Contacts of the helix formed by residues 159 - 192 (chain B) in PDB entry 2YPT
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 THR 159 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 3.5 8.0 - - - -
157B GLN 3.9 1.3 + - - +
158B GLN* 1.3 74.8 - - - +
160B LEU* 1.3 67.3 + - - +
161B GLY* 3.2 6.8 + - - +
162B PHE* 3.3 25.6 + - + +
163B PHE* 3.1 18.7 + - - +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 6.2 0.7 - - + -
94A LEU* 4.7 13.2 - - + -
143B LEU* 4.7 16.8 - - + -
147B PHE* 3.6 31.2 - - + -
159B THR* 1.3 75.0 + - - +
161B GLY* 1.3 56.6 + - - +
163B PHE* 3.6 1.7 + - - +
164B MET* 3.0 46.4 + - + +
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Residues in contact with GLY 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B THR* 3.2 8.3 + - - -
160B LEU* 1.3 77.5 - - - +
162B PHE* 1.4 54.5 + - - +
164B MET* 3.4 4.8 + - - +
165B LYS* 2.8 42.4 + - - +
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 3.3 21.1 - - + -
159B THR* 3.3 29.5 + - + +
161B GLY* 1.4 71.3 - - - +
163B PHE* 1.3 59.3 + - - +
165B LYS* 4.0 5.9 - - + +
166B ASP* 2.9 51.0 + - - +
169B LYS* 5.4 4.0 - - - -
223B PHE 4.1 9.9 - - - -
224B ASP* 5.2 0.9 - - - -
259B LYS* 4.8 18.6 - - + -
260B ARG* 3.7 46.9 - - + -
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Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.5 19.5 - - + -
142B SER* 3.2 28.9 - - - -
143B LEU* 3.6 46.4 - - + -
146B THR* 3.6 30.5 - - + -
147B PHE* 3.6 14.1 - + + -
158B GLN* 3.5 23.9 + - - +
159B THR 3.1 16.6 + - - +
160B LEU 3.7 2.9 - - - +
162B PHE* 1.3 76.4 - - - +
164B MET* 1.4 64.2 + - - +
166B ASP* 3.5 3.4 + - - +
167B ALA* 3.0 29.9 + - + +
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Residues in contact with MET 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.7 29.6 - - + +
94A LEU* 3.9 19.3 - - + +
95A PHE* 3.8 49.6 - - + +
139B LEU* 4.6 5.6 - - + -
143B LEU* 5.2 0.2 - - - -
160B LEU* 3.0 35.6 + - + +
161B GLY* 3.7 5.6 - - - +
163B PHE* 1.4 82.1 - - + +
165B LYS* 1.4 64.3 + - - +
167B ALA* 3.2 14.1 + - - +
168B ILE* 3.2 27.1 + - + +
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLY 2.8 24.1 + - - +
162B PHE* 4.0 6.1 - - + +
164B MET* 1.4 73.3 - - + +
166B ASP* 1.3 57.7 + - - +
168B ILE* 3.7 9.7 + - + +
169B LYS* 3.1 39.4 + - + +
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Residues in contact with ASP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 5.3 0.2 - - - +
162B PHE* 2.9 29.0 + - + +
163B PHE* 3.8 6.1 - - - +
165B LYS* 1.3 75.2 - - - +
167B ALA* 1.4 54.6 - - - +
169B LYS* 3.5 27.2 + - - +
170B LYS* 2.9 38.4 + - - +
223B PHE* 3.6 13.9 - - - +
260B ARG* 2.8 44.1 + - - +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.8 18.3 - - + -
139B LEU* 4.0 22.0 - - + -
163B PHE* 3.0 21.9 + - + +
164B MET* 3.2 9.6 + - - +
166B ASP* 1.4 75.6 - - - +
168B ILE* 1.4 56.7 + - - +
170B LYS* 4.0 4.9 - - - +
171B PHE* 3.0 29.5 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU 4.5 5.8 - - - +
95A PHE* 3.7 45.8 - - + +
164B MET* 3.2 34.4 + - + +
165B LYS* 4.0 9.2 - - + +
167B ALA* 1.4 71.3 - - - +
169B LYS* 1.4 55.9 + - - +
171B PHE* 3.2 2.9 + - + +
172B VAL* 2.8 53.0 + - + +
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Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PHE* 5.4 4.0 - - - -
165B LYS* 3.1 28.8 + - + +
166B ASP* 3.5 29.2 + - - +
168B ILE* 1.4 74.8 - - - +
170B LYS* 1.4 61.9 + - - +
172B VAL* 3.4 5.2 + - - +
173B VAL* 3.1 28.5 + - + +
222B LEU* 2.8 32.2 + - + +
223B PHE* 3.7 20.1 + - + +
