - - + +
137R ALA* 1.3 69.2 + - + +
138R MET 3.4 0.7 - - - -
139R PRO* 3.5 14.0 - - - +
212R ILE* 3.9 29.2 - - + -
215R VAL* 4.6 27.9 - - + +
216R LEU* 5.1 5.2 - - + -
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Residues in contact with ALA 137 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R TYR* 2.8 60.8 + - + +
136R VAL* 1.3 75.1 - - + +
138R MET* 1.3 62.7 + - + +
139R PRO* 3.3 7.7 - - - +
215R VAL* 5.7 6.7 - - + -
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Residues in contact with MET 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R TYR* 5.0 11.2 - - + -
134R THR* 3.0 33.1 + - + +
137R ALA* 1.3 88.4 - - + +
139R PRO* 1.3 57.8 - - - +
140R MET 2.9 11.3 + - - -
141R LEU* 3.2 44.3 + - + +
142R TYR 4.2 1.4 + - - -
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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) + - + + + + + -
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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