Contacts of the helix formed by residues 153 - 179 (chain A) in PDB entry 1HBX
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 ASN 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.7 2.5 - - - +
152A ASP* 1.3 72.6 - - - +
154A LYS* 1.3 68.2 + - - +
155A LEU* 2.8 20.4 + - - +
156A ARG* 2.9 38.2 + - + +
157A ARG* 2.8 19.4 + - - +
68G VAL* 6.0 4.2 - - - +
69G LYS* 6.0 1.2 - - - +
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASP 2.6 12.0 + - - +
153A ASN* 1.3 72.2 - - - +
155A LEU* 1.3 57.2 + - - +
157A ARG* 3.6 21.8 + - - +
158A TYR* 2.9 29.8 + - + +
190A GLU* 3.9 18.4 + - - +
191A THR* 6.3 1.2 - - - +
-10W G 5.2 9.4 - - - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN* 2.8 17.5 + - - +
154A LYS* 1.3 71.8 - - - +
156A ARG* 1.3 62.1 + - - +
157A ARG 2.9 2.0 + - - -
158A TYR* 2.9 14.2 + - + +
159A THR* 2.6 38.3 + - - +
65G TYR* 4.2 31.6 - - + -
68G VAL* 4.5 16.6 - - + -
69G LYS* 3.7 36.8 - - + -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.4 35.4 - - - +
151A ILE* 3.5 31.9 - - + +
153A ASN* 2.9 34.4 + - + +
155A LEU* 1.3 75.7 - - - +
157A ARG* 1.3 62.4 + - - +
159A THR* 3.3 8.3 + - - -
160A THR* 3.0 26.8 + - - -
-5C G 2.6 51.9 + - + +
-4C G 4.3 1.8 + - - -
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PHE* 3.1 31.0 - - - -
151A ILE* 2.9 40.4 + - + +
152A ASP* 3.3 21.4 + - - +
153A ASN 2.8 13.5 + - - +
154A LYS* 3.6 25.0 + - - +
155A LEU 2.9 0.6 + - - -
156A ARG* 1.3 76.6 - - - +
158A TYR* 1.3 65.1 + - - +
159A THR 3.0 0.7 + - - -
160A THR* 3.1 4.4 + - - +
161A PHE* 2.8 23.0 + - - +
190A GLU* 2.5 47.0 + - - -
178B LEU 4.1 1.1 - - - +
179B THR* 4.1 22.2 - - + +
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS* 2.9 21.2 + - + +
155A LEU* 2.9 15.7 + - + +
157A ARG* 1.3 74.2 - - - +
159A THR* 1.3 64.2 + - - +
161A PHE* 3.5 13.6 + + + +
162A SER* 2.8 40.6 + - - -
189A SER* 6.3 0.9 - - - -
190A GLU* 6.1 5.8 - - + -
191A THR* 4.6 13.9 - - + -
-10W G 3.2 13.1 - - + +
-9W A 2.8 73.3 + + + +
-8W A 4.9 3.8 - - - -
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 2.6 35.6 + - - +
156A ARG* 3.4 8.7 + - - -
158A TYR* 1.3 77.5 - - - +
160A THR* 1.3 58.4 + - - +
162A SER* 2.5 32.6 + - - -
163A LYS* 3.0 23.7 + - + -
-7C C 5.2 11.9 - - - +
-6C A 5.3 5.6 - - - +
-5C G 5.1 14.1 - - + +
-4C G 6.5 0.2 - - + -
-7W G 5.3 4.9 - - - +
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.3 19.3 - - + +
156A ARG* 3.0 15.2 + - - -
157A ARG 3.7 2.2 - - - +
159A THR* 1.3 79.4 - - - +
161A PHE* 1.3 58.3 + - - +
163A LYS* 4.5 2.9 - - - +
164A ARG* 2.8 49.7 + - - +
178B LEU* 4.3 5.6 - - + -
179B THR* 4.0 17.7 - - + -
-5C G 5.6 0.3 + - - -
-4C G 2.4 43.7 + - - +
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Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 2.8 20.5 + - + +
158A TYR* 3.7 14.8 - + + +
160A THR* 1.3 73.6 - - - +
162A SER* 1.3 63.2 + - - +
165A LYS* 2.9 50.1 + - + +
187A VAL* 3.3 35.4 - - + -
189A SER* 3.8 31.0 - - - -
190A GLU 5.8 0.2 - - - -
195A TYR* 4.6 3.1 - + - -
175B LEU* 3.9 10.1 - - + -
179B THR* 3.4 32.3 - - + -
181B THR* 3.6 22.4 - - + -
-8W A 5.8 0.2 - - - -
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Residues in contact with SER 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 2.8 31.8 + - - -
159A THR* 2.5 18.0 + - - -
