Contacts of the helix formed by residues 198 - 220 (chain D) in PDB entry 1XFB
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 198 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ASP 3.8 1.2 + - - -
197D HIS* 1.3 77.5 - - - +
199D LEU* 1.3 66.0 + - - +
200D LYS* 3.1 37.7 + - - +
201D ARG* 3.2 26.3 + - - +
202D CYS 3.3 8.3 + - - -
236D PRO* 4.1 3.1 - - - -
240D CYS* 4.0 15.5 - - - -
242D ILE* 4.3 8.8 - - + +
244D TYR* 3.4 14.7 + - - +
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ASP* 1.3 73.1 - - - +
200D LYS* 1.3 65.6 + - - +
202D CYS* 3.1 4.0 + - - +
203D GLN* 3.0 21.3 + - - +
234D VAL* 3.3 19.5 - - + +
235D THR* 3.2 33.2 - - - -
236D PRO* 3.8 13.5 - - + +
244D TYR* 3.3 44.3 + - + -
248D GLU* 3.7 27.8 - - + +
249D ILE* 4.4 5.8 - - + -
252D ALA* 3.9 13.0 - - + -
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Residues in contact with LYS 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 4.2 23.8 - - - +
198D ASP* 3.1 21.1 + - - +
199D LEU* 1.3 78.8 - - - +
201D ARG* 1.3 63.4 + - - +
203D GLN* 3.1 10.8 + - - +
204D TYR* 3.0 21.9 + - - +
244D TYR* 4.8 0.2 + - - -
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Residues in contact with ARG 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 2.8 50.1 + - - +
4A SER* 3.7 19.5 + - - +
157B ARG* 3.8 13.3 - - - +
154D ILE* 3.4 19.3 - - + +
155D SER 3.3 24.5 + - - -
156D GLU* 4.6 1.0 + - - +
159D PRO* 4.8 2.4 - - - +
197D HIS* 3.7 22.9 - - + +
198D ASP* 3.2 19.8 + - - +
200D LYS* 1.3 79.5 - - - +
202D CYS* 1.3 63.5 + - - +
204D TYR* 3.1 7.5 + - - +
205D VAL* 2.9 36.2 + - + +
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Residues in contact with CYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ILE* 4.1 17.5 - - - -
191D ILE* 5.2 4.7 - - - -
192D LEU 6.1 0.2 - - - -
197D HIS* 4.0 11.1 - - + -
198D ASP 3.3 3.0 + - - +
199D LEU 3.1 8.5 + - - +
201D ARG* 1.3 78.0 - - - +
203D GLN* 1.3 58.9 + - - +
205D VAL* 4.0 0.7 - - - +
206D THR* 2.8 41.6 + - - -
232D ASN* 4.2 6.7 - - - -
233D MET 4.4 0.7 - - - -
234D VAL* 3.5 11.7 - - - -
235D THR* 3.2 43.5 - - - +
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Residues in contact with GLN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D LEU* 3.0 12.6 + - - +
200D LYS* 3.4 13.5 - - - +
202D CYS* 1.3 76.8 - - - +
204D TYR* 1.3 57.0 + - - +
206D THR* 3.2 3.3 + - - -
207D GLU* 2.6 58.1 + - - +
234D VAL* 3.8 15.2 - - + +
252D ALA* 3.4 37.2 - - - +
255D THR* 3.7 15.0 - - - +
256D ALA* 3.9 6.2 - - + +
259D ARG* 3.2 16.2 - - - +
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Residues in contact with TYR 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 3.0 50.8 + + - +
4A SER* 3.4 31.2 - - - -
5A TYR 5.3 0.9 - - - -
221A HIS* 3.1 29.8 - + + -
200D LYS 3.0 12.9 + - - +
201D ARG* 3.3 10.3 - - - +
203D GLN* 1.3 75.2 - - - +
205D VAL* 1.3 68.5 + - + +
207D GLU* 3.1 13.5 + - - +
208D LYS* 3.0 55.3 + - + +
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Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 4.0 23.8 - - + +
154D ILE* 3.9 25.4 - - + -
159D PRO* 3.6 31.6 - - + -
164D ILE* 6.0 0.7 - - + -
191D ILE* 3.7 16.4 - - + -
201D ARG* 2.9 29.2 + - + +
202D CYS 4.0 0.2 - - - +
204D TYR* 1.3 78.4 - - + +
206D THR* 1.3 63.7 + - - +
208D LYS* 3.2 5.6 + - + +
209D VAL* 2.9 25.6 + - + +
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Residues in contact with THR 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ILE* 3.4 17.0 - - + +
