Contacts of the helix formed by residues 134 - 160 (chain F) in PDB entry 6BCR
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 CYS 134 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ARG* 5.1 0.2 - - - +
132F VAL 4.4 7.2 - - - -
133F ALA* 1.3 81.3 - - - +
135F GLY* 1.3 67.9 + - - +
136F ASP 3.6 0.2 + - - -
137F ASP* 3.4 13.4 + - - +
138F ARG* 3.1 14.1 + - - +
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Residues in contact with GLY 135 (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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134F CYS* 1.3 74.8 - - - +
136F ASP* 1.3 59.5 + - - -
138F ARG* 2.9 21.5 + - - +
139F LYS* 3.1 11.0 + - - +
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Residues in contact with ASP 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER 5.4 2.1 - - - +
74B LYS* 4.2 33.4 - - + +
134F CYS 3.6 0.2 + - - -
135F GLY* 1.3 73.5 - - - -
137F ASP* 1.3 62.7 + - - +
139F LYS* 3.1 16.1 + - + +
140F GLN* 2.9 25.1 + - - +
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Residues in contact with ASP 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN* 3.8 30.1 - - + +
91F ARG* 3.6 29.5 + - - -
133F ALA* 3.6 10.4 - - - +
134F CYS 3.4 9.9 + - - +
135F GLY 3.2 0.4 - - - -
136F ASP* 1.3 80.0 - - - +
138F ARG* 1.3 56.0 + - - +
140F GLN* 4.0 5.0 - - - +
141F THR* 2.6 41.4 + - - -
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Residues in contact with ARG 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ALA* 2.8 36.9 + - - +
131F GLU* 4.5 6.9 + - - +
133F ALA* 3.5 29.0 + - - +
134F CYS* 3.1 17.8 + - - +
135F GLY 2.9 12.8 + - - +
137F ASP* 1.3 74.7 - - - +
139F LYS* 1.3 65.8 + - - +
141F THR* 3.2 2.6 + - - -
142F ILE* 2.8 49.1 + - + +
180F GLU 5.1 2.0 + - - -
181F ILE* 3.5 31.9 + - - +
183F ASN* 4.9 5.7 + - - -
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Residues in contact with LYS 139 (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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135F GLY 3.1 9.5 + - - +
136F ASP* 3.1 20.3 + - - +
138F ARG* 1.3 78.2 - - - +
140F GLN* 1.3 61.0 + - + +
142F ILE* 3.3 8.2 + - - +
143F ASP* 2.9 48.8 + - - +
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Residues in contact with GLN 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLU* 4.2 8.1 - - - +
5A GLU* 5.9 3.1 - - - -
74B LYS* 6.0 3.2 - - - +
136F ASP 2.9 15.6 + - - +
137F ASP* 4.1 5.6 - - - +
139F LYS* 1.3 80.4 - - + +
141F THR* 1.3 57.8 + - - +
143F ASP* 3.2 13.8 + - - +
144F ASN* 2.9 65.2 + - - +
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Residues in contact with THR 141 (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 ARG* 5.7 1.0 + - - -
126F PHE* 3.1 35.9 - - + +
129F LEU* 3.5 15.9 - - + +
130F ALA* 3.5 19.7 - - - +
133F ALA* 4.4 2.2 - - - +
137F ASP* 2.6 36.0 + - - -
138F ARG* 3.6 4.7 - - - -
140F GLN* 1.3 76.9 - - - +
142F ILE* 1.3 61.3 + - - +
144F ASN* 3.3 9.8 + - - +
145F SER* 3.0 22.9 + - - -
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Residues in contact with ILE 142 (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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130F ALA* 3.8 11.4 - - + -
138F ARG* 2.8 50.9 + - + +
139F LYS* 3.6 7.0 - - - +
141F THR* 1.3 77.3 - - - +
143F ASP* 1.3 62.6 + - - +
145F SER* 3.3 6.6 + - - -
146F GLN* 2.9 30.8 + - - +
177F PHE* 3.8 8.2 - - + -
181F ILE* 3.6 26.2 - - + +
182F LEU* 3.7 29.2 - - + -
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Residues in contact with ASP 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F LYS* 2.9 45.9 + - - +
140F GLN* 3.6 18.1 + - - +
142F ILE* 1.3 81.7 - - - +
144F ASN* 1.3 60.0 + - - +
146F GLN* 3.5 11.5 + - - +
