Contacts of the helix formed by residues 113 - 148 (chain A) in PDB entry 6JOD
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 GLY 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TRP* 2.4 35.4 + - - +
111A LEU 3.2 6.1 + - - -
112A PHE* 1.3 78.3 - - - +
114A PRO* 1.3 76.1 - - - +
115A VAL* 3.4 3.4 - - - -
116A MET 3.6 1.0 + - - -
117A CYS* 3.1 6.8 + - - +
184A VAL* 4.0 1.6 - - - -
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Residues in contact with PRO 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY* 1.3 81.9 - - - +
115A VAL* 1.3 72.0 + - + +
117A CYS* 3.1 3.3 + - - +
118A LYS* 2.9 28.8 + - - +
183A ASP* 3.5 22.3 - - - +
184A VAL* 3.7 23.1 - - + +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE 5.1 2.5 - - - +
113A GLY* 4.8 0.9 - - - -
114A PRO* 1.3 85.1 - - + +
116A MET* 1.3 70.9 + - + +
118A LYS* 3.4 7.9 + - - +
119A VAL* 2.9 37.5 + - + +
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Residues in contact with MET 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TRP* 3.7 5.2 - - + -
112A PHE* 3.2 46.2 - - + +
113A GLY 3.6 1.7 + - - +
114A PRO 3.2 0.6 - - - -
115A VAL* 1.3 86.3 - - + +
117A CYS* 1.3 57.6 + - - +
119A VAL* 4.5 7.2 - - - +
120A PHE* 2.9 63.1 + - + +
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Residues in contact with CYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TRP* 3.5 11.8 - - - +
113A GLY 3.1 7.1 + - - +
114A PRO 3.1 8.3 + - - +
116A MET* 1.3 72.9 - - - +
118A LYS* 1.3 65.6 + - - +
121A GLY 3.0 19.3 + - - +
182A ARG* 3.3 18.0 - - - +
183A ASP* 3.5 21.3 - - - -
184A VAL* 3.5 17.7 - - + -
195A CYS* 2.0 54.3 - - - -
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PRO 2.9 15.6 + - - +
115A VAL* 3.4 11.7 - - - +
117A CYS* 1.3 75.5 - - - +
119A VAL* 1.3 59.1 + - + +
122A SER* 2.7 37.6 + - - -
178A THR 5.0 0.6 - - - +
179A PHE* 3.0 32.6 + - + +
180A TYR* 2.8 33.9 + - - +
181A PHE* 3.5 3.6 - - - +
182A ARG* 3.1 28.0 + - - +
183A ASP* 4.1 20.1 - - - +
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 2.9 27.4 + - + +
116A MET* 4.1 9.9 - - - +
118A LYS* 1.3 76.1 - - + +
120A PHE* 1.3 76.4 + - + +
122A SER* 3.2 5.9 + - - -
123A PHE* 2.9 36.4 + - + +
179A PHE* 6.4 0.7 - - - -
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 4.3 15.2 - - + +
99A LEU* 3.5 37.9 - - + -
100A TRP* 3.5 20.3 - - + -
110A TRP* 4.5 8.1 - + + -
112A PHE* 5.6 1.3 - + + -
116A MET* 2.9 56.3 + - + +
117A CYS 4.7 0.2 - - - +
119A VAL* 1.3 87.6 - - + +
121A GLY* 1.3 61.5 + - - +
123A PHE* 3.8 7.5 - + + +
124A LEU* 2.9 28.8 + - - +
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TRP* 4.0 12.8 - - - -
117A CYS 3.0 17.5 + - - -
120A PHE* 1.3 75.8 - - - +
122A SER* 1.3 59.5 + - - +
124A LEU* 3.2 4.5 + - - +
125A THR* 3.0 31.5 + - - -
178A THR* 3.5 7.7 - - - +
182A ARG* 3.8 16.2 - - - -
7B PRO 4.8 3.4 - - - +
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LYS 2.7 25.6 + - - -
119A VAL* 3.2 7.1 + - - -
121A GLY* 1.3 74.0 - - - +
123A PHE* 1.3 58.3 + - - +
125A THR* 4.0 1.1 - - - +
126A LEU* 2.9 31.9 + - - +
175A SER* 4.0 5.5 + - - -
178A THR* 3.9 13.6 + - - +
179A PHE* 3.7 44.4 - - - -
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.3 56.1 - - + -
93A LEU* 5.6 0.2 - - - -
95A ALA* 5.9 0.7 - - + -
96A THR* 3.8 19.7 - - + -