202D CYS* 2.8 28.2 + - - -
203D GLN* 3.5 5.6 - - - -
205D VAL* 1.3 76.1 - - - +
207D GLU* 1.3 65.1 + - - +
209D VAL* 3.8 0.7 - - - +
210D LEU* 2.9 46.1 + - + +
231D PRO* 5.8 2.0 - - + -
232D ASN* 3.3 28.9 + - - +
234D VAL* 4.4 8.8 - - + +
256D ALA* 4.1 15.3 - - + -
257D LEU* 5.9 0.9 - - + -
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Residues in contact with GLU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 5.6 0.4 - - - -
203D GLN* 2.6 52.1 + - - +
204D TYR* 3.4 12.7 + - + +
206D THR* 1.3 77.7 - - - +
208D LYS* 1.3 61.2 + - + +
210D LEU* 4.8 0.2 - - - -
211D ALA* 2.9 31.1 + - - +
256D ALA* 3.7 23.3 - - - +
259D ARG* 3.0 31.2 + - - +
260D THR* 3.4 15.7 - - + +
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Residues in contact with LYS 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A HIS* 6.5 0.2 - - + -
218A SER* 2.6 42.4 + - - +
219A ASP* 4.8 1.3 - - - +
221A HIS* 3.2 20.3 + - - +
164D ILE* 4.7 14.1 - - + +
204D TYR* 3.0 60.6 + - + +
205D VAL* 3.7 7.6 - - - +
207D GLU* 1.3 75.3 - - + +
209D VAL* 1.3 66.1 + - - +
211D ALA* 3.4 5.6 + - - +
212D ALA* 3.1 22.5 + - - +
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Residues in contact with VAL 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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152D LEU* 3.3 37.0 - - + -
159D PRO* 4.8 0.9 - - + -
164D ILE* 4.4 21.3 - - + +
189D PRO* 4.2 15.3 - - + +
191D ILE* 3.6 19.3 - - + -
205D VAL* 2.9 28.6 + - + +
206D THR 3.8 2.9 - - - +
208D LYS* 1.3 76.6 - - - +
210D LEU* 1.3 65.2 + - + +
212D ALA* 3.0 5.5 + - - +
213D VAL* 2.9 37.1 + - + +
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D PRO* 4.0 16.8 - - + -
206D THR* 2.9 39.0 + - + +
207D GLU 4.0 0.2 - - - +
209D VAL* 1.3 77.3 - - + +
211D ALA* 1.3 65.8 + - - +
213D VAL* 2.9 17.0 + - + +
214D TYR* 2.9 23.4 + - + -
229D LEU* 3.9 33.7 - - + -
231D PRO* 4.7 7.4 - - + -
256D ALA 5.0 0.9 - - - +
257D LEU* 3.8 26.0 - - + -
260D THR* 3.5 28.5 - - - +
261D VAL* 4.5 0.2 - - + -
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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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215A LYS* 4.0 12.1 - - + +
218A SER* 3.6 29.8 - - - +
207D GLU 2.9 20.3 + - - +
208D LYS 3.6 5.4 - - - +
209D VAL 3.3 0.2 - - - -
210D LEU* 1.3 76.0 - - - +
212D ALA* 1.3 60.8 + - - +
214D TYR* 3.8 3.8 + - - +
215D LYS* 3.3 21.3 + - - +
260D THR* 4.1 14.7 - - + +
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Residues in contact with ALA 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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215A LYS* 4.2 18.1 - - - +
164D ILE* 3.5 30.3 - - + +
165D LEU* 6.1 0.4 - - - -
168D ALA* 4.1 9.0 - - + +
208D LYS 3.1 8.1 + - - +
209D VAL 3.0 8.6 + - - +
211D ALA* 1.3 74.9 - - - +
213D VAL* 1.3 66.8 + - - +
215D LYS* 3.2 3.7 + - - +
216D ALA* 3.0 24.3 + - - +
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Residues in contact with VAL 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ALA* 4.0 16.1 - - + +
171D LEU* 4.2 11.9 - - + -
187D VAL* 3.9 28.5 - - + -
189D PRO* 4.1 18.2 - - + -
209D VAL* 2.9 34.9 + - + +
210D LEU* 3.3 12.3 - - + +
212D ALA* 1.3 77.6 - - - +
214D TYR* 1.3 66.0 + - + +
216D ALA* 3.3 3.6 + - - +
217D LEU* 3.0 34.9 + - + +
229D LEU* 5.3 0.7 - - + -
