Contacts of the helix formed by residues 197 - 221 (chain D) in PDB entry 1XPM
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 197 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D TYR 4.3 6.3 - - - +
184D ASP 2.9 13.5 + - - +
186D TRP* 5.0 2.8 - - + -
196D VAL* 1.3 71.6 - - - +
198D GLY* 1.3 66.2 + - - +
199D ALA* 3.9 5.7 + - - +
200D LEU* 2.9 42.3 + - + +
201D SER* 2.8 19.8 + - - -
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Residues in contact with GLY 198 (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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196D VAL* 3.5 9.0 + - - +
197D ASP* 1.3 70.0 + - - +
199D ALA* 1.3 61.0 + - - +
201D SER* 2.5 24.7 + - - -
202D LYS* 3.5 9.0 + - - +
4402D CAA 3.6 36.7 - - - +
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Residues in contact with ALA 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ASP* 3.4 5.4 + - - +
198D GLY* 1.3 73.5 - - - +
200D LEU* 1.3 63.9 + - - +
202D LYS* 3.1 27.6 + - - +
203D ASP* 3.4 14.9 + - - +
4402D CAA 4.9 1.0 - - - +
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Residues in contact with LEU 200 (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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182D VAL* 4.2 21.8 - - + -
183D TYR* 3.9 23.1 - - + +
184D ASP* 4.4 4.7 - - + -
197D ASP* 2.9 31.9 + - + +
199D ALA* 1.3 77.5 - - - +
201D SER* 1.3 63.7 + - - +
203D ASP* 3.1 16.0 + - + +
204D ALA* 2.9 23.8 + - + +
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Residues in contact with SER 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ASP* 3.6 25.7 - - - +
185D PHE* 5.4 0.9 - - - -
196D VAL* 4.6 5.4 - - - -
197D ASP 2.8 15.4 + - - -
198D GLY* 2.5 25.6 + - - -
200D LEU* 1.3 73.5 - - - +
202D LYS* 1.3 57.9 + - - +
204D ALA* 3.9 1.0 - - - +
205D TYR* 3.0 28.9 + - - +
4402D CAA 3.4 42.3 + - - +
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Residues in contact with LYS 202 (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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198D GLY 3.9 15.0 - - - +
199D ALA* 3.1 15.6 + - - +
200D LEU 3.1 0.6 - - - -
201D SER* 1.3 84.2 + - - +
203D ASP* 1.3 67.4 + - - +
205D TYR* 3.5 0.9 + - - +
206D ILE* 3.1 34.4 + - + +
236D PHE* 4.7 13.7 - - + -
239D MET* 3.8 30.5 - - + +
242D LYS* 6.3 2.7 - - + -
4402D CAA 4.9 37.3 + - + +
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Residues in contact with ASP 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ALA 3.4 10.4 + - - +
200D LEU* 3.1 18.6 + - + +
202D LYS* 1.3 79.1 - - - +
204D ALA* 1.3 57.3 + - - +
206D ILE* 3.4 6.7 + - - +
207D ARG* 2.8 32.5 + - - +
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Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D VAL* 4.3 19.1 - - + -
184D ASP* 4.0 15.0 - - + +
200D LEU* 2.9 18.0 + - + +
201D SER 3.9 2.9 - - - +
203D ASP* 1.3 76.2 - - - +
205D TYR* 1.3 66.4 + - - +
207D ARG* 3.9 6.2 - - - +
208D SER* 3.0 25.6 + - - -
305D TYR* 3.4 18.2 - - - +
309D SER* 5.0 1.8 + - - +
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Residues in contact with TYR 205 (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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201D SER 3.0 19.3 + - - +
202D LYS* 3.8 5.8 - - - +
204D ALA* 1.3 78.5 - - - +
206D ILE* 1.3 63.6 + - - +
208D SER* 3.4 2.9 + - - -
209D PHE* 3.1 19.2 + - + +
232D PHE* 3.6 17.6 - + - +
233D HIS* 2.9 40.5 + + - +
239D MET* 3.9 25.6 - - + -
240D GLY* 4.6 3.1 - - - -
243D ALA* 3.6 26.0 - - + -
303D PHE* 4.2 18.1 - + - -
305D TYR* 3.5 29.1 + + + -
4402D CAA 3.3 33.0 - - + -