147F GLY* 2.9 25.8 + - - -
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Residues in contact with ASN 144 (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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2A GLU* 3.3 22.8 + - - +
122F LYS* 5.8 0.3 - - - -
126F PHE* 3.7 41.8 - - + -
140F GLN* 2.9 47.9 + - - +
141F THR* 3.7 5.6 - - - +
142F ILE 3.2 0.2 - - - -
143F ASP* 1.3 75.8 - - - +
145F SER* 1.3 65.7 + - - +
147F GLY* 3.4 1.3 + - - -
148F ALA* 3.1 23.7 + - - +
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Residues in contact with SER 145 (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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123F GLY* 2.9 21.5 + - - -
126F PHE* 3.6 24.2 - - - +
127F ARG* 3.8 7.4 + - - -
130F ALA* 5.7 0.2 - - - -
141F THR 3.0 11.2 + - - -
142F ILE* 3.6 8.1 - - - -
144F ASN* 1.3 75.7 - - - +
146F GLN* 1.3 62.7 + - - +
148F ALA* 3.1 4.2 + - - +
149F TYR* 2.9 39.0 + - - -
177F PHE* 3.4 15.9 - - - -
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Residues in contact with GLN 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F ILE* 2.9 18.3 + - - +
143F ASP* 3.8 11.6 - - - +
145F SER* 1.3 75.9 - - - +
147F GLY* 1.3 58.7 + - - +
149F TYR* 3.8 5.2 - - - +
150F GLN* 2.8 38.7 + - + +
174F PHE* 4.4 5.4 - - + -
177F PHE* 3.8 20.3 - - + -
178F TYR* 3.4 27.1 + - - -
182F LEU* 3.7 27.0 - - - +
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Residues in contact with GLY 147 (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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143F ASP 2.9 18.2 + - - -
144F ASN* 3.9 1.8 - - - -
146F GLN* 1.3 76.5 - - - +
148F ALA* 1.3 61.5 + - - +
150F GLN* 3.9 5.6 - - - +
151F GLU* 3.1 25.1 + - - +
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Residues in contact with ALA 148 (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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119F LEU* 3.5 32.4 - - + +
122F LYS* 3.8 21.8 - - + -
123F GLY* 3.5 14.8 - - - +
144F ASN 3.1 13.8 + - - +
145F SER 3.6 4.5 - - - +
147F GLY* 1.3 74.3 - - - +
149F TYR* 1.3 65.8 + - - +
151F GLU* 3.4 2.2 + - - +
152F ALA* 3.1 23.4 + - - +
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Residues in contact with TYR 149 (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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119F LEU 4.8 0.2 - - - -
120F LYS* 3.7 14.8 - - + -
123F GLY* 3.4 10.8 - - - -
124F ASP* 2.5 33.7 + - - -
127F ARG* 2.9 19.9 + - - -
145F SER* 2.9 42.1 + - - +
146F GLN 3.8 0.4 - - - +
148F ALA* 1.3 75.8 - - - +
150F GLN* 1.3 58.7 + - - +
152F ALA* 3.3 4.4 + - - +
153F PHE* 2.8 29.6 + - - +
170F LEU* 3.7 25.3 - - + +
173F ASN* 4.0 16.6 - - + +
174F PHE* 3.5 36.7 - + + -
177F PHE* 3.7 22.4 - + + -
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Residues in contact with GLN 150 (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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146F GLN* 2.8 28.0 + - + +
147F GLY* 3.9 5.6 - - - +
149F TYR* 1.3 73.6 - - - +
151F GLU* 1.3 63.0 + - - +
153F PHE* 3.1 15.4 + - - +
154F ASP* 2.9 55.7 + - - +
157F LYS* 5.4 1.0 - - - +
174F PHE* 3.7 23.0 - - + -
178F TYR* 4.5 7.3 + - - -
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Residues in contact with GLU 151 (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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115F LYS* 4.3 10.6 + - - -
119F LEU* 3.7 30.8 - - + +
147F GLY 3.1 17.6 + - - +
148F ALA* 3.9 3.7 - - - +
150F GLN* 1.3 76.6 - - - +
152F ALA* 1.3 65.1 + - - +
154F ASP* 3.2 9.7 + - + +
155F ILE* 3.0 41.0 + - + +
