Contacts of the helix formed by residues 159 - 192 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PHE* 3.5 8.0 - - - -
157D GLN 4.0 1.3 + - - +
158D GLN* 1.3 74.6 - - - +
160D LEU* 1.3 67.8 + - - +
161D GLY* 3.2 6.2 + - - +
162D PHE* 3.3 26.0 + - + +
163D PHE* 3.1 18.9 + - - +
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D LEU* 4.7 17.3 - - + -
147D PHE* 3.6 30.9 - - + -
159D THR* 1.3 75.6 + - - +
161D GLY* 1.3 57.4 + - - +
163D PHE* 3.6 1.9 + - - +
164D MET* 3.0 46.0 + - + +
90E THR* 6.5 1.1 - - + -
91E LEU* 6.1 1.3 - - + -
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Residues in contact with GLY 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D THR* 3.2 8.3 + - - -
160D LEU* 1.3 77.1 - - - +
162D PHE* 1.4 54.8 + - - +
164D MET* 3.4 4.8 + - - +
165D LYS* 2.8 50.2 + - - +
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Residues in contact with PHE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D GLN* 3.3 22.2 - - + -
159D THR* 3.3 29.7 + - + +
161D GLY* 1.4 70.6 - - - +
163D PHE* 1.4 58.2 + - - +
165D LYS* 4.0 6.4 - - + +
166D ASP* 2.9 51.4 + - - +
169D LYS* 5.0 6.5 - - - -
223D PHE 4.1 9.9 - - - -
224D ASP* 5.2 1.1 - - - -
259D LYS* 4.8 18.8 - - + -
260D ARG* 3.7 46.2 - - + -
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU* 4.5 20.4 - - + -
142D SER* 3.2 28.7 - - - -
143D LEU* 3.6 44.4 - - + -
146D THR* 3.6 32.5 - - + -
147D PHE* 3.7 14.1 - + + -
158D GLN* 3.5 21.4 + - - +
159D THR 3.1 16.2 + - - +
160D LEU 3.7 2.7 - - - +
162D PHE* 1.4 76.6 - - - +
164D MET* 1.3 64.4 + - - +
166D ASP* 3.8 3.0 - - - +
167D ALA* 3.0 29.5 + - + +
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Residues in contact with MET 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU* 4.6 13.2 - - + -
143D LEU* 5.2 0.4 - - + -
160D LEU* 3.0 34.6 + - + +
161D GLY* 3.7 5.8 - - - +
162D PHE 3.4 0.2 - - - -
163D PHE* 1.3 83.1 - - + +
165D LYS* 1.4 65.6 + - + +
167D ALA* 3.2 14.9 + - + +
168D ILE* 3.2 39.0 + - + +
91E LEU* 3.7 45.5 - - + +
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Residues in contact with LYS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D GLY* 2.8 30.2 + - - +
162D PHE* 4.0 6.3 - - + +
164D MET* 1.4 71.5 - - - +
166D ASP* 1.3 56.8 + - - +
168D ILE* 3.7 10.5 + - + +
169D LYS* 3.0 42.2 + - + +
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Residues in contact with ASP 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D GLN* 5.3 0.2 - - - +
162D PHE* 2.9 28.0 + - + +
163D PHE* 3.8 5.8 - - - +
165D LYS* 1.3 74.6 - - - +
167D ALA* 1.4 56.8 + - - +
169D LYS* 3.4 27.7 + - - +
170D LYS* 2.9 34.8 + - - +
223D PHE* 3.6 14.6 - - - +
260D ARG* 2.7 44.3 + - - +
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Residues in contact with ALA 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU* 4.1 29.6 - - + -
163D PHE* 3.0 22.5 + - + +
164D MET* 3.2 11.6 + - + +
166D ASP* 1.4 76.1 - - - +
168D ILE* 1.4 57.9 + - + +
170D LYS* 3.9 4.6 - - - +
171D PHE* 3.0 29.2 + - - +
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D MET* 3.2 40.5 + - + +
165D LYS* 4.0 8.5 - - + +
167D ALA* 1.4 73.1 - - + +
169D LYS* 1.4 56.2 + - - +
171D PHE* 3.2 8.5 + - + +
172D VAL* 2.8 53.2 + - + +
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Residues in contact with LYS 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D PHE* 5.0 7.2 - - - -
165D LYS* 3.0 34.4 + - + +
166D ASP* 3.4 31.0 + - - +
168D ILE* 1.4 74.5 - - - +
170D LYS* 1.4 56.3 + - - +
172D VAL* 3.5 5.0 + - - +
173D VAL* 3.1 33.5 + - + +
222D LEU* 3.3 29.0 + - + +
223D PHE* 3.6 20.2 + - + +
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Residues in contact with LYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ASP* 2.9 22.3 + - - +
167D ALA* 3.9 4.9 - - - +
169D LYS* 1.4 70.1 - - - +
171D PHE* 1.4 55.0 + - - +
173D VAL* 3.3 3.3 + - - +