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 2.9 22.9 + - - +
167B ALA* 4.0 5.2 - - - +
169B LYS* 1.4 69.6 - - - +
171B PHE* 1.4 54.9 + - - +
173B VAL* 3.3 3.5 + - - +
174B THR* 2.7 40.0 + - - +
223B PHE* 3.5 23.1 - - + -
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.7 26.7 - + + -
100A TYR* 4.0 27.8 - + - -
131B THR* 3.4 23.1 - - - -
132B LEU* 4.0 20.0 - - + -
135B ALA* 3.8 20.4 - - + -
167B ALA 3.0 20.0 + - - +
168B ILE* 3.2 6.0 + - + +
170B LYS* 1.4 74.6 - - - +
172B VAL* 1.4 68.1 + - + +
174B THR* 3.4 8.5 + - + -
175B GLN* 3.2 60.1 + - + +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE* 2.8 38.8 + - + +
169B LYS* 3.7 6.1 - - - +
171B PHE* 1.4 78.4 - - + +
173B VAL* 1.3 65.9 + - + +
175B GLN* 3.3 8.6 + - - +
176B CYS* 3.2 37.2 + - - -
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LYS* 3.1 18.6 + - + +
170B LYS 3.8 3.4 - - - +
172B VAL* 1.3 78.6 - - + +
174B THR* 1.4 63.1 + - - +
176B CYS* 3.3 9.0 + - - +
177B ILE* 3.3 41.2 + - + +
219B ILE* 4.9 10.8 - - + -
222B LEU* 4.3 18.2 - - + -
223B PHE* 3.9 29.2 - - + -
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 6.0 2.2 - - + -
170B LYS* 2.7 26.3 + - - +
171B PHE* 3.5 10.1 - - + -
172B VAL 3.3 0.2 - - - -
173B VAL* 1.4 75.2 - - - +
175B GLN* 1.4 62.3 + - - +
177B ILE* 3.2 9.0 + - - +
178B LEU* 2.9 45.1 + - + +
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Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 3.7 7.2 + - + +
128B LEU* 3.4 27.7 - - + +
131B THR* 3.0 38.9 + - - +
171B PHE* 3.2 44.4 + - + +
172B VAL* 3.3 8.0 + - - +
174B THR* 1.4 82.7 - - - +
176B CYS* 1.4 59.0 + - - +
177B ILE 3.1 0.2 - - - -
178B LEU* 4.2 7.3 - - - +
179B LEU* 2.9 47.0 + - + +
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Residues in contact with CYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 3.2 31.5 + - - +
173B VAL* 3.7 12.6 - - - +
174B THR 3.3 0.2 - - - -
175B GLN* 1.4 76.0 - - - +
177B ILE* 1.3 58.8 + - + +
179B LEU* 5.5 0.2 - - - -
180B PRO* 3.4 21.6 - - - +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 3.3 33.2 + - + +
174B THR* 3.2 8.4 + - - +
175B GLN 3.1 0.6 - - - -
176B CYS* 1.3 81.0 - - + +
178B LEU* 1.3 66.0 + - - +
180B PRO* 3.4 7.5 - - - +
181B VAL* 3.3 33.4 - - + +
207B VAL* 6.4 0.4 - - + -
211B LEU* 5.9 7.2 - - + -
219B ILE* 5.2 10.1 - - + -
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.7 24.2 - - + -
131B THR* 3.8 28.9 - - + +
174B THR* 2.9 25.9 + - + +
175B GLN* 3.8 13.2 - - - +
177B ILE* 1.3 77.2 - - - +
179B LEU* 1.3 57.2 + - + +
181B VAL* 3.7 3.5 - - - +
182B SER* 2.6 50.8 + - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.7 29.0 - - + +
127B LEU* 4.6 13.0 - - + -
128B LEU* 3.7 47.6 - - + -
175B GLN* 2.9 34.6 + - + +
176B CYS* 5.5 0.2 - - - -
178B LEU* 1.3 76.2 - - + +
180B PRO* 1.4 61.8 - - + +
182B SER* 4.4 4.0 - - - -
183B SER* 2.9 29.3 + - - -
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Residues in contact with PRO 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B CYS* 3.4 24.9 - - - +
177B ILE* 3.4 14.6 - - - +
179B LEU* 1.4 93.2 - - + +
181B VAL* 1.4 59.2 + - + +
183B SER* 2.9 18.1 + - - +
184B LEU* 3.2 26.3 + - + +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 3.3 28.7 + - + +
178B LEU* 3.3 4.9 + - - +
180B PRO* 1.4 76.0 - - + +
182B SER* 1.4 55.7 + - - +
184B LEU* 3.5 1.8 + - + -
185B LEU* 2.9 37.5 + - + +
203B PHE* 3.5 18.6 - - + -
204B THR* 6.3 2.0 - - + -
207B VAL* 4.0 36.8 - - + -
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.5 4.3 - - - -
127B LEU* 3.4 31.3 - - - +
