Contacts of the helix formed by residues 158 - 181 (chain B) in PDB entry 6YB9
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 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 4.4 9.2 - - - -
156B LEU* 3.3 8.5 + - - -
157B ILE* 1.3 72.9 - - - +
159B GLN* 1.3 67.0 + - - -
160B THR 3.2 2.7 - - - -
161B GLU* 2.9 17.3 + - - -
162B VAL* 3.0 27.7 + - - +
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Residues in contact with GLN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU* 5.2 4.7 - - - +
146B ILE* 3.9 35.5 - - + +
158B GLY* 1.3 70.0 - - - +
160B THR* 1.3 61.2 + - - +
162B VAL* 3.3 2.1 + - - +
163B ASP* 2.9 53.3 + - - +
414B LYS* 3.5 13.9 - - - +
421B ARG* 6.4 0.2 - - - +
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Residues in contact with THR 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLY 3.2 0.6 - - - -
159B GLN* 1.3 80.6 - - - +
161B GLU* 1.3 74.6 + - - +
163B ASP* 3.5 2.6 + - - +
164B ILE* 3.0 50.9 + - + +
414B LYS* 4.2 31.7 + - + +
415B GLN* 4.4 7.9 - - - +
418B LYS* 4.2 15.9 - - + +
421B ARG* 3.5 27.3 + - - -
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 4.1 15.6 - - + +
156B LEU 3.4 17.5 - - - +
157B ILE* 4.1 9.9 - - + -
158B GLY* 2.9 38.2 + - - +
160B THR* 1.3 87.0 - - - +
162B VAL* 1.3 61.0 + - - +
164B ILE* 3.3 9.7 + - + +
165B MET* 3.0 34.1 + - - +
203B ILE* 3.7 25.7 - - + +
415B GLN* 5.1 3.3 + - - +
418B LYS* 2.7 29.6 + - - -
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 3.9 11.0 - - + -
142B GLU* 3.9 37.5 - - + +
145B LEU* 3.7 37.5 - - + -
146B ILE* 4.1 17.7 - - + -
157B ILE* 3.9 13.7 - - + +
158B GLY 3.0 14.6 + - - +
159B GLN* 3.7 4.7 - - - +
161B GLU* 1.3 74.3 - - - +
163B ASP* 1.3 63.4 + - - +
165B MET* 3.3 4.4 + - - +
166B SER* 3.0 24.0 + - - -
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU* 5.1 6.7 - - - +
159B GLN* 2.9 33.3 + - - +
160B THR 3.8 4.3 - - - +
162B VAL* 1.3 76.8 - - - +
164B ILE* 1.3 61.1 + - - +
166B SER* 3.6 5.0 + - - -
167B HIS* 3.0 54.1 + - - +
410B TRP* 3.6 16.8 - - - -
414B LYS* 2.9 25.8 + - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B THR* 3.0 40.0 + - + +
161B GLU* 3.6 9.6 - - + +
162B VAL 3.2 0.4 - - - -
163B ASP* 1.3 74.1 - - - +
165B MET* 1.3 64.5 + - + +
167B HIS* 3.5 1.9 + - - +
168B ALA* 2.9 31.3 + - + +
203B ILE* 5.2 15.7 - - + +
407B LEU* 5.0 1.0 - - - +
410B TRP* 4.0 19.5 - - + -
411B ILE* 4.0 33.0 - - + -
414B LYS* 4.5 8.7 - - + -
415B GLN* 3.9 22.9 - - - +
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Residues in contact with MET 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.8 37.9 - - + -
98B TRP* 2.9 54.5 - - + +
145B LEU* 5.5 0.4 - - + -
157B ILE* 5.0 6.7 - - - -
161B GLU 3.0 23.2 + - - +
162B VAL* 3.3 1.5 + - - -
164B ILE* 1.3 75.3 - - - +
166B SER* 1.3 54.0 + - - +
168B ALA* 4.3 1.3 - - - -
169B THR* 2.6 38.5 + - - -
194B PHE* 3.5 42.3 - - + -
203B ILE* 3.9 18.4 - - + -
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 3.8 15.8 - - - -
126B VAL* 3.7 28.0 - - - +
128B LEU* 5.5 0.9 - - - +
142B GLU* 3.6 21.2 + - - -
162B VAL 3.0 17.9 + - - -
163B ASP* 3.7 6.5 - - - -