119A VAL* 2.9 26.3 + - + +
120A PHE* 3.8 12.1 - + + +
121A GLY 3.2 0.2 - - - -
122A SER* 1.3 74.0 + - - +
124A LEU* 1.3 65.6 + - - +
126A LEU* 3.3 17.6 + - + +
127A ASN* 2.9 34.4 + - + +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.5 10.8 - - + +
96A THR* 3.1 27.6 - - - +
100A TRP* 3.3 30.7 - - + +
120A PHE 2.9 20.0 + - - +
121A GLY 3.4 4.5 - - - +
123A PHE* 1.3 78.3 - - - +
125A THR* 1.3 57.5 + - - +
127A ASN 3.2 2.1 + - - -
128A MET* 2.9 34.7 + - + +
308A PHE* 3.4 38.6 - - + -
7B PRO* 3.8 26.0 - - + +
8B PHE* 4.2 7.4 - - + +
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Residues in contact with THR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLY 3.0 11.3 + - - -
122A SER 4.0 2.2 - - - -
124A LEU* 1.3 75.2 - - - +
126A LEU* 1.3 63.2 + - - +
128A MET* 3.2 3.5 + - - +
129A PHE* 2.9 49.1 + - + -
174A SER 4.7 0.2 - - - +
175A SER* 3.6 11.2 - - - -
178A THR* 3.2 38.5 + - - +
7B PRO 4.8 2.3 + - - -
8B PHE* 3.4 32.8 + - + -
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A SER 2.9 19.9 + - - +
123A PHE* 3.6 17.7 - - + +
125A THR* 1.3 78.7 - - - +
127A ASN* 1.3 68.3 + - - +
129A PHE 3.5 0.4 + - - +
130A ALA* 2.9 24.4 + - - +
168A TRP* 4.1 15.5 - - + +
171A ALA* 3.5 10.9 - - + +
172A CYS* 3.5 49.4 - - - +
175A SER* 3.8 13.9 - - - +
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Residues in contact with ASN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA* 2.9 28.7 - - - +
92A LEU* 3.1 18.8 - - - +
93A LEU* 3.1 33.1 + - + +
123A PHE* 2.9 30.6 + - + +
124A LEU 3.2 0.2 + - - -
126A LEU* 1.3 83.9 - - - +
128A MET* 1.3 61.5 + - - +
130A ALA* 3.9 3.2 - - - +
131A SER* 2.9 30.0 + - - -
168A TRP* 3.8 22.8 - - - -
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Residues in contact with MET 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.5 31.0 - - + -
124A LEU* 2.9 23.9 + - + +
125A THR* 3.2 7.2 + - - +
127A ASN* 1.3 76.2 - - - +
129A PHE* 1.3 59.0 + - + +
131A SER* 3.3 3.0 + - - -
132A ILE* 2.9 37.1 + - + +
269A TRP* 3.4 37.0 - - + -
304A ILE* 4.8 2.9 - - + +
308A PHE* 3.5 34.8 - - + +
311A SER* 4.6 2.5 - - - -
8B PHE* 3.5 39.9 - - + -
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR* 2.9 37.8 + - + +
126A LEU 3.9 0.2 - - - +
128A MET* 1.3 79.2 - - + +
130A ALA* 1.3 56.8 + - - +
132A ILE* 4.6 6.5 - - + +
133A PHE* 2.9 46.6 + + + -
171A ALA* 3.7 20.0 - - + -
174A SER* 3.2 48.7 - - - -
175A SER 3.7 2.2 - - - -
214A MET 6.2 0.2 - - - -
215A LYS* 5.2 13.5 - - + -
218A LEU* 4.3 18.2 - - + -
219A GLY* 4.2 23.6 - - - -
8B PHE* 4.5 16.4 - + - -
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Residues in contact with ALA 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA* 4.0 6.1 - - + -
126A LEU 2.9 19.1 + - - +
127A ASN* 3.9 3.8 - - - +
128A MET 3.3 0.2 - - - -
129A PHE* 1.3 74.4 - - - +
131A SER* 1.3 59.1 + - - +
133A PHE* 3.8 2.7 - - - +
134A PHE* 2.9 42.5 + - + -
167A VAL* 5.1 2.2 - - + -
168A TRP* 3.7 38.8 - - + -
171A ALA* 3.6 8.7 - - + +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.3 19.7 - - - +
89A ALA* 4.0 5.7 - - - +
90A ASP* 2.8 30.2 + - - -
93A LEU* 4.7 0.4 - - - -
127A ASN 2.9 19.1 + - - -
128A MET* 3.7 4.9 - - - -
130A ALA* 1.3 76.4 - - - +
132A ILE* 1.3 60.0 + - - +
134A PHE 3.2 0.9 + - - -
135A ILE* 2.9 39.9 + - - +