178B LEU* 2.6 38.2 + - - +
179B LEU* 3.9 3.4 - - - -
181B VAL* 1.4 70.3 - - - +
183B SER* 1.4 59.0 + - - +
185B LEU* 3.2 10.3 + - - +
186B LEU* 2.9 42.8 + - - +
385B LEU* 5.2 3.6 - - - -
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ILE* 4.1 20.3 - - - +
124B LEU* 3.7 23.4 - - - +
179B LEU 2.9 18.6 + - - -
180B PRO* 2.9 17.5 + - - +
182B SER* 1.4 75.0 - - - +
184B LEU* 1.4 57.1 + - - +
186B LEU* 3.4 4.0 + - - +
187B TYR* 2.9 28.5 + - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B PRO* 3.2 25.0 + - + +
181B VAL* 4.9 0.9 - - + -
183B SER* 1.4 79.3 + - - +
185B LEU* 1.4 64.9 + - - +
187B TYR* 3.3 17.2 + - + +
188B ILE* 3.1 32.3 + - + +
203B PHE* 3.5 29.4 - - + -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL* 2.9 22.4 + - + +
182B SER* 3.2 10.3 + - - +
184B LEU* 1.4 74.6 - - - +
186B LEU* 1.4 62.4 + - + +
188B ILE* 3.5 6.5 + - - +
189B ILE* 3.4 20.3 + - - +
200B ALA* 4.0 18.4 - - + +
203B PHE* 3.7 14.8 - - + -
204B THR* 3.8 30.1 - - + -
360B PHE* 4.0 13.7 - - + -
388B LEU* 4.4 27.8 - - + +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 5.2 0.7 - - - +
120B ILE* 4.0 19.7 - - + +
123B SER* 3.7 28.0 - - - +
124B LEU* 5.1 2.9 - - + -
182B SER* 2.9 28.7 + - - +
183B SER* 3.7 9.0 - - - +
185B LEU* 1.4 73.3 - - + +
187B TYR* 1.3 59.3 + - - +
189B ILE* 3.4 5.3 + - - +
190B LYS* 3.0 34.8 + - + +
384B THR* 3.8 17.4 - - + +
385B LEU* 3.5 50.9 - - + +
388B LEU* 4.2 8.7 - - + -
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Residues in contact with TYR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 6.5 0.2 - - + -
120B ILE* 4.0 18.3 - - + +
183B SER 2.9 18.4 + - - +
184B LEU* 3.3 21.7 + - + +
186B LEU* 1.3 76.5 - - - +
188B ILE* 1.3 62.4 + - + +
190B LYS* 4.8 0.4 - - - -
191B ILE* 2.8 76.1 + - + +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.1 21.2 + - + +
185B LEU* 3.8 4.9 - - - +
187B TYR* 1.3 84.4 - - + +
189B ILE* 1.3 57.5 + - - +
191B ILE* 5.1 0.2 - - - -
192B GLY* 2.9 30.7 + - - +
196B PHE* 4.1 4.8 - - - +
199B TYR* 3.8 17.9 - - + +
200B ALA* 3.5 33.9 - - + +
203B PHE* 3.6 42.2 - - + -
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU 3.4 11.0 + - - +
186B LEU* 3.8 7.2 - - - +
187B TYR 3.4 0.2 - - - -
188B ILE* 1.3 79.7 - - - +
190B LYS* 1.4 59.2 + - - +
192B GLY 3.2 14.6 - - - +
196B PHE* 4.0 33.4 - - + +
200B ALA* 5.4 5.2 - - + -
363B PHE* 5.3 5.6 - - + -
367B ILE* 5.9 2.0 - - + -
384B THR* 4.0 20.4 - - + -
388B LEU* 6.1 2.5 - - + -
----------------------------------------------------------
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 4.9 15.3 - - + +
119B GLU* 4.3 10.1 - - - +
120B ILE* 4.8 16.2 - - + -
186B LEU 3.0 20.8 + - - +
187B TYR* 4.0 3.6 - - - +
189B ILE* 1.4 77.8 - - - +
191B ILE* 1.4 64.3 + - + +
192B GLY 4.2 1.6 - - - +
384B THR* 3.6 26.2 - - + +
----------------------------------------------------------
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 4.6 24.0 - - + -
120B ILE* 6.2 0.2 - - + -
187B TYR* 2.8 65.2 + - + +
188B ILE* 5.1 0.7 - - - -
190B LYS* 1.4 76.6 - - + +
192B GLY* 1.3 64.6 - - - +
----------------------------------------------------------
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 2.9 22.0 + - - +
189B ILE 3.2 16.6 - - - +
190B LYS 4.2 1.6 - - - +
191B ILE* 1.3 80.9 - - - +
193B GLY* 1.3 56.7 + - - -
196B PHE* 3.5 10.3 - - - +
199B TYR* 4.4 13.2 - - - -
----------------------------------------------------------
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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