Contacts of the helix formed by residues 197 - 219 (chain D) in PDB entry 1XDM
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 1.3 59.8 + - - +
199D GLU* 3.9 16.3 + - + +
200D HIS* 2.9 78.2 + - - +
201D CYS* 3.9 2.6 + - - +
243D TYR* 3.4 10.1 - - - -
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Residues in contact with LEU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ASP* 1.3 68.6 - - - +
199D GLU* 1.3 72.4 + - - +
200D HIS 3.1 2.2 + - - -
201D CYS* 3.3 6.6 + - - +
202D GLN* 3.1 21.2 + - - +
233D VAL* 3.8 7.3 - - + +
234D THR* 3.2 36.8 - - - +
243D TYR* 2.7 62.8 + - + -
247D GLN* 4.1 24.0 - - + +
248D VAL* 4.9 0.7 - - - +
251D ALA* 4.3 15.3 - - + -
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Residues in contact with GLU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ASP* 3.9 18.8 - - + +
198D LEU* 1.3 78.0 - - - +
200D HIS* 1.3 64.7 + - - +
202D GLN* 3.1 13.3 + - - +
203D TYR* 2.9 26.1 + - - +
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Residues in contact with HIS 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ASP* 2.9 43.2 + - - +
199D GLU* 1.3 76.8 - - - +
201D CYS* 1.3 57.6 + - - +
203D TYR* 3.3 5.6 + - - +
204D VAL* 2.6 39.4 + - + +
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Residues in contact with CYS 201 (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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197D ASP 4.9 1.8 - - - +
198D LEU 3.3 9.5 + - - +
200D HIS* 1.3 79.0 - - + +
202D GLN* 1.3 53.2 + - - +
204D VAL* 3.1 8.0 + - - +
205D THR* 2.7 50.0 + - - -
231D ASN* 4.9 2.9 - - - -
232D MET 4.6 3.4 - - - -
233D VAL* 4.0 11.4 - - + -
234D THR 3.7 37.9 - - - +
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Residues in contact with GLN 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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365C SO4 3.0 18.1 + - - -
198D LEU 3.1 13.0 + - - +
199D GLU* 3.1 14.5 + - - +
201D CYS* 1.3 75.5 - - - +
203D TYR* 1.3 61.0 + - - +
205D THR* 3.8 4.8 - - - -
206D GLU* 3.0 46.3 + - - +
233D VAL* 4.1 14.5 - - + +
251D ALA* 3.1 36.1 - - - +
254D THR* 3.0 10.4 - - - +
255D ALA* 4.2 1.5 - - + +
258D ARG* 2.9 28.9 + - - -
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Residues in contact with TYR 203 (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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217C ASN* 5.5 8.7 - - - -
218C ASP 5.5 2.4 + - - -
220C HIS* 4.1 32.7 - + + +
199D GLU 2.9 15.9 + - - +
200D HIS* 3.7 5.6 - - - +
202D GLN* 1.3 74.7 - - - +
204D VAL* 1.3 74.5 + - + +
206D GLU* 3.5 11.9 + - + +
207D LYS* 3.2 40.7 + - + +
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Residues in contact with VAL 204 (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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158D PRO* 4.5 24.9 - - + -
163D ILE* 5.9 1.3 - - + -
200D HIS* 2.6 37.2 + - + +
201D CYS* 3.5 7.6 - - - +
203D TYR* 1.3 82.8 - - + +
205D THR* 1.3 65.3 + - - +
207D LYS* 3.0 17.9 + - - +
208D VAL* 3.0 30.3 + - + +
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Residues in contact with THR 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 CYS* 2.7 41.5 + - - -
202D GLN 3.8 4.9 - - - -
204D VAL* 1.3 73.1 - - - +
206D GLU* 1.3 58.3 + - - +
208D VAL* 3.4 7.8 + - - +
209D LEU* 2.9 56.2 + - + +
230D PRO* 6.1 2.7 - - + -
231D ASN* 4.0 20.8 + - - +
233D VAL* 3.9 17.1 - - + +
255D ALA* 4.6 5.2 - - + -
256D LEU* 5.9 1.1 - - + -