161A PHE* 1.3 76.0 - - - +
163A LYS* 1.3 70.8 + - - -
165A LYS* 3.1 8.1 + - - +
166A THR* 2.8 29.8 + - - -
-9W A 5.2 0.5 - - - +
-8W A 4.6 28.8 + - - -
-7W G 6.1 1.3 - - - -
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Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A THR* 3.0 22.8 + - + +
160A THR 4.0 4.5 - - - +
162A SER* 1.3 84.2 - - - +
164A ARG* 1.3 61.9 + - - +
166A THR* 3.3 8.0 + - - +
167A GLY* 3.2 15.4 + - - -
-6C A 4.2 4.9 - - - +
-5C G 2.8 26.9 + - - -
-4C G 3.2 26.9 + - + +
-3C A 3.9 37.1 - - + +
-7W G 4.8 11.4 - - + +
-6W T 3.3 32.2 + - + -
-5W C 4.1 1.8 - - - +
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 4.3 13.1 - - - +
146A ILE* 5.0 5.7 - - - +
160A THR* 2.8 30.4 + - - +
163A LYS* 1.3 68.6 - - - +
165A LYS* 1.3 64.8 + - - +
166A THR 3.1 1.6 - - - -
167A GLY* 3.0 10.6 + - - -
168A ILE* 3.0 18.1 + - - +
171B LYS* 4.2 15.1 + - + +
174B GLU* 4.2 24.2 + - - +
175B LEU* 3.9 28.9 - - + +
178B LEU* 3.0 34.4 - - - +
-4C G 3.4 23.0 + - - +
-3C A 3.0 44.2 + - - +
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 2.9 52.0 + - + +
162A SER* 3.6 5.6 - - - +
164A ARG* 1.3 77.5 - - - +
166A THR* 1.3 70.6 + - - +
168A ILE* 3.6 7.8 - - - +
169A MET* 3.2 37.0 + - + +
187A VAL* 4.7 5.2 - - + -
195A TYR* 3.3 51.1 - - + +
175B LEU* 4.5 6.1 - - + +
-8W A 3.5 24.3 + - - -
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER 2.8 22.6 + - - -
163A LYS* 3.4 11.9 - - - +
165A LYS* 1.3 88.0 + - - +
167A GLY* 1.3 58.1 + - - +
169A MET* 3.6 4.5 - - - +
170A LYS* 3.2 22.4 + - + +
-8W A 4.8 7.6 - - - +
-7W G 4.1 21.8 + - - +
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Residues in contact with GLY 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LYS 3.2 4.8 + - - -
164A ARG 3.0 6.7 + - - -
166A THR* 1.3 77.4 - - - +
168A ILE* 1.3 53.8 + - - -
169A MET 3.0 2.0 - - - -
170A LYS* 2.6 27.6 + - - +
171A LYS* 2.7 24.5 + - - +
-3C A 3.7 16.2 - - - -
-2C T 5.4 8.5 - - - -
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG 3.0 14.0 + - - +
165A LYS* 3.6 16.6 - - - +
167A GLY* 1.3 69.7 - - - -
169A MET* 1.3 67.9 + - + +
171A LYS* 2.9 11.1 + - - +
172A ALA* 2.7 33.4 + - - +
185A LEU* 3.7 29.4 - - + -
187A VAL* 4.8 1.8 - - + -
168B ILE* 4.1 17.9 - - + +
171B LYS* 4.0 16.6 - - + +
172B ALA* 3.5 41.7 - - + +
175B LEU* 4.2 16.8 - - + -
183B VAL* 4.9 0.4 - - + -
185B LEU* 5.4 0.9 - - + -
-3C A 4.1 3.2 + - - -
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Residues in contact with MET 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS* 3.2 46.9 - - + +
166A THR* 3.6 5.2 - - - +
168A ILE* 1.3 81.7 - - + +
170A LYS* 1.3 67.1 + - - +
172A ALA* 3.3 9.6 + - - +
173A TYR* 3.3 10.2 + - - +
185A LEU* 4.0 14.4 - - + -
187A VAL* 4.1 16.6 - - + -
195A TYR* 3.9 21.3 - - + -
196A THR 3.8 27.6 - - - +
197A PHE* 3.9 18.0 - - + -
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A THR* 3.2 14.5 + - + +
167A GLY* 2.6 21.2 + - - +
169A MET* 1.3 73.2 - - - +
171A LYS* 1.3 61.2 + - + +
173A TYR* 2.9 28.3 + - + +
174A GLU* 3.2 32.5 + - + +
-2C T 2.4 43.2 + - - +
-1C T 3.9 5.1 + - - -
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLY* 2.7 18.1 + - - +
168A ILE* 3.1 12.3 - - - +
170A LYS* 1.3 77.0 - - + +
172A ALA* 1.3 67.5 + - - +
173A TYR 2.9 1.0 + - - -