311A SER* 4.0 12.1 + - - -
314A ASN* 4.3 1.0 + - - -
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A MET* 2.9 25.5 + - + +
129A PHE* 4.2 8.1 - - + +
131A SER* 1.3 77.3 - - - +
133A PHE* 1.3 66.3 + - + +
135A ILE* 3.1 12.7 + - + +
136A THR* 3.0 22.2 + - - -
219A GLY* 3.4 24.7 - - - +
223A PRO* 3.6 35.7 - - + -
227A ILE* 5.3 0.2 - - - +
265A PHE* 3.8 12.6 - - + -
269A TRP* 3.8 45.1 - - + +
273A HIS* 5.2 0.9 - - + -
8B PHE* 5.8 1.8 - - + -
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE* 2.9 35.7 + + + +
130A ALA 4.1 0.2 - - - +
132A ILE* 1.3 82.2 - - + +
134A PHE* 1.3 56.9 + - - +
136A THR* 3.5 8.1 + - + +
137A CYS* 2.9 27.7 + - - +
167A VAL* 3.7 20.3 - - + +
170A MET* 4.0 25.4 - - + -
171A ALA* 3.9 31.6 - - + -
174A SER* 3.9 20.4 - - - -
218A LEU* 3.4 30.7 - - + -
223A PRO* 4.5 10.3 - - + -
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 4.7 17.0 - + - +
85A ASN* 3.4 39.7 - - + -
86A LEU* 3.9 31.9 - - + -
89A ALA* 4.7 0.7 - - + -
130A ALA* 2.9 29.3 + - + +
131A SER 3.6 4.0 - - - +
132A ILE 3.1 0.2 - - - -
133A PHE* 1.3 75.3 - - - +
135A ILE* 1.3 59.9 + - - +
137A CYS* 3.7 7.6 - - + +
138A MET* 2.9 36.7 + - + +
164A VAL* 4.2 6.5 - - + -
167A VAL* 3.6 35.9 - - + -
168A TRP* 3.7 35.2 - + - -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 4.0 9.2 - - + -
131A SER* 2.9 25.4 + - - +
132A ILE* 3.5 15.0 - - + +
134A PHE* 1.3 76.0 - - - +
136A THR* 1.3 61.1 + - - +
138A MET* 3.2 5.6 + - - +
139A SER* 3.0 26.7 + - - +
227A ILE* 3.7 22.9 - - + -
261A VAL* 4.5 8.1 - - + -
265A PHE* 4.3 20.4 - - + -
269A TRP* 5.8 0.2 - - - +
310A ASN* 4.5 9.0 - - - +
314A ASN* 3.1 33.4 - - - +
318A TYR* 3.5 21.4 + - + +
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE 3.0 9.9 + - - -
133A PHE* 3.7 12.3 - - + +
135A ILE* 1.3 77.2 - - - +
137A CYS* 1.3 58.2 - - - +
139A SER* 3.2 3.1 + - - -
140A VAL* 2.9 30.4 + - + +
223A PRO* 3.4 34.6 + - + +
226A PHE* 3.6 38.4 - - + -
227A ILE* 3.8 10.7 - - - +
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Residues in contact with CYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 3.4 40.4 - - - -
133A PHE 2.9 18.5 + - - +
134A PHE* 3.7 12.3 - - + +
135A ILE 3.3 0.2 - - - -
136A THR* 1.3 77.6 - - - +
138A MET* 1.3 57.7 + - + +
140A VAL* 3.5 7.6 + - - +
141A ASP* 2.9 26.3 + - - +
163A ILE* 4.2 12.3 - - - -
167A VAL* 4.7 9.6 - - + -
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Residues in contact with MET 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 4.1 13.2 - - - +
82A TYR* 3.5 37.2 - - + +
83A ILE* 3.5 25.6 - - + -
86A LEU* 4.1 21.3 - - - -
134A PHE* 2.9 22.5 + - - +
135A ILE 3.7 3.8 - - - +
137A CYS* 1.3 73.7 - - - +
139A SER* 1.3 61.3 + - - +
141A ASP* 3.3 7.8 + - - +
142A ARG* 2.9 42.1 + - - +
318A TYR* 3.4 35.2 - - + -
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Residues in contact with SER 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE 3.0 15.0 + - - -
136A THR 3.6 7.6 - - - -
138A MET* 1.3 73.5 - - - +
140A VAL* 1.3 59.0 + - - +
142A ARG* 3.3 10.5 + - - +
143A TYR* 2.9 28.6 + - - +
226A PHE 5.5 0.2 - - - -
227A ILE* 3.9 29.0 - - - +
230A CYS* 3.5 22.0 - - - +
234A ILE* 4.3 1.8 - - - +
261A VAL* 4.4 5.5 - - - +
318A TYR* 4.4 8.0 + - - -