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Residues in contact with GLU 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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217C ASN* 4.2 11.8 + - - +
220C HIS* 5.6 5.4 + - - -
202D GLN* 3.0 50.0 + - - +
203D TYR* 3.6 13.7 - - + +
205D THR* 1.3 80.8 - - - +
207D LYS* 1.3 52.6 + - - +
210D ALA* 2.8 34.5 + - - +
255D ALA* 3.3 21.1 - - + -
258D ARG* 3.4 31.2 + - - +
259D THR* 3.3 21.4 - - + +
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Residues in contact with LYS 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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214C LYS* 5.7 1.8 - - - -
217C ASN* 4.1 16.7 + - - +
218C ASP* 5.3 11.4 - - - +
158D PRO* 4.7 16.2 + - - +
160D SER* 4.7 16.4 + - - +
163D ILE* 3.1 32.3 - - + +
203D TYR* 3.2 32.6 + - + +
204D VAL* 3.0 12.7 + - - +
206D GLU* 1.3 74.8 - - - +
208D VAL* 1.3 67.5 + - - +
210D ALA* 3.7 1.2 - - - +
211D ALA* 2.8 29.9 + - + +
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Residues in contact with VAL 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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163D ILE* 4.0 28.3 - - + +
166D ASN* 4.7 11.0 - - - +
188D PRO* 4.0 25.4 - - + -
189D GLU* 4.9 11.0 - - + +
204D VAL* 3.0 33.4 - - + +
205D THR* 3.6 7.2 - - - +
207D LYS* 1.3 74.8 - - - +
209D LEU* 1.3 58.9 + - + +
211D ALA* 3.0 6.9 + - - +
212D VAL* 2.9 35.5 + - + +
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Residues in contact with LEU 209 (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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188D PRO* 4.5 18.8 - - + -
205D THR* 2.9 43.9 + - + +
206D GLU 3.4 3.4 - - - +
208D VAL* 1.3 73.6 - - + +
210D ALA* 1.3 59.0 + - - +
211D ALA 2.9 4.5 - - - -
212D VAL* 2.8 24.0 + - + +
213D TYR* 3.1 29.4 + - + -
228D LEU* 4.1 11.7 - - + -
230D PRO* 5.5 5.2 - - + -
256D LEU* 4.0 17.9 - - + +
259D THR* 3.6 24.5 - - + +
260D VAL* 3.7 22.7 - - + -
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Residues in contact with ALA 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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213C TYR 5.6 2.2 - - - +
214C LYS* 3.6 12.7 - - + +
217C ASN* 3.0 42.2 - - + +
206D GLU 2.8 12.4 + - - +
207D LYS 4.1 1.6 - - - +
209D LEU* 1.3 73.6 - - - +
211D ALA* 1.3 56.0 + - - +
213D TYR* 4.4 3.0 - - - +
214D LYS* 3.3 23.0 + - - +
258D ARG 5.2 0.9 - - - +
259D THR* 4.1 19.5 - - + +
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Residues in contact with ALA 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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214C LYS* 4.5 16.2 - - - +
163D ILE* 3.4 24.7 - - + -
164D GLN* 6.0 0.9 - - - -
167D ALA* 3.4 14.0 - - + +
207D LYS* 2.8 21.3 + - + +
208D VAL 3.0 8.5 - - - +
210D ALA* 1.3 79.0 - - - +
212D VAL* 1.3 60.6 + - - +
214D LYS* 3.8 5.5 - - - +
215D ALA* 3.3 14.0 + - - +
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Residues in contact with VAL 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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166D ASN* 4.5 6.5 - - - +
167D ALA* 4.1 8.5 - - + +
170D LEU* 4.0 25.1 - - + -
186D VAL* 4.0 18.4 - - + -
188D PRO* 4.5 10.5 - - + -
208D VAL* 2.9 31.4 + - + +
209D LEU* 2.8 11.5 + - + +
211D ALA* 1.3 76.5 - - - +
213D TYR* 1.3 63.9 + - + +
214D LYS 2.9 4.0 - - - -
215D ALA* 2.9 4.9 + - - +
216D LEU* 2.7 48.4 + - + +
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Residues in contact with TYR 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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186D VAL* 5.0 3.6 - - + +