174A GLU* 4.1 18.8 + - - +
175A LEU* 3.1 25.7 + - + +
143B ARG* 5.9 1.2 - - - +
164B ARG* 4.6 8.6 - - + +
168B ILE* 3.9 25.4 - - + -
171B LYS* 3.8 28.9 - - - +
-2C T 4.7 20.0 + - - +
-1C T 5.6 1.2 + - - -
2W T 3.6 7.5 + - - -
3W A 2.3 38.0 + - - +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE 2.7 15.7 + - - +
169A MET 3.6 9.0 - - - +
170A LYS 3.3 0.4 - - - -
171A LYS* 1.3 72.5 - - - +
173A TYR* 1.3 54.4 + - - +
175A LEU* 4.0 1.6 - - - +
176A SER* 2.7 32.9 + - - -
183A VAL* 4.1 13.9 - - + +
185A LEU* 3.9 20.0 - - + -
197A PHE* 3.6 27.5 - - + -
168B ILE* 3.6 13.6 - - + +
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Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A MET 3.3 6.6 + - - +
170A LYS* 2.9 18.2 + - + +
172A ALA* 1.3 78.0 - - - +
174A GLU* 1.3 74.9 + - + +
175A LEU 2.9 0.5 + - - -
176A SER* 2.4 24.6 + - - -
177A THR* 2.7 48.6 + - + +
197A PHE* 3.9 23.3 - + + -
148B MET* 4.1 21.3 + - + +
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Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS* 3.2 46.8 + - + +
171A LYS* 3.3 15.2 + - - +
173A TYR* 1.3 82.0 - - + +
175A LEU* 1.3 54.3 + - - +
177A THR* 3.9 0.4 - - - -
178A LEU* 2.5 42.1 + - - +
143B ARG* 5.9 0.3 + - - -
148B MET* 3.3 39.0 - - + +
164B ARG* 3.3 24.8 + - - +
-2C T 4.3 6.9 + - - -
-1C T 5.0 2.4 - - - +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LYS* 3.1 16.4 + - + +
172A ALA 4.0 2.7 - - - +
173A TYR 3.1 0.6 - - - -
174A GLU* 1.3 75.2 - - - +
176A SER* 1.3 67.3 + - - +
177A THR 2.9 0.3 + - - -
178A LEU* 4.6 2.7 - - - -
179A THR* 2.8 50.8 + - + +
181A THR* 4.3 6.3 - - - +
183A VAL* 4.5 5.2 - - + -
161B PHE* 3.7 18.2 - - + +
164B ARG* 4.0 31.7 - - + +
165B LYS* 4.4 5.4 - - - -
168B ILE* 4.1 30.5 - - + -
187B VAL* 4.2 23.1 - - + -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA 2.7 13.7 + - - -
173A TYR* 2.4 30.0 + - - -
175A LEU* 1.3 79.6 - - - +
177A THR* 1.3 53.6 + - - +
180A GLY* 2.8 29.9 + - - -
181A THR* 3.2 30.5 + - - +
183A VAL* 3.5 11.0 - - - +
197A PHE* 3.6 7.4 - - - -
199A THR* 3.6 14.1 - - - -
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TYR* 2.7 59.4 + - + +
174A GLU 3.4 4.9 - - - -
175A LEU 2.9 0.8 + - - -
176A SER* 1.3 73.4 + - - +
178A LEU* 1.3 67.0 + - - +
179A THR 3.3 0.5 + - - -
180A GLY* 3.3 9.4 + - - -
148B MET* 3.9 32.5 - - - +
149B GLU* 4.4 4.5 - - - -
150B PHE* 3.6 13.3 + - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU 2.5 18.8 + - - +
175A LEU 3.9 1.3 - - - +
177A THR* 1.3 73.7 - - - +
179A THR* 1.3 61.0 + - + +
146B ILE* 4.0 14.6 - - + -
147B LYS 3.5 18.8 - - - +
148B MET* 3.8 24.2 - - + -
149B GLU 3.6 7.4 - - - +
150B PHE* 3.2 3.5 - - - -
151B ILE* 2.7 62.2 + - + +
160B THR* 4.5 2.7 - - + -
164B ARG* 3.3 50.7 - - - +
4W G 4.4 0.7 - - - +
----------------------------------------------------------
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 2.8 30.7 + - + +
178A LEU* 1.3 74.5 - - + +
180A GLY* 1.3 61.2 + - - +
181A THR* 2.7 39.0 + - - +
150B PHE* 3.4 8.6 - - - -
157B ARG* 3.3 31.9 - - + +
160B THR* 3.5 30.7 - - + -
161B PHE* 3.6 15.6 - - + +
190B GLU* 4.8 3.3 - - - +
----------------------------------------------------------
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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