Contacts of the helix formed by residues 170 - 194 (chain D) in PDB entry 5XVO
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 170 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D PHE* 3.8 15.2 - - - -
168D GLN* 3.2 24.5 + - + +
169D GLU* 1.3 76.8 - - - +
171D ASP* 1.3 65.5 + - - +
172D ILE* 2.9 13.5 + - + +
173D ASN* 2.7 51.0 + - - +
174D ALA* 3.1 20.4 + - - +
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Residues in contact with ASP 171 (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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170D ASN* 1.3 75.9 - - - +
172D ILE* 1.3 63.9 + - + +
174D ALA* 3.7 6.2 - - - +
175D GLY 3.1 17.2 + - - -
233D ARG 5.9 0.2 - - - +
235D GLU 4.1 3.1 - - - +
236D ALA* 4.0 8.0 - - - +
237D PHE* 3.6 30.7 + - - +
240D MET* 3.1 28.9 - - + +
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Residues in contact with ILE 172 (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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160D PHE* 3.7 49.1 - - + -
164D PHE* 4.0 18.6 - - + -
170D ASN* 2.9 11.0 + - - +
171D ASP* 1.3 77.3 - - + +
173D ASN* 1.3 59.8 + - - +
175D GLY* 3.4 1.7 + - - -
176D LEU* 3.0 33.1 + - + +
229D ILE* 3.9 8.4 - - + +
233D ARG* 4.0 31.9 - - + +
240D MET* 4.0 9.4 - - + -
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Residues in contact with ASN 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D PHE* 3.2 23.5 - - - -
166D ARG* 2.7 43.6 + - - +
167D GLU 5.2 0.4 - - - -
168D GLN* 2.8 39.8 + - - +
170D ASN* 2.7 27.2 + - - +
172D ILE* 1.3 71.5 - - - +
174D ALA* 1.3 56.5 + - - +
176D LEU* 3.1 3.1 + - - +
177D ASN* 2.8 47.5 + - - +
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Residues in contact with ALA 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LEU* 5.4 4.2 - - + +
170D ASN 3.1 16.0 + - - +
171D ASP* 3.7 9.4 - - - +
173D ASN* 1.3 77.8 - - - +
175D GLY* 1.3 57.0 + - - +
177D ASN* 3.5 9.0 + - - +
178D TYR* 3.0 30.5 + - - +
237D PHE* 3.6 24.7 - - + -
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Residues in contact with GLY 175 (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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171D ASP 3.1 12.0 + - - -
172D ILE 3.7 2.2 - - - -
174D ALA* 1.3 79.2 - - - +
176D LEU* 1.3 63.8 + - - +
178D TYR* 3.4 1.5 + - - +
179D GLY 3.0 18.2 + - - -
229D ILE* 2.8 22.7 - - - +
237D PHE* 3.6 13.7 - - - -
240D MET* 4.1 8.3 - - - -
244D LEU* 3.4 8.8 - - - +
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Residues in contact with LEU 176 (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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156D PHE* 3.4 28.7 - - + -
160D PHE* 4.6 4.7 - - + -
164D PHE* 4.5 0.2 - - + -
166D ARG* 4.0 13.5 - - - +
172D ILE* 3.0 27.3 + - + +
173D ASN* 3.5 23.6 - - - +
175D GLY* 1.3 75.0 - - - +
177D ASN* 1.3 58.6 + - - +
179D GLY* 3.2 2.1 + - - -
180D TYR* 2.8 43.1 + - + +
225D VAL* 3.9 6.9 - - + +
226D ASP* 3.2 35.4 - - - +
229D ILE* 2.9 22.9 - - + +
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Residues in contact with ASN 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C TYR* 5.9 2.9 - - - +
166D ARG* 2.7 34.1 + - - +
173D ASN* 2.8 33.5 + - - +
174D ALA* 3.7 8.1 - - - +
176D LEU* 1.3 75.2 - - - +
178D TYR* 1.3 61.5 + - - +
180D TYR* 3.2 7.1 + - - +
181D THR* 2.9 29.4 + - - -
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Residues in contact with TYR 178 (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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41D LEU* 4.0 12.8 - - - +
43D GLU* 4.6 1.6 + - - +
67D CYS* 5.7 0.9 - - - -
71D ARG 4.0 8.4 + - - -
72D LEU* 4.2 10.5 - - + -
73D PRO* 3.4 34.3 - - + +
174D ALA 3.0 18.5 + - - +
175D GLY* 3.6 6.5 - - - +
177D ASN* 1.3 77.8 - - - +
179D GLY* 1.3 63.6 + - - +
181D THR* 3.2 9.0 + - - -
182D LEU* 3.1 47.0 + - + +
237D PHE* 4.4 4.9 - + + -
241D LYS* 3.5 48.6 + - + +
