Contacts of the helix formed by residues 166 - 192 (chain D) in PDB entry 3P9K
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 ASP 166 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D VAL* 4.1 6.4 - - - +
162D TYR* 2.8 48.1 + - + +
163D HIS* 3.4 5.2 + - - +
164D GLY 3.6 0.2 - - - -
165D THR* 1.3 80.9 - - - +
167D PRO* 1.3 52.9 - - - +
168D ARG* 3.1 17.4 + - - +
169D PHE* 3.1 24.3 + - + +
170D ASN* 2.8 33.8 + - - +
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Residues in contact with PRO 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D GLY 5.9 1.6 - - - +
165D THR 3.7 7.9 - - - +
166D ASP* 1.3 86.9 - - - +
168D ARG* 1.3 63.0 + - - +
170D ASN* 3.6 9.4 + - + +
171D ARG* 3.2 23.7 + - - +
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Residues in contact with ARG 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASP* 2.8 42.6 + - - -
131D LYS* 5.4 3.0 - - - +
132D VAL* 3.4 19.4 - - - +
166D ASP* 3.1 13.1 + - - +
167D PRO* 1.3 80.5 - - - +
169D PHE* 1.3 70.4 + - - +
171D ARG* 3.1 39.0 + - - +
172D VAL* 3.2 23.8 + - - +
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Residues in contact with PHE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D MET* 4.2 6.5 - - + -
130D ASP* 3.4 39.7 - - + -
132D VAL* 3.9 19.5 - - + -
133D LEU* 3.4 35.7 - - + -
151D PHE* 5.9 1.1 - + - -
162D TYR* 4.4 6.5 - + + -
163D HIS* 3.7 34.3 - + - -
166D ASP* 3.1 25.0 + - + +
168D ARG* 1.3 82.3 - - - +
170D ASN* 1.3 57.5 + - - +
171D ARG 3.0 2.2 - - - -
172D VAL* 3.0 16.4 + - + +
173D PHE* 2.7 41.6 + + + +
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Residues in contact with ASN 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D HIS* 3.3 39.3 + - - +
164D GLY* 5.5 0.2 - - - -
166D ASP 2.8 18.8 + - - +
167D PRO* 3.6 10.4 + - + +
168D ARG 3.3 0.2 - - - -
169D PHE* 1.3 77.7 - - - +
171D ARG* 1.3 57.6 - - - +
173D PHE* 3.5 5.5 + - - +
174D ASN* 3.1 43.7 + - - +
231D HIS* 3.9 8.9 - - - -
232D VAL* 5.6 0.9 - - - +
235D GLU* 2.7 36.7 + - - +
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Residues in contact with ARG 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D PRO 3.2 11.6 + - - +
168D ARG* 3.1 34.4 + - - +
169D PHE 3.0 0.6 - - - -
170D ASN* 1.3 78.9 - - - +
172D VAL* 1.3 83.4 + - - +
173D PHE 3.1 0.2 - - - -
174D ASN* 4.0 5.7 - - - +
175D GLU* 2.8 45.1 + - + +
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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
----------------------------------------------------------
123D ALA 4.6 2.1 - - - +
126D LEU* 4.2 11.7 - - + +
127D MET* 3.7 32.9 - - + +
130D ASP* 4.5 3.8 - - - +
168D ARG* 3.2 30.2 + - - +
169D PHE* 3.0 22.3 + - + +
171D ARG* 1.3 98.9 - - - +
173D PHE* 1.3 62.4 + - - +
175D GLU* 3.5 4.5 + - - +
176D GLY* 3.1 19.1 + - - -
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Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D MET* 3.7 21.7 - - + +
133D LEU* 5.7 1.6 - - + -
160D PHE* 4.3 3.1 - + - -
163D HIS* 3.3 45.5 - + + +
169D PHE* 2.7 28.0 + + + +
170D ASN* 3.6 5.6 - - - +
172D VAL* 1.3 74.8 - - - +
174D ASN* 1.3 73.6 + - - +
176D GLY* 3.1 2.6 + - - -
177D MET* 3.0 53.7 + - + +
404D SAH 3.9 25.6 - - + -
604D CIY 3.5 39.3 - + - -
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Residues in contact with ASN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D HIS* 5.5 0.2 + - - -
170D ASN* 3.1 29.0 + - - +
171D ARG* 4.0 4.6 - - - +
173D PHE* 1.3 89.9 - - - +
175D GLU* 1.3 60.4 + - - +
177D MET* 3.7 5.9 - - - +
178D LYS* 2.8 32.3 + - - +
207D GLY* 5.5 1.7 - - - -
208D VAL* 4.0 29.2 + - + +
232D VAL* 5.4 9.8 - - - +
235D GLU* 3.1 26.7 + - - -
404D SAH 5.2 3.8 + - - -
