Contacts of the helix formed by residues 238 - 260 (chain D) in PDB entry 4HYY
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 GLU 238 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D PHE* 4.4 25.6 - - + +
234D SER 5.2 2.4 + - - +
235D GLY 3.8 15.0 - - - +
236D ARG* 4.1 3.8 - - - -
237D GLY* 1.3 78.1 + - - +
239D LEU* 1.3 63.2 + - - +
240D ALA* 3.2 4.3 - - - +
241D GLU* 3.3 34.7 + - + +
242D ARG* 3.4 6.9 + - - +
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Residues in contact with LEU 239 (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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233D PHE 4.1 18.6 - - - +
234D SER* 5.4 1.1 - - - -
236D ARG* 3.5 58.6 - - + +
237D GLY* 3.1 8.9 + - - +
238D GLU* 1.3 74.1 - - - +
240D ALA* 1.3 56.2 + - - +
241D GLU 3.0 1.6 - - - -
242D ARG* 3.8 27.8 - - - +
243D GLN* 2.6 49.9 + - + +
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Residues in contact with ALA 240 (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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234C SER 6.0 1.1 - - - -
237C GLY 6.5 0.7 - - - -
238C GLU* 5.5 12.3 - - + -
237D GLY 4.4 3.0 + - - +
238D GLU* 4.9 3.1 - - - -
239D LEU* 1.3 78.7 - - - +
241D GLU* 1.3 55.6 + - - +
243D GLN* 4.1 5.6 - - - +
244D GLN* 3.1 35.0 + - - +
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Residues in contact with GLU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D PHE* 4.0 23.5 - - + -
238D GLU* 3.3 33.3 + - + +
239D LEU 3.0 1.2 - - - -
240D ALA* 1.3 75.3 - - - +
242D ARG* 1.3 65.6 + - - +
243D GLN 3.1 1.2 + - - -
244D GLN* 3.1 24.3 + - - +
245D LYS* 3.0 42.6 + - - +
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Residues in contact with ARG 242 (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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226D MET* 4.6 11.9 - - - +
229D PHE* 3.5 30.1 - - + +
230D ARG* 4.4 21.8 + - - +
233D PHE* 3.2 49.1 + - + +
234D SER* 5.5 2.8 - - - -
238D GLU 3.4 4.2 + - - +
239D LEU* 3.3 26.4 + - - +
241D GLU* 1.3 76.5 - - - +
243D GLN* 1.3 75.8 + - - +
245D LYS* 3.4 1.7 + - - +
246D LEU* 2.7 41.4 + - + +
288D ILE* 5.8 3.4 - - - +
289D GLY* 4.6 20.8 - - - +
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Residues in contact with GLN 243 (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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231C VAL 5.4 2.5 - - - +
232C ASP 6.5 0.4 - - - -
234C SER* 3.4 28.7 + - - +
239D LEU* 2.6 39.8 + - + +
240D ALA* 4.1 6.5 - - - +
242D ARG* 1.3 107.6 + - - +
244D GLN* 1.3 56.7 + - - +
246D LEU* 3.2 7.6 + - - +
247D ALA* 2.7 38.7 + - - +
289D GLY 5.4 3.9 + - - +
290D GLY* 6.1 1.8 - - - -
292D ILE* 3.4 32.2 - - + +
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Residues in contact with GLN 244 (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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232C ASP 5.4 8.9 + - - +
233C PHE* 6.0 4.2 - - - -
240D ALA* 3.1 22.5 + - - +
241D GLU* 3.3 23.2 - - - +
243D GLN* 1.3 72.8 - - - +
245D LYS* 1.3 59.7 + - + +
247D ALA* 3.8 4.1 - - - +
248D GLN* 2.9 46.0 + - - +
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Residues in contact with LYS 245 (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 GLU* 4.0 24.8 + - + -
200D MET* 5.3 5.1 - - + +
229D PHE* 3.9 17.0 - - + -
233D PHE* 3.7 25.7 - - + -
241D GLU* 3.0 32.8 + - - +
242D ARG 3.6 3.6 - - - +
244D GLN* 1.3 75.7 - - + +
246D LEU* 1.3 64.6 + - - +
248D GLN* 3.2 22.5 + - + +
249D MET* 3.0 23.9 + - - +
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Residues in contact with LEU 246 (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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226D MET* 4.0 34.8 - - + -
229D PHE* 3.7 37.1 - - + -
242D ARG* 2.7 26.8 + - + +
243D GLN* 3.8 13.7 - - - +
245D LYS* 1.3 70.7 - - - +
247D ALA* 1.3 62.6 + - - +
249D MET* 3.2 17.0 + - + +
250D LEU* 2.9 35.9 + - + +
289D GLY* 4.4 7.9 - - - +
292D ILE* 3.9 24.5 - - + -
293D LEU 4.8 0.7 - - - +
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Residues in contact with ALA 247 (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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231C VAL* 4.1 23.1 - - + +
232C ASP* 4.6 9.9 - - - +
243D GLN 2.7 22.7 + - - +
244D GLN* 3.8 4.3 - - - +
246D LEU* 1.3 72.9 - - - +
248D GLN* 1.3 64.3 + - - +
250D LEU* 3.2 2.8 + - - +
251D SER* 2.9 27.4 + - - -
292D ILE* 3.8 21.1 - - + -
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Residues in contact with GLN 248 (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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200D MET* 3.7 17.2 - - + +
244D GLN* 2.9 29.3 + - - +
245D LYS* 3.3 34.6 + - + +
247D ALA* 1.3 76.8 - - - +
249D MET* 1.3 62.9 + - - +
251D SER* 3.3 7.7 + - - -
252D ARG* 3.1 24.9 + - - +
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Residues in contact with MET 249 (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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199D GLN* 3.4 23.6 - - - +
200D MET* 3.6 22.9 - - + +
203D LEU* 3.6 28.2 - - + +
222D ILE* 5.6 0.2 - - - -
225D ILE* 3.5 34.1 - - + +
229D PHE* 4.2 15.9 - - + -
245D LYS 3.0 15.3 + - - +
246D LEU* 3.2 16.1 + - + +
248D GLN* 1.3 76.5 - - - +
250D LEU* 1.3 86.2 + - + +
252D ARG* 3.1 4.9 + - - +
253D LEU* 2.9 26.2 + - + +
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Residues in contact with LEU 250 (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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121D ILE* 4.3 4.0 - - + +
225D ILE* 3.9 13.0 - - + -
246D LEU* 2.9 45.7 + - + +
247D ALA* 3.9 3.8 - - - +
249D MET* 1.3 91.7 - - + +
251D SER* 1.3 64.3 + - - +
253D LEU* 3.3 15.4 + - + +
254D GLN* 3.1 27.2 + - - +
292D ILE* 4.1 10.3 - - + +
293D LEU* 3.8 40.8 - - + -
296D ALA* 3.8 17.9 - - + -
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Residues in contact with SER 251 (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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194C TYR* 3.5 30.6 - - - +
195C THR* 4.0 14.6 - - - +
247D ALA 2.9 14.0 + - - -
248D GLN* 3.3 11.1 + - - -
250D LEU* 1.3 78.7 - - - +
252D ARG* 1.3 63.6 + - - +
254D GLN* 3.4 11.9 + - - +
255D LYS* 3.1 31.7 + - - +
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Residues in contact with ARG 252 (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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200D MET* 3.7 22.7 - - + -
203D LEU* 5.5 3.8 - - + -
204D ASP* 3.0 30.0 + - - +
207D ALA* 3.5 27.6 - - - +
248D GLN* 3.1 18.5 + - + +
249D MET 3.1 8.