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Residues in contact with VAL 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 2.9 23.5 + - + +
137A CYS* 3.7 8.5 - - - +
139A SER* 1.3 75.5 - - - +
141A ASP* 1.3 59.1 + - - +
143A TYR* 3.3 2.0 + - + +
144A GLN* 2.9 52.4 + - + +
226A PHE* 3.9 27.6 - - + -
230A CYS* 3.7 19.5 - - - -
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Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 3.8 12.3 - - - +
79A SER* 3.7 27.2 + - - -
82A TYR* 3.8 21.7 - - + -
137A CYS 2.9 19.1 + - - +
138A MET* 3.6 5.7 - - - +
139A SER 3.2 0.2 - - - -
140A VAL* 1.3 77.5 - - - +
142A ARG* 1.3 58.7 + - - +
145A SER* 2.9 34.5 + - - -
155A ARG* 2.3 39.2 + - - +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 6.2 2.9 - - - -
83A ILE* 6.2 0.2 - - - +
138A MET* 2.9 28.0 + - + +
139A SER* 3.7 5.6 - - - +
141A ASP* 1.3 78.9 - - - +
143A TYR* 1.3 58.2 + - - +
145A SER* 2.8 20.0 + - - +
146A VAL* 2.9 24.4 + - + +
234A ILE* 3.7 17.9 - - + -
257A MET* 4.9 8.9 + - - +
258A ALA* 4.6 17.4 - - - +
261A VAL* 3.8 24.0 - - - +
317A LEU 4.9 3.0 + - - -
318A TYR* 3.2 42.2 + - - +
321A VAL* 5.8 3.2 - - - +
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER 2.9 17.2 + - - +
140A VAL* 3.6 4.7 - - + +
142A ARG* 1.3 77.0 - - - +
144A GLN* 1.3 71.8 + - + +
146A VAL* 3.1 3.1 + - - +
147A ILE* 3.0 63.8 + - + +
229A THR 4.9 3.4 - - - -
230A CYS* 3.8 34.3 - - - -
233A GLY* 3.8 21.9 - - - -
234A ILE* 3.5 17.6 - - + +
237A HIS* 4.4 3.0 + + - -
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Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 2.9 35.2 + - + +
141A ASP 3.8 0.4 - - - +
143A TYR* 1.3 90.7 - - + +
145A SER* 1.3 57.9 + - - +
147A ILE* 4.2 5.8 - - - +
148A TYR* 3.4 31.0 + - + +
151A LEU* 4.2 5.2 - - + +
155A ARG* 3.5 26.3 + - - +
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 2.9 19.4 + - - -
142A ARG* 2.8 23.7 + - - +
144A GLN* 1.3 77.7 - - - +
146A VAL* 1.3 61.8 + - - +
148A TYR 2.9 22.5 - - - +
149A PRO* 4.1 4.0 - - - +
151A LEU* 5.4 4.7 - - - -
155A ARG* 4.2 11.0 - - - +
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Residues in contact with VAL 146 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ARG* 2.9 23.9 + - + +
143A TYR 3.1 3.6 + - - +
145A SER* 1.3 80.2 - - - +
147A ILE* 1.3 65.9 + - - +
148A TYR 3.5 0.2 + - - -
149A PRO* 4.3 10.4 - - - +
234A ILE* 4.2 26.5 - - + +
237A HIS* 3.8 31.7 - - + +
238A LEU* 4.5 20.6 - - + -
241A THR* 6.5 0.4 - - + -
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Residues in contact with ILE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.0 57.8 + - + +
144A GLN* 4.7 3.4 - - - +
146A VAL* 1.3 76.1 - - - +
148A TYR* 1.3 83.7 + - + +
149A PRO* 3.1 12.0 - - - +
237A HIS* 3.3 36.1 - - + +
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Residues in contact with TYR 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLN* 3.4 18.3 + - + +
145A SER* 2.9 18.5 - - - +
146A VAL 3.3 0.2 - - - -
147A ILE* 1.3 103.2 - - + +
149A PRO* 1.3 65.1 - - - +
150A PHE* 3.3 19.1 + + + -
151A LEU* 3.7 38.7 + - + +
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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) + - + + + + + -
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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