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Residues in contact with GLU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ALA* 4.1 8.1 - - + -
171D ARG* 2.8 29.7 + - + +
172D VAL* 3.7 6.1 - - - +
174D ASN* 1.3 77.9 - - - +
176D GLY* 1.3 62.9 + - - +
178D LYS* 4.0 24.4 + - - +
179D ASN* 2.9 55.9 + - - +
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Residues in contact with GLY 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ALA* 3.8 24.9 - - - +
124D LEU* 3.5 25.6 - - - +
127D MET* 4.6 2.9 - - - -
172D VAL 3.1 15.4 + - - -
173D PHE 3.1 4.2 + - - -
175D GLU* 1.3 79.0 - - - +
177D MET* 1.3 60.5 + - - +
179D ASN* 3.9 1.6 - - - +
180D HIS* 3.3 16.8 + - - +
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Residues in contact with MET 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 4.0 4.5 - - + -
127D MET* 3.5 38.1 - - + -
173D PHE* 3.0 40.6 + - + +
174D ASN* 3.8 5.8 - - - +
176D GLY* 1.3 75.5 - - - +
178D LYS* 1.3 60.3 + - - +
180D HIS* 3.5 3.1 + - - +
181D SER* 2.9 33.4 + - - -
262D LYS* 4.8 0.2 + - - -
263D TRP* 3.8 20.4 - - + -
404D SAH 3.3 25.5 - - + +
604D CIY 3.7 41.7 - - + +
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Residues in contact with LYS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D VAL* 5.7 2.5 - - + -
174D ASN 2.8 19.2 + - - +
175D GLU* 3.8 28.3 + - - +
177D MET* 1.3 74.7 - - - +
179D ASN* 1.3 67.9 + - - +
181D SER* 3.2 4.8 + - - -
182D ILE* 2.9 54.7 + - + +
208D VAL* 4.6 17.5 - - + -
210D ALA* 4.4 15.0 - - + -
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Residues in contact with ASN 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLY 4.3 1.8 + - - +
119D VAL* 3.0 24.9 - - - +
120D SER* 3.0 40.9 + - - +
123D ALA* 3.7 16.9 - - + +
124D LEU* 5.7 1.1 - - + +
175D GLU* 2.9 48.4 + - - +
176D GLY 3.9 4.5 - - - +
178D LYS* 1.3 82.2 - - - +
180D HIS* 1.3 61.5 + - - +
182D ILE* 3.6 1.9 + - - +
183D ILE* 3.3 26.9 + - - +
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Residues in contact with HIS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 4.3 11.5 - - + +
121D MET* 4.0 21.9 - - + +
124D LEU* 3.8 21.5 - - + +
176D GLY 3.3 14.7 + - - +
177D MET 3.9 3.6 - - - +
178D LYS 3.2 0.4 - - - -
179D ASN* 1.3 79.1 - - - +
181D SER* 1.3 58.0 + - - +
183D ILE* 3.4 4.4 + - - +
184D ILE* 3.0 62.1 + - + +
262D LYS* 3.2 26.9 + - - +
263D TRP* 3.7 42.5 - + + -
293D VAL* 6.3 0.4 - - + -
351D ALA 5.6 2.0 + - - -
353D ALA* 5.5 4.5 - - + -
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Residues in contact with SER 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D MET 2.9 13.8 + - - -
178D LYS* 3.2 5.4 + - - -
180D HIS* 1.3 74.3 - - - +
182D ILE* 1.3 58.1 + - - +
185D THR* 2.7 40.4 + - - -
210D ALA* 5.2 3.6 - - - -
211D THR* 3.2 26.8 + - - -
262D LYS* 3.2 22.2 + - - +
404D SAH 2.6 26.2 + - - -
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Residues in contact with ILE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASP* 4.1 23.2 - - + +
119D VAL* 3.9 32.8 - - + -
178D LYS* 2.9 48.7 + - + +
179D ASN 4.0 3.4 - - - +
181D SER* 1.3 76.7 - - - +
183D ILE* 1.3 61.8 + - - +
185D THR* 4.4 3.8 - - - -
186D LYS* 3.5 21.1 + - - +
210D ALA* 4.4 14.8 - - + -
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Residues in contact with ILE 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C CYS* 5.2 7.6 - - - -
111D PHE* 6.1 5.6 - - + -
115D ASN* 4.5 8.1 - - - +
119D VAL* 3.5 17.5 - - + +
120D SER* 3.9 28.3 - - - -
121D MET* 3.6 33.9 - - + +
179D ASN 3.3 15.8 + - - +
180D HIS 3.7 6.1 - - - +
181D SER 3.1 0.8 - - - -
182D ILE* 1.3 78.4 - - - +
184D ILE* 1.3 69.3 + - + +
186D LYS* 3.5 13.9 + - - +
187D LYS* 3.5 17.5 + - + +