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Residues in contact with ILE 206 (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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202D LYS* 3.1 19.9 + - + +
203D ASP* 4.0 6.7 - - - +
205D TYR* 1.3 76.2 - - - +
207D ARG* 1.3 66.8 + - - +
209D PHE* 3.2 5.5 + - + +
210D GLN* 2.9 52.5 + - - +
239D MET* 3.9 21.8 - - + -
242D LYS* 4.4 11.4 - - + +
243D ALA* 4.1 20.2 - - + +
246D SER* 3.8 15.0 - - - +
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Residues in contact with ARG 207 (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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178D TYR* 3.2 19.4 + - - -
180D GLU* 2.7 32.9 + - - +
203D ASP 2.8 19.1 + - - +
204D ALA* 3.9 5.8 - - - +
206D ILE* 1.3 76.9 - - - +
208D SER* 1.3 58.4 + - - +
210D GLN* 3.3 9.4 + - - +
211D GLN* 2.9 63.4 + - + +
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Residues in contact with SER 208 (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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178D TYR* 4.3 17.6 + - - -
204D ALA 3.0 18.6 + - - -
205D TYR 3.6 1.1 - - - -
207D ARG* 1.3 76.3 - - - +
209D PHE* 1.3 59.5 + - - +
211D GLN* 4.0 0.5 - - - +
212D SER* 2.7 34.3 + - - -
303D PHE* 3.7 1.7 - - - -
305D TYR* 3.5 23.5 - - - -
309D SER* 4.8 5.4 + - - -
310D VAL 4.0 0.3 - - - -
311D GLY* 3.3 31.9 + - - -
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Residues in contact with PHE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D TYR* 3.1 13.4 + - + +
206D ILE* 3.5 10.1 - - - +
208D SER* 1.3 77.5 - - - +
210D GLN* 1.3 58.7 + - - +
212D SER* 3.7 0.9 - - - -
213D TRP* 2.8 36.6 + - + +
230D LEU* 4.4 3.1 - - + -
232D PHE* 3.3 30.7 - + - -
243D ALA* 3.6 29.8 - - + -
246D SER* 4.3 6.5 - - - -
247D ILE* 3.3 42.2 - - + -
303D PHE* 3.4 48.9 - + + -
313D PHE* 4.1 17.9 - + - -
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Residues in contact with GLN 210 (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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206D ILE* 2.9 28.8 + - + +
207D ARG* 3.9 8.0 - - - +
209D PHE* 1.3 78.3 - - + +
211D GLN* 1.3 64.4 + - - +
213D TRP* 3.9 3.9 - - - +
214D ASN* 2.8 46.1 + - - +
246D SER* 3.4 40.7 + - - +
247D ILE* 4.4 12.2 - - + +
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Residues in contact with GLN 211 (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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101C PHE* 4.1 9.7 - - + -
178D TYR* 3.7 43.6 + - + +
207D ARG* 2.9 53.7 + - + +
210D GLN* 1.3 84.9 + - - +
212D SER* 1.3 62.2 + - - +
214D ASN* 3.6 13.8 + - - +
215D GLU* 3.2 23.7 + - - +
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Residues in contact with SER 212 (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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101C PHE* 5.4 0.4 - - - -
176D VAL* 3.6 12.0 - - - +
177D ALA 5.7 0.4 - - - -
178D TYR* 3.5 22.5 + - - +
208D SER 2.7 21.2 + - - -
209D PHE 3.7 2.7 - - - -
211D GLN* 1.3 75.7 - - - +
213D TRP* 1.3 65.7 + - - +
215D GLU* 3.4 2.3 + - - +
216D TYR* 3.0 23.9 + - - +
303D PHE* 3.8 11.6 - - - -
311D GLY 3.7 14.7 + - - -
313D PHE* 4.2 19.5 - - - -
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Residues in contact with TRP 213 (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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209D PHE* 2.8 26.6 + - + +
210D GLN* 3.9 2.2 - - - +
212D SER* 1.3 76.0 - - - +
214D ASN* 1.3 73.8 + - - +
216D TYR* 3.2 17.2 + + - +
217D ALA* 2.8 42.6 + - + +
222D LYS 4.6 0.7 - - - -
223D SER* 3.7 27.8 - - - -
224D LEU* 3.5 41.3 - - + +