165B MET* 1.3 74.8 - - - +
167B HIS* 1.3 67.5 + - - +
169B THR* 3.4 4.2 + - - -
170B GLN* 3.4 16.5 + - - +
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Residues in contact with HIS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASP* 3.0 43.1 + - - +
164B ILE 4.0 1.1 - - - +
166B SER* 1.3 79.6 - - - +
168B ALA* 1.3 65.7 + - - +
170B GLN* 3.4 12.9 + - - +
171B ALA* 3.1 22.5 + - - +
403B ARG* 4.8 2.1 + - - -
407B LEU* 3.9 12.5 - - + +
410B TRP* 3.5 47.7 + + + -
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 6.3 0.2 - - + -
164B ILE* 2.9 23.0 + - + +
165B MET* 3.8 4.0 - - - +
167B HIS* 1.3 74.3 - - - +
169B THR* 1.3 60.6 + - - +
171B ALA* 3.3 0.7 + - - +
172B ILE* 2.9 41.6 + - + +
194B PHE* 3.9 20.6 - - + -
407B LEU* 3.9 24.8 - - + +
411B ILE* 5.4 1.6 - - + -
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Residues in contact with THR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 3.4 34.3 - - + +
99B VAL 4.3 5.8 - - - +
100B CYS* 4.0 19.5 - - + -
126B VAL* 4.1 14.8 - - + -
165B MET 2.6 22.8 + - - -
166B SER 3.6 6.1 - - - -
167B HIS 3.3 0.4 - - - -
168B ALA* 1.3 76.6 - - - +
170B GLN* 1.3 62.1 + - - +
172B ILE* 3.5 0.3 + - - +
173B PHE* 3.0 22.9 + - - +
190B MET* 3.7 5.2 - - + +
192B ILE* 4.0 16.6 - - + -
194B PHE* 3.5 7.1 - - - -
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Residues in contact with GLN 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B CYS* 4.1 8.7 - - - -
123B PRO* 3.9 24.8 - - - +
124B PRO* 2.9 36.5 + - + +
126B VAL* 4.2 11.2 - - + +
166B SER 3.4 9.7 + - - +
167B HIS* 3.7 14.5 - - - +
168B ALA 3.3 0.4 - - - -
169B THR* 1.3 77.8 - - - +
171B ALA* 1.3 55.1 + - - +
173B PHE* 3.3 3.8 + - - +
174B GLU* 2.9 50.9 + - - +
403B ARG* 4.5 6.0 + - - +
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 4.8 4.7 - - + -
167B HIS 3.1 15.0 + - - +
168B ALA 3.3 4.2 + - - +
170B GLN* 1.3 72.8 - - - +
172B ILE* 1.3 66.3 + - - +
174B GLU* 3.3 1.7 + - - +
175B ILE* 3.0 32.1 + - + +
403B ARG* 3.6 39.1 - - + +
407B LEU* 4.0 23.1 - - + -
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.1 25.7 - - + +
73B ILE* 3.9 35.7 - - + -
168B ALA* 2.9 27.6 + - + +
169B THR 3.8 3.1 - - - +
171B ALA* 1.3 76.4 - - - +
173B PHE* 1.3 62.3 + - - +
175B ILE* 3.4 3.0 + - - +
176B LEU* 3.0 25.9 + - + +
190B MET* 3.7 20.6 - - + -
192B ILE* 3.9 22.0 - - + -
194B PHE* 4.3 12.3 - - + -
205B LEU* 4.2 11.7 - - + -
209B ILE* 4.4 8.5 - - + -
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B CYS* 3.6 24.2 - - + -
102B ARG* 3.6 23.6 - - + -
124B PRO* 4.1 16.8 - - + -
169B THR 3.0 18.1 + - - +
170B GLN 3.5 3.8 - - - +
172B ILE* 1.3 77.0 - - - +
174B GLU* 1.3 55.4 + - - +
176B LEU* 3.3 2.7 + - - +
177B GLU* 2.7 62.0 + - + +
187B LEU* 3.6 35.7 - - + -
188B VAL 4.0 0.2 - - - -
189B ASP* 3.8 22.9 - - - -
190B MET* 3.5 34.4 - - + +
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A GLU* 4.9 14.5 - - - +
506A EDO 4.7 1.0 + - - -
102B ARG* 4.7 3.8 - - - +
123B PRO* 5.7 0.7 - - - +
124B PRO* 4.2 23.0 - - + +
170B GLN* 2.9 33.9 + - - +
171B ALA 3.3 3.8 + - - +
173B PHE* 1.3 75.8 - - + +