350D TYR* 5.7 5.2 - - + -
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D MET* 5.0 2.5 - - + -
180D HIS* 3.0 48.7 + - + +
181D SER 4.1 1.3 - - - +
183D ILE* 1.3 83.4 - - + +
185D THR* 1.3 60.5 + - - +
187D LYS* 3.2 6.8 + - + +
188D LEU* 2.8 30.4 + - + +
262D LYS* 4.2 9.6 - - + -
293D VAL* 4.1 17.9 - - + -
349D ILE* 4.7 8.7 - - + -
350D TYR* 4.2 23.8 - - + +
351D ALA* 4.5 12.6 - - + +
353D ALA* 4.1 19.7 - - + -
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Residues in contact with THR 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D SER* 2.7 32.3 + - - -
182D ILE* 4.4 3.8 - - - -
184D ILE* 1.3 72.9 - - - +
186D LYS* 1.3 62.6 + - - +
188D LEU* 3.6 11.4 - - + +
189D LEU* 3.0 28.0 + - + +
211D THR* 3.6 33.9 + - + +
214D ALA* 3.8 29.6 - - + -
215D ILE* 4.1 15.9 - - + -
262D LYS* 5.0 2.9 - - - +
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Residues in contact with LYS 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLU* 5.2 9.2 - - - +
117D ASP* 4.1 26.9 + - - +
182D ILE 3.5 12.0 + - - +
183D ILE* 3.5 10.9 + - - +
184D ILE 3.2 0.6 - - - -
185D THR* 1.3 81.4 - - - +
187D LYS* 1.3 66.8 + - + +
189D LEU* 3.4 14.6 + - - +
190D GLU* 3.3 36.6 + - + +
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Residues in contact with LYS 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ILE* 3.5 12.9 + - + +
184D ILE* 3.2 10.2 + - + +
186D LYS* 1.3 81.0 - - + +
188D LEU* 1.3 65.8 + - - +
190D GLU* 3.0 36.2 + - + +
191D LEU* 3.1 25.8 - - + +
349D ILE* 4.0 15.7 - - + +
350D TYR* 3.9 50.9 + - + -
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE* 2.8 19.5 + - + +
185D THR* 3.6 13.9 - - + +
186D LYS 3.2 0.2 - - - -
187D LYS* 1.3 71.8 - - - +
189D LEU* 1.3 57.8 + - + +
190D GLU 2.9 5.3 + - - -
191D LEU 4.6 0.2 - - - +
192D TYR* 2.8 63.1 + - + +
195D PHE* 3.9 28.3 - - + -
211D THR* 5.8 1.8 - - + -
215D ILE* 4.9 7.2 - - + -
260D LEU* 5.2 3.4 - - + -
291D VAL* 5.8 0.9 - - + -
293D VAL* 4.3 25.1 - - + -
349D ILE* 3.8 29.1 - - + +
355D ALA* 4.0 11.0 - - + -
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Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D THR* 3.0 35.4 + - + +
186D LYS* 3.7 8.3 - - - +
187D LYS 3.3 0.2 - - - -
188D LEU* 1.3 76.2 - - + +
190D GLU* 1.3 60.4 + - + +
192D TYR 4.3 9.6 - - - +
193D HIS* 6.1 1.2 - - - -
195D PHE* 4.5 8.5 - - + -
214D ALA* 3.9 22.2 - - + +
215D ILE* 3.9 20.9 - - + -
218D HIS* 4.1 35.5 + - + +
219D TYR* 4.0 29.9 + - + +
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Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D LYS* 3.3 38.8 - - + +
187D LYS* 3.0 35.7 + - - +
188D LEU 2.9 0.8 - - - -
189D LEU* 1.3 82.8 - - + +
191D LEU* 1.3 72.2 + - + +
192D TYR 3.8 0.4 - - - -
193D HIS* 5.1 8.2 + - - -
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Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D LYS* 3.1 20.5 + - + +
190D GLU* 1.3 102.1 - - + +
192D TYR* 1.3 62.0 + - - +
193D HIS* 4.1 12.6 + - - -
347D THR* 4.4 12.8 - - + +
348D TYR* 4.0 8.3 - - + +
349D ILE* 3.1 47.6 - - + +
350D TYR* 5.9 0.7 - - + -
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Residues in contact with TYR 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D LEU* 2.8 37.1 + - + +
189D LEU* 4.3 10.0 - - - +
190D GLU 3.8 0.6 - - - -
191D LEU* 1.3 79.8 - - - +
193D HIS* 1.3 66.8 + - - +
194D GLY* 3.3 38.4 - - - -
195D PHE* 3.8 39.2 + + - -
219D TYR* 4.5 7.6 + - - -
289D LYS* 3.4 1.7 - - - -
291D VAL* 3.1 29.8 - - + +
347D THR* 4.7 13.2 - - + -
349D ILE* 4.5 4.3 - - + -
355D ALA* 4.1 18.2 - - + -
357D GLU* 2.6 33.9 + - + +
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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