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Residues in contact with ALA 152 (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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116F VAL* 3.6 23.1 - - + +
119F LEU* 3.6 24.3 - - + +
120F LYS 4.0 5.4 - - - +
148F ALA 3.1 13.6 + - - +
149F TYR 3.5 8.3 - - - +
151F GLU* 1.3 76.4 - - - +
153F PHE* 1.3 56.9 + - - +
155F ILE* 3.5 0.4 + - - -
156F SER* 2.9 32.6 + - - -
170F LEU* 3.4 18.1 - - + +
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Residues in contact with PHE 153 (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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149F TYR 2.8 17.7 + - - +
150F GLN* 3.1 22.6 + - - +
152F ALA* 1.3 74.5 - - - +
154F ASP* 1.3 61.7 + - - +
156F SER* 3.0 19.8 + - - -
157F LYS* 3.0 55.2 + - + +
167F ARG* 5.5 5.6 - - + -
170F LEU* 3.5 17.2 - - + +
171F ALA* 4.4 16.2 - - + -
174F PHE* 3.8 21.3 - + + -
191F LEU* 3.7 39.7 - - + -
195F ALA* 5.9 1.8 - - + -
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Residues in contact with ASP 154 (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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150F GLN* 2.9 45.5 + - - +
151F GLU* 3.2 9.0 + - + +
153F PHE* 1.3 75.0 - - - +
155F ILE* 1.3 66.9 - - + +
157F LYS* 3.2 12.9 + - - +
158F LYS* 3.0 23.7 + - - +
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Residues in contact with ILE 155 (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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112F PRO* 4.0 24.7 - - + +
115F LYS* 3.9 35.9 - - + +
116F VAL* 3.4 22.2 - - + -
119F LEU* 4.0 17.7 - - + -
151F GLU* 3.0 25.1 + - + +
154F ASP* 1.3 76.3 - - + +
156F SER* 1.3 58.4 + - - +
158F LYS* 3.1 7.0 + - - -
159F GLU* 2.8 36.0 + - + +
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Residues in contact with SER 156 (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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116F VAL* 3.8 21.1 - - - +
152F ALA 2.9 16.6 + - - -
153F PHE* 3.0 19.1 + - - -
154F ASP 3.2 0.2 - - - -
155F ILE* 1.3 76.6 - - - +
157F LYS* 1.3 61.2 + - - +
160F MET* 2.9 42.5 + - - +
167F ARG* 3.6 32.0 + - - +
170F LEU* 3.9 5.8 - - - +
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Residues in contact with LYS 157 (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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150F GLN* 5.4 1.2 - - - +
153F PHE* 3.0 64.0 + - + +
154F ASP* 3.7 10.7 + - - +
156F SER* 1.3 83.1 + - - +
158F LYS* 1.3 60.9 + - - +
160F MET 4.3 2.1 - - - +
167F ARG* 3.7 34.6 + - - +
194F THR* 6.4 2.2 - - - -
198F GLU* 5.7 2.5 - - - +
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Residues in contact with LYS 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F ASP 3.0 15.1 + - - +
155F ILE* 3.7 6.1 - - + +
157F LYS* 1.3 79.1 - - - +
159F GLU* 1.3 84.5 + - + +
160F MET 3.8 0.4 - - - -
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Residues in contact with GLU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PRO* 3.8 39.1 - - + +
155F ILE* 2.8 23.1 + - + +
158F LYS* 1.3 110.7 - - + +
160F MET* 1.3 65.4 + - + +
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Residues in contact with MET 160 (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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112F PRO* 3.6 15.5 - - + +
113F GLU* 3.7 16.4 - - + +
116F VAL* 3.3 40.8 - - + -
155F ILE 5.1 0.4 - - - +
156F SER* 2.9 18.3 + - - +
157F LYS 4.3 3.3 - - - +
158F LYS 3.8 0.2 - - - -
159F GLU* 1.3 82.7 - - + +
161F GLN* 1.3 64.6 + - - +
162F PRO* 4.3 0.2 - - - +
164F HIS* 4.1 35.0 - - + -
166F ILE* 4.6 4.9 - - + -
167F ARG* 2.7 49.0 + - - -
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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