227D PHE* 3.5 25.4 - + - -
247D ILE* 4.3 25.9 - - + +
313D PHE* 3.5 35.8 - + + +
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Residues in contact with ASN 214 (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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210D GLN* 2.8 34.4 + - - +
211D GLN* 3.9 17.0 - - - +
213D TRP* 1.3 90.5 + - - +
215D GLU* 1.3 58.0 + - - +
217D ALA* 3.4 5.3 + - - +
218D LYS* 3.0 27.9 + - - +
247D ILE* 6.0 0.3 - - - +
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Residues in contact with GLU 215 (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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101C PHE* 3.5 50.6 - - + -
176D VAL* 3.8 11.4 - - + -
211D GLN 3.2 8.0 + - - +
212D SER 4.0 2.9 - - - +
214D ASN* 1.3 75.6 - - - +
216D TYR* 1.3 60.9 + - - +
218D LYS* 3.3 22.7 + - - +
219D ARG* 2.7 74.2 + - - +
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Residues in contact with TYR 216 (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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174D ASP* 2.7 59.9 + - + -
176D VAL* 3.6 11.8 - - + +
212D SER 3.0 18.4 + - - +
213D TRP* 3.4 20.6 - + - +
215D GLU* 1.3 76.3 - - - +
217D ALA* 1.3 58.8 + - - +
219D ARG* 3.3 3.5 + - - +
220D GLN* 2.9 39.3 + - + +
222D LYS* 3.5 31.7 - - + +
227D PHE* 3.6 22.2 - + - -
313D PHE* 3.5 29.8 - + + -
314D TYR* 4.2 3.6 - - - -
315D SER* 3.6 9.6 - - - -
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Residues in contact with ALA 217 (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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213D TRP* 2.8 38.9 + - + +
214D ASN* 3.7 7.0 - - - +
216D TYR* 1.3 79.5 - - - +
218D LYS* 1.3 58.2 + - - +
221D GLY* 2.8 27.4 + - - -
222D LYS 3.2 28.8 + - - +
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Residues in contact with LYS 218 (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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214D ASN 3.0 17.1 + - - +
215D GLU* 3.6 25.4 + - - +
216D TYR 3.2 0.2 - - - -
217D ALA* 1.3 79.9 - - - +
219D ARG* 1.3 63.8 + - + +
221D GLY* 3.6 6.4 + - - -
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Residues in contact with ARG 219 (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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99C GLN* 5.2 1.4 + - - +
101C PHE* 3.7 31.1 + - - +
131C GLU* 5.8 1.8 + - - -
175D ALA 4.7 4.6 + - - -
176D VAL* 3.6 29.8 - - - +
215D GLU* 2.7 47.9 + - - +
216D TYR* 3.9 3.1 - - - +
218D LYS* 1.3 77.1 - - + +
220D GLN* 1.3 76.0 + - + +
221D GLY 3.8 0.2 + - - -
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Residues in contact with GLN 220 (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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173D GLU 4.7 3.9 + - - +
174D ASP* 3.5 32.4 + - + +
216D TYR* 2.9 43.6 + - + +
219D ARG* 1.3 94.4 + - + +
221D GLY* 1.3 64.2 + - - +
222D LYS* 3.5 27.7 - - + +
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Residues in contact with GLY 221 (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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217D ALA 2.8 11.4 + - - -
218D LYS 3.6 4.8 + - - -
219D ARG 3.5 2.8 - - - -
220D GLN* 1.3 79.8 - - - +
222D LYS* 1.3 60.1 + - - +
226D ASP* 4.7 1.0 - - - +
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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
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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) + - + + + + + -
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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