244D LEU* 3.7 14.8 - - + -
245D PHE* 3.6 23.2 - + - -
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Residues in contact with GLY 179 (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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175D GLY 3.0 8.6 + - - -
176D LEU 3.7 2.5 - - - -
178D TYR* 1.3 80.9 - - - +
180D TYR* 1.3 61.8 + - - +
182D LEU* 3.1 19.0 + - - +
183D LEU* 3.2 16.1 + - - +
225D VAL* 4.1 16.2 - - - +
244D LEU* 3.7 23.3 - - - -
247D LEU* 4.8 1.1 - - - +
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Residues in contact with TYR 180 (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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156D PHE* 3.7 13.9 - + - -
166D ARG* 3.4 35.0 - - - -
176D LEU* 2.8 24.2 + - + +
177D ASN* 3.6 6.1 - - - +
179D GLY* 1.3 76.6 - - - +
181D THR* 1.3 57.2 + - - +
183D LEU* 3.3 4.5 + - - +
184D LEU* 2.9 25.9 + - - +
218D MET* 3.5 15.5 - - + +
222D ARG* 3.4 59.2 + - + +
225D VAL* 3.6 24.9 - - + -
226D ASP* 2.5 27.6 + - - -
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Residues in contact with THR 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PHE* 3.6 44.9 - - + -
81C TYR* 4.5 11.8 + - - +
65D LEU* 5.8 1.1 - - + -
73D PRO* 3.9 19.8 - - + +
177D ASN* 2.9 17.0 + - - +
178D TYR* 3.2 8.6 + - - -
180D TYR* 1.3 74.6 - - - +
182D LEU* 1.3 67.1 + - + +
184D LEU* 3.2 8.8 + - + +
185D SER* 2.8 27.6 + - - +
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Residues in contact with LEU 182 (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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41D LEU* 5.7 1.1 - - + -
63D LEU* 5.0 0.7 - - - +
65D LEU* 4.2 23.6 - - + -
73D PRO* 5.6 5.2 - - + -
178D TYR* 3.1 46.4 + - + +
179D GLY* 3.1 12.5 + - - +
181D THR* 1.3 79.6 - - + +
183D LEU* 1.3 63.6 + - - +
185D SER* 3.2 14.3 + - - -
186D ILE* 3.2 18.8 + - + +
244D LEU* 4.4 10.8 - - + +
245D PHE* 4.7 9.4 - - + -
247D LEU* 4.4 16.2 - - + -
248D PHE* 4.2 33.7 - - + -
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Residues in contact with LEU 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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179D GLY 3.2 10.5 + - - +
180D TYR* 3.5 7.4 - - + +
182D LEU* 1.3 77.6 - - + +
184D LEU* 1.3 66.8 + - - +
186D ILE* 3.1 18.6 + - + +
187D PHE* 3.2 26.7 + - + -
218D MET* 3.8 20.0 - - + -
221D PHE* 3.6 37.0 - - + +
222D ARG* 4.1 4.7 - - - +
224D LEU* 5.5 1.1 - - + -
225D VAL* 3.2 31.2 - - + -
247D LEU* 4.8 9.0 - - + -
261D LEU* 3.9 28.0 - - + -
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Residues in contact with LEU 184 (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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80C PHE* 3.9 28.9 - - + -
76D LYS* 4.4 0.2 - - - -
180D TYR 2.9 14.7 + - - +
181D THR* 3.2 14.1 + - + +
183D LEU* 1.3 75.8 - - - +
185D SER* 1.3 57.5 + - - +
187D PHE* 3.2 2.6 + - - -
188D ALA* 2.8 31.6 + - + +
211D PHE* 3.7 32.3 - - + -
214D ALA* 3.6 28.5 - - + +
215D SER* 3.6 26.9 - - - +
218D MET* 3.8 12.5 - - - -
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Residues in contact with SER 185 (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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80C PHE* 3.5 11.3 - - - -
63D LEU* 3.7 18.5 - - - +
65D LEU* 3.4 19.8 - - - +
76D LYS* 3.1 30.0 + - - +
181D THR* 2.8 15.1 + - - +
182D LEU* 3.5 8.4 - - - -
183D LEU 3.1 0.2 - - - -
184D LEU* 1.3 74.7 - - - +
186D ILE* 1.3 66.7 + - - +
189D ARG* 3.1 23.9 + - - +
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Residues in contact with ILE 186 (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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63D LEU* 4.4 12.6 - - + -
182D LEU* 3.2 14.8 + - + +
183D LEU* 3.1 17.3 + - + +
185D SER* 1.3 78.2 - - - +
187D PHE* 1.3 61.9 - - + +
189D ARG* 3.5 8.2 + - - +
190D GLU* 3.2 29.5 + - + +
247D LEU* 6.1 0.9 - - + -