175B ILE* 1.3 56.9 + - - +
177B GLU* 3.5 14.1 - - - +
178B LYS* 2.8 31.7 + - - +
399B TRP* 3.9 21.0 - - + -
403B ARG* 3.1 41.1 + - - +
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 5.0 6.7 - - + -
68B LEU* 3.8 18.4 - - + -
71B ALA* 4.6 5.2 - - + -
73B ILE* 3.9 33.4 - - + -
171B ALA 3.0 21.5 + - - +
172B ILE 3.7 3.4 - - - +
174B GLU* 1.3 76.2 - - - +
176B LEU* 1.3 56.5 + - + +
178B LYS* 3.4 2.4 + - - +
179B SER* 2.6 40.4 + - - +
399B TRP* 4.0 10.8 - - + -
400B SER* 3.6 38.0 + - - +
403B ARG* 4.0 16.2 - - + -
404B ALA* 4.2 7.9 - - + +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.8 38.1 - - + -
67B LEU* 4.0 18.2 - - + -
68B LEU* 3.9 17.3 - - + -
172B ILE* 3.0 19.7 + - + +
173B PHE* 3.8 0.9 - - - +
175B ILE* 1.3 72.1 - - - +
177B GLU* 1.3 65.7 + - - +
179B SER* 3.2 4.7 + - - -
180B TRP* 3.1 32.8 + - + -
187B LEU* 3.6 15.5 - - + -
190B MET* 4.2 19.1 - - - -
209B ILE* 4.1 15.0 - - + -
214B TRP* 4.1 17.7 - - + -
259B LEU* 5.5 0.9 - - + -
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLY 4.7 0.5 - - - +
506A EDO 3.6 23.6 + - - -
102B ARG* 2.7 60.8 + - - +
173B PHE* 2.7 35.4 + - + +
174B GLU* 3.5 10.6 - - - +
176B LEU* 1.3 74.1 - - - +
178B LYS* 1.3 61.5 + - - +
180B TRP* 3.4 9.4 + - - +
181B LEU* 3.4 17.8 + - + +
185B CYS 4.9 1.0 - - - +
186B THR* 6.0 0.5 - - - +
187B LEU* 3.4 27.9 + - + +
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A GLU 4.5 1.8 + - - -
320A GLY* 5.4 1.0 - - - -
345A TYR* 3.1 31.3 + - - -
506A EDO 3.1 30.6 + - - +
174B GLU 2.8 19.7 + - - +
175B ILE 3.8 4.0 - - - +
177B GLU* 1.3 73.3 - - - +
179B SER* 1.3 61.8 + - - +
181B LEU* 3.4 16.6 - - + +
182B PRO* 3.3 17.3 - - - +
392B GLY 5.6 2.2 - - - +
396B HIS* 4.1 20.8 - - + +
399B TRP* 3.4 53.2 - - + +
400B SER* 5.2 0.7 - - - +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.8 19.8 - - - +
175B ILE* 2.6 23.5 + - - +
176B LEU* 3.6 6.1 - - - -
177B GLU 3.2 0.4 - - - -
178B LYS* 1.3 76.3 - - - +
180B TRP* 1.3 57.2 + - - +
181B LEU 3.4 0.2 - - - -
182B PRO* 3.4 14.0 - - - +
183B GLN* 4.7 1.9 + - - +
259B LEU* 3.5 32.9 - - - +
396B HIS* 3.3 32.0 + - - -
400B SER* 4.1 6.8 + - - -
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Residues in contact with TRP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.9 0.2 - - - +
176B LEU* 3.1 27.5 + - + +
177B GLU 3.4 4.2 + - - +
178B LYS 3.3 0.2 - - - -
179B SER* 1.3 74.4 - - - +
181B LEU* 1.3 65.3 + - - +
182B PRO* 3.4 1.6 - - - -
183B GLN* 3.0 33.3 + - + +
185B CYS* 3.4 42.5 + - + +
187B LEU* 4.3 14.1 - - + -
214B TRP* 3.6 38.7 - + - -
216B LEU* 3.7 39.5 - - + +
251B TRP* 4.9 2.2 - + - -
252B VAL* 4.0 16.2 - - + -
255B ARG* 4.3 12.6 - - + -
256B VAL* 4.2 20.0 - - + -
259B LEU* 3.7 31.8 - - + +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLY* 4.3 21.1 - - - +
506A EDO 4.1 28.7 - - - +
177B GLU* 3.4 12.6 + - + +
178B LYS* 3.4 18.8 - - + +
180B TRP* 1.3 76.2 - - - +
182B PRO* 1.4 64.6 - - + +
184B ASN* 2.8 28.3 + - - -
185B CYS 4.0 11.9 - - - +
186B THR* 5.6 3.8 - - - +
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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