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Residues in contact with TYR 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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187D VAL* 5.7 1.4 - - + +
210D LEU* 2.9 24.7 + - + +
211D ALA* 4.5 3.4 - - - +
213D VAL* 1.3 77.4 - - + +
215D LYS* 1.3 65.9 + - - +
217D LEU* 3.2 18.1 + - + +
218D SER* 2.9 22.2 + - - -
224D LEU* 3.6 34.8 - - + +
227D THR* 5.1 2.7 + - - -
228D LEU 5.2 0.9 - - - -
229D LEU* 3.4 40.9 - - + +
260D THR 3.9 17.5 - - - +
261D VAL* 3.7 21.6 - - + +
262D PRO* 3.7 19.1 - - + -
265D VAL* 3.5 25.1 - - + +
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Residues in contact with LYS 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA* 4.1 18.6 - - + +
212A ALA* 4.3 23.3 - - - +
215A LYS* 4.1 29.4 - - + -
211D ALA 3.3 16.4 + - - +
212D ALA 3.2 5.5 + - - +
214D TYR* 1.3 77.0 - - - +
216D ALA* 1.3 58.8 + - - +
218D SER* 3.2 9.7 + - - -
219D ASP* 2.9 67.2 + - - +
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Residues in contact with ALA 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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168D ALA* 3.4 35.7 - - + +
169D ASN* 4.3 4.3 - - - +
172D ALA* 3.8 6.5 - - + -
212D ALA 3.0 12.2 + - - +
213D VAL 3.4 7.2 - - - +
215D LYS* 1.3 74.6 - - - +
217D LEU* 1.3 66.2 + - - +
219D ASP* 2.9 11.1 + - - +
220D HIS* 2.9 29.6 + - + -
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Residues in contact with LEU 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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168D ALA 5.8 0.2 - - - +
171D LEU* 5.5 0.2 - - + -
172D ALA* 3.7 22.7 - - + +
175D ALA* 3.9 9.0 - - + -
187D VAL* 4.4 17.7 - - + -
213D VAL* 3.0 27.9 + - + +
214D TYR* 3.2 39.5 + - + +
216D ALA* 1.3 75.7 - - - +
218D SER* 1.3 63.4 + - - +
220D HIS 3.2 1.2 + - - -
221D HIS 3.1 3.8 + - - -
222D VAL* 3.0 59.4 + - + +
224D LEU* 4.0 14.6 - - + -
227D THR* 5.5 2.5 - - - +
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Residues in contact with SER 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU 5.9 0.2 - - - -
208A LYS* 3.0 34.7 + - - +
211A ALA* 3.8 25.1 - - - +
214D TYR 2.9 12.5 + - - -
215D LYS* 3.3 13.2 - - - +
217D LEU* 1.3 76.2 - - - +
219D ASP* 1.3 62.5 + - - +
221D HIS* 2.9 17.7 + - - +
222D VAL 5.0 3.4 - - - +
224D LEU* 6.0 0.4 - - - +
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Residues in contact with ASP 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LYS* 5.0 2.0 - - - +
162C LEU* 3.3 25.1 - - + +
165C LEU* 3.5 30.8 - - + +
215D LYS* 2.9 52.6 + - - +
216D ALA* 2.9 10.4 + - - +
218D SER* 1.3 77.4 + - - +
220D HIS* 1.3 62.1 + - + +
221D HIS* 3.4 11.8 + - - -
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Residues in contact with HIS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 5.5 3.0 - - + +
117C ALA 4.0 3.6 - - - +
162C LEU* 3.7 29.8 - - + +
165C LEU* 4.0 3.4 - - + +
166C GLU* 3.7 21.1 - - + -
169D ASN* 2.8 29.0 + - - -
172D ALA* 3.4 29.6 - - + +
173D ARG* 3.8 27.4 + - + +
176D SER* 3.7 19.2 + - - -
216D ALA* 2.9 22.8 + - - +
217D LEU 3.2 2.9 + - - +
218D SER 3.1 0.2 - - - -
219D ASP* 1.3 78.6 - - + +
221D HIS* 1.3 76.3 + - - +
222D VAL* 3.3 3.7 + - + -
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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) + - + + + + + -
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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