248D PHE* 3.7 32.1 - - + -
261D LEU* 4.0 25.1 - - + -
262D THR* 4.5 19.3 - - + -
265D ALA* 3.5 30.3 - - + -
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Residues in contact with PHE 187 (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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183D LEU* 3.2 29.3 + - + +
184D LEU 3.2 5.2 + - - +
186D ILE* 1.3 82.7 - - + +
188D ALA* 1.3 67.0 + - - +
190D GLU* 3.8 2.7 - - - +
191D LEU* 3.0 28.4 + - - +
214D ALA* 4.2 19.7 - - + +
217D LEU* 4.1 16.4 - - + -
218D MET* 3.8 18.2 - - + -
221D PHE* 3.5 48.9 - + + -
261D LEU* 5.8 1.6 - - + -
265D ALA* 3.6 32.3 - - + -
268D TYR* 4.2 9.2 - + - -
269D THR* 3.4 20.9 - - - -
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Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 5.3 6.7 - - + -
76D LYS* 2.4 39.0 - - - +
78D LEU* 6.0 2.7 - - + -
184D LEU* 2.8 13.4 + - + +
187D PHE* 1.3 78.7 - - - +
189D ARG* 1.3 60.0 + - - +
191D LEU* 3.8 1.9 - - - +
192D VAL* 3.2 29.1 + - + +
198D THR* 3.9 12.4 - - + +
211D PHE* 5.4 2.5 - - + -
214D ALA* 3.8 15.8 - - + +
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Residues in contact with ARG 189 (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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38D ASP* 3.0 48.4 + - - +
39D VAL* 4.7 2.6 - - - +
61D LYS* 3.1 31.9 + - + -
62D ILE 4.7 0.2 - - - -
63D LEU* 3.4 32.5 - - + +
76D LYS* 4.0 2.6 - - - +
79D PRO* 6.2 4.0 - - + -
185D SER 3.1 14.2 + - - +
186D ILE* 3.6 8.5 + - - +
187D PHE 3.2 0.2 - - - -
188D ALA* 1.3 80.9 - - - +
190D GLU* 1.3 80.5 + - - +
192D VAL* 3.4 6.1 + - - +
193D GLN* 3.1 32.0 + - + +
262D THR* 3.5 22.6 - - - +
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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
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186D ILE* 3.2 18.2 + - + +
187D PHE* 3.3 3.3 + - - +
189D ARG* 1.3 103.8 + - - +
191D LEU* 1.3 62.1 + - - +
193D GLN* 3.2 27.4 + - - +
194D THR* 3.1 25.8 + - - +
262D THR* 4.0 5.4 - - - +
265D ALA* 4.0 17.7 - - + +
266D THR* 3.1 38.9 + - - +
269D THR* 3.7 23.1 - - - +
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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 PHE 3.0 19.2 + - - +
188D ALA 3.8 3.6 - - - +
190D GLU* 1.3 75.7 - - - +
192D VAL* 1.3 65.0 + - - +
194D THR* 2.7 24.4 + - - -
196D CYS* 3.2 19.1 + - + +
198D THR* 3.9 12.8 - - + -
213D LEU* 3.6 34.1 - - + +
214D ALA* 3.6 34.8 - - + +
217D LEU* 3.8 14.8 - - + -
269D THR* 3.8 20.4 - - + -
273D VAL* 4.2 15.3 - - + -
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Residues in contact with VAL 192 (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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78D LEU* 3.8 27.1 - - + -
79D PRO* 3.7 33.4 - - + +
80D PHE 5.3 0.7 - - - -
82D GLY* 3.5 28.7 + - - +
188D ALA 3.2 14.2 + - - +
189D ARG* 3.7 9.2 - - - +
191D LEU* 1.3 77.2 - - - +
193D GLN* 1.3 61.8 + - - +
195D GLY* 3.0 13.9 + - - -
196D CYS 3.7 12.1 - - - +
197D PHE* 5.9 0.2 - - - -
198D THR* 4.0 11.7 - - + +
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Residues in contact with GLN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LYS* 3.5 43.2 + - + +
82D GLY* 3.9 10.1 - - - +
83D ARG* 3.0 26.7 + - - +
189D ARG* 3.1 24.1 + - + +
190D GLU* 3.2 32.7 - - - +
192D VAL* 1.3 78.6 - - - +
194D THR* 1.3 57.0 + - + +
266D THR* 5.4 7.2 - - + +
270D LYS* 5.9 5.5 - - - +
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Residues in contact with THR 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ARG* 3.6 18.9 + - - +
89D GLN* 3.4 18.9 - - - +
190D GLU 3.1 17.7 - - - +
191D LEU* 2.7 14.5 + - - +
193D GLN* 1.3 78.7 - - + +
195D GLY* 1.3 56.4 + - - +
196D CYS* 3.3 19.6 - - - -
269D THR* 4.3 14.1 - - + -
270D LYS* 4.4 26.9 - - + -
273D VAL* 4.1 12.8 - - + +
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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