209D LEU* 3.1 26.6 + - + +
210D ALA* 5.1 1.6 - - - +
212D VAL* 1.3 81.3 - - + +
214D LYS* 1.3 56.7 + - - +
216D LEU* 3.5 23.6 - - + +
217D ASN* 2.8 30.2 + - - +
223D LEU* 4.0 19.3 - - + +
226D THR* 5.1 5.6 - - + -
227D LEU 4.4 3.1 + - - -
228D LEU* 3.3 34.9 - - + +
259D THR 4.1 6.1 - - - +
260D VAL* 3.5 30.5 - - + +
261D PRO* 3.7 29.6 - - + -
264D VAL* 3.8 26.9 - - + +
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Residues in contact with LYS 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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207C LYS 4.8 0.6 + - - -
210C ALA* 3.6 11.9 + - + +
211C ALA* 3.2 39.8 - - - +
214C LYS* 3.4 35.3 - - + +
210D ALA 3.3 20.7 + - - +
211D ALA* 3.8 6.5 - - - +
212D VAL 2.9 0.6 - - - -
213D TYR* 1.3 76.4 - - - +
215D ALA* 1.3 66.0 + - - +
217D ASN* 3.1 6.5 + - - +
218D ASP* 2.8 63.5 + - - +
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Residues in contact with ALA 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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167D ALA* 3.7 19.5 - - + -
168D ASN* 3.8 16.4 - - - +
171D ALA* 3.7 16.8 - - + -
211D ALA 3.3 11.0 + - - +
212D VAL 2.9 8.2 + - - +
214D LYS* 1.3 78.7 - - - +
216D LEU* 1.3 58.7 + - - +
218D ASP* 2.9 13.3 + - - +
219D HIS* 2.9 32.8 + - - -
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Residues in contact with LEU 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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171D ALA* 3.9 15.7 - - - +
174D ALA* 3.9 14.1 - - + -
186D VAL* 4.3 17.0 - - + -
212D VAL* 2.7 44.9 + - + +
213D TYR* 3.5 31.0 - - + +
215D ALA* 1.3 72.6 - - - +
217D ASN* 1.3 62.4 + - - +
219D HIS* 3.0 11.6 + - - +
220D HIS 3.0 9.2 + - - -
221D VAL* 3.1 54.1 + - + -
223D LEU* 4.4 9.6 - - + -
226D THR* 6.0 0.9 - - + -
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Residues in contact with ASN 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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203C TYR* 5.7 2.6 - - - -
206C GLU* 4.0 9.1 + - - +
207C LYS* 4.2 18.5 + - - +
210C ALA* 3.7 28.8 - - + +
258C ARG* 4.8 7.5 + - - +
259C THR* 4.0 19.2 - - - +
213D TYR 2.8 23.5 + - - +
214D LYS* 3.1 7.8 + - - +
216D LEU* 1.3 73.2 - - - +
218D ASP* 1.3 64.7 + - - +
220D HIS* 3.3 14.8 + - - +
221D VAL 5.1 2.9 - - - +
223D LEU* 5.2 6.0 - - + +
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Residues in contact with ASP 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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161A LEU* 3.4 37.4 - - + +
203C TYR* 5.6 2.1 + - - -
207C LYS* 4.6 17.6 - - - +
210C ALA* 5.6 0.3 - - - +
214D LYS* 2.8 54.5 + - - +
215D ALA* 2.9 11.5 + - - +
217D ASN* 1.3 79.0 - - - +
219D HIS* 1.3 59.5 + - + +
220D HIS* 3.1 8.5 + - - +
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Residues in contact with HIS 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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161A LEU* 4.3 22.0 - - + +
165A GLU* 3.2 29.7 + - + -
168D ASN* 4.1 12.0 + - - -
171D ALA* 3.1 45.4 - - + +
172D ARG* 3.5 22.4 - - + +
175D SER* 4.1 16.2 + - - -
215D ALA* 2.9 20.8 + - + +
216D LEU 3.0 4.2 + - - +
218D ASP* 1.3 79.1 - - + +
220D HIS* 1.3 70.3 + - - +
221D VAL* 3.2 3.8 + - + -
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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
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Atomic class I II III IV V VI VII VIII
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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