174D THR* 2.7 40.6 + - - +
223D PHE* 3.5 20.4 - - + -
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Residues in contact with PHE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU 4.9 0.2 - - - -
131D THR* 3.6 25.8 - - - -
132D LEU* 3.9 29.6 - - + -
135D ALA* 3.8 20.6 - - + -
167D ALA 3.0 19.6 + - - +
168D ILE* 3.6 10.1 - - + +
170D LYS* 1.4 75.7 - - - +
172D VAL* 1.4 68.5 + - + +
174D THR* 3.4 7.8 + - + -
175D GLN* 3.1 61.2 + - + +
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Residues in contact with VAL 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ILE* 2.8 38.5 + - + +
169D LYS* 3.7 5.8 - - - +
171D PHE* 1.4 74.3 - - + +
173D VAL* 1.3 68.0 + - + +
175D GLN* 3.3 7.9 + - - +
176D CYS* 3.2 39.2 + - - -
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Residues in contact with VAL 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LYS 3.1 20.6 + - - +
170D LYS 3.7 3.6 - - - +
172D VAL* 1.3 76.6 - - + +
174D THR* 1.4 62.4 + - - +
176D CYS* 3.4 8.2 + - - +
177D ILE* 3.3 35.0 + - + +
219D ILE* 3.8 22.0 - - + -
222D LEU* 4.3 16.8 - - + -
223D PHE* 3.7 27.8 - - + -
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Residues in contact with THR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D THR* 6.0 2.2 - - + -
170D LYS* 2.7 24.1 + - - +
171D PHE* 3.5 9.8 - - + -
172D VAL 3.3 0.2 - - - -
173D VAL* 1.4 76.8 - - - +
175D GLN* 1.4 61.5 + - - +
177D ILE* 3.1 8.7 + - - +
178D LEU* 2.8 44.8 + - + +
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Residues in contact with GLN 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 3.4 30.5 - - + +
131D THR* 3.0 36.1 + - - +
171D PHE* 3.1 43.4 + - + +
172D VAL* 3.3 7.6 + - - +
174D THR* 1.4 81.3 - - - +
176D CYS* 1.4 59.4 + - - +
177D ILE 3.2 0.2 - - - -
178D LEU* 3.7 17.9 - - - +
179D LEU* 3.0 42.0 + - + +
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Residues in contact with CYS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D VAL* 3.2 33.6 + - - +
173D VAL* 3.7 8.3 - - - +
174D THR 3.3 0.4 - - - -
175D GLN* 1.4 76.7 - - - +
177D ILE* 1.3 59.9 + - + +
179D LEU* 5.5 0.2 - - - -
180D PRO* 3.3 22.4 - - - +
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Residues in contact with ILE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D VAL* 3.4 33.0 - - + +
174D THR* 3.1 8.8 + - - +
176D CYS* 1.3 81.3 - - + +
178D LEU* 1.3 66.4 + - - +
180D PRO* 3.4 6.7 - - - +
181D VAL* 3.3 29.5 - - + +
211D LEU* 3.9 34.3 - - + -
219D ILE* 3.9 27.4 - - + -
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D LEU* 3.8 29.4 - - + +
131D THR* 3.9 20.0 - - + +
174D THR* 2.8 24.8 + - + +
175D GLN* 3.7 25.4 - - - +
177D ILE* 1.3 77.6 - - - +
179D LEU* 1.3 61.6 + - + +
181D VAL* 3.8 2.8 - - - +
182D SER* 2.8 46.7 + - - +
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 3.7 33.9 - - + +
127D LEU* 5.2 2.9 - - + -
128D LEU* 3.6 50.0 - - + +
175D GLN* 3.0 26.3 + - + +
176D CYS* 5.5 0.2 - - - -
178D LEU* 1.3 91.7 - - + +
180D PRO* 1.4 62.1 - - + +
182D SER* 4.5 1.1 - - - -
183D SER* 3.0 31.1 + - - -
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Residues in contact with PRO 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D CYS* 3.3 29.4 - - - +
177D ILE 3.4 9.9 - - - +
179D LEU* 1.4 91.3 - - + +
181D VAL* 1.4 60.2 + - + +
183D SER* 2.7 21.1 + - - +
184D LEU* 3.1 25.3 + - + +
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Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ILE* 3.3 28.6 + - + +
178D LEU* 3.3 3.9 + - - +
180D PRO* 1.4 76.9 - - + +
182D SER* 1.4 59.9 + - - +
184D LEU* 5.0 0.4 - - - -
185D LEU* 3.0 30.7 + - + +
203D PHE* 3.4 18.3 - - + -
204D THR* 6.2 2.5 - - + -
207D VAL* 4.0 36.8 - - + -
211D LEU* 5.0 2.2 - - + -
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Residues in contact with SER 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 4.5 4.5 - - - -
127D LEU* 3.4 30.1 - - - +
178D LEU* 2.8 34.5 + - - +
179D LEU* 3.9 3.6 - - - -
181D VAL* 1.4 72.2 - - - +
183D SER* 1.4 58.8 + - - +
185D LEU* 3.8 8.2 - - - +
186D LEU* 2.9 42.6 + - - +
385D LEU* 5.2 3.3 - - - +
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Residues in contact with SER 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ILE* 4.5 18.3 - - - +
124D LEU* 3.8 24.1 - - - +
179D LEU 3.0 16.2 + - - -
180D PRO* 2.7 25.8 + - - +
182D SER* 1.4 75.9 - - - +
184D LEU* 1.4 57.9 + - - +
186D LEU* 3.6 3.7 + - - +
187D TYR* 3.1 27.4 + - - +
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D PRO* 3.1 22.0 + - + +
181D VAL* 5.0 0.7 - - - +
183D SER* 1.4 80.2 + - - +
185D LEU* 1.4 63.5 + - - +
187D TYR* 3.3 16.1 - - + +
188D ILE* 3.1 32.8 + - + +
203D PHE* 3.5 30.7 - - + -
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D VAL* 3.0 22.7 + - + +
182D SER* 3.4 7.4 + - - +
184D LEU* 1.4 76.0 - - - +
186D LEU* 1.4 61.8 + - + +
188D ILE* 3.3 6.4 + - - +
189D ILE* 3.2 28.1 + - + +
200D ALA* 3.7 30.7 - - + +
203D PHE* 3.7 16.5 - - + -
204D THR* 3.8 18.6 - - + -
360D PHE* 4.0 12.3 - - + -
388D LEU* 4.2 28.7 - - + -
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Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D GLU* 5.3 0.4 - - - +
120D ILE* 4.0 21.1 - - + +
123D SER* 3.7 28.3 - - - +
124D LEU* 5.0 3.6 - - + -
182D SER* 2.9 28.4 + - - +
183D SER* 3.9 7.6 - - - +
185D LEU* 1.4 76.3 - - + +
187D TYR* 1.4 56.2 + - - +
189D ILE* 3.5 7.3 + - - +
190D LYS* 3.0 34.6 + - + +
384D THR* 3.7 17.7 - - + -
385D LEU* 3.5 49.1 - - + +
388D LEU* 4.3 7.2 - - + -
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Residues in contact with TYR 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PRO* 6.5 0.2 - - + -
120D ILE* 4.0 19.0 - - + +
183D SER 3.1 15.5 + - - +
184D LEU* 3.3 22.7 - - + +
186D LEU* 1.4 75.5 - - - +
188D ILE* 1.3 61.2 + - + +
190D LYS* 3.5 1.0 + - - -
191D ILE* 2.8 76.6 + - + +
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Residues in contact with ILE 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D LEU* 3.1 21.0 + - + +
185D LEU* 3.7 6.1 - - - +
187D TYR* 1.3 83.4 - - + +
189D ILE* 1.3 58.4 + - - +
191D ILE* 5.1 0.4 - - - -
192D GLY* 2.9 30.5 + - - +
196D PHE* 4.1 4.1 - - - +
199D TYR* 3.8 18.4 - - + +
200D ALA* 3.6 33.2 - - + +
203D PHE* 3.6 41.5 - - + -
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Residues in contact with ILE 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LEU* 3.2 37.6 + - + +
186D LEU* 3.9 4.5 - - - +
187D TYR 3.4 0.2 - - - -
188D ILE* 1.3 75.4 - - - +
190D LYS* 1.3 60.4 + - - +
192D GLY 3.3 14.4 - - - +
196D PHE* 3.7 38.8 - - + +
200D ALA* 4.1 16.8 - - + -
360D PHE* 4.7 4.0 - - + -
363D PHE* 4.3 11.2 - - + -
367D ILE* 4.4 7.0 - - + -
384D THR* 3.7 22.2 - - + -
388D LEU* 4.1 29.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PRO* 4.9 18.6 - - + +
119D GLU* 4.4 10.1 - - + +
120D ILE* 4.9 10.8 - - + -
186D LEU* 3.0 21.1 + - + +
187D TYR* 4.0 3.8 - - - +
189D ILE* 1.3 78.1 - - - +
191D ILE* 1.4 64.6 + - + +
192D GLY 4.2 1.4 - - - +
384D THR* 3.6 26.7 - - + +
----------------------------------------------------------
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D PRO* 4.6 23.8 - - + -
120D ILE* 6.2 0.2 - - + -
187D TYR* 2.8 64.3 + - + +
188D ILE* 4.8 0.7 - - - +
190D LYS* 1.4 75.8 - - + +
192D GLY* 1.3 65.7 + - - +
193D GLY 4.0 0.2 + - - -
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Residues in contact with GLY 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 2.9 22.1 + - - +
189D ILE 3.3 16.1 - - - +
190D LYS 4.2 1.7 - - - +
191D ILE* 1.3 80.3 - - - +
193D GLY* 1.3 56.9 + - - -
196D PHE* 3.5 12.0 - - - +
199D TYR* 4.5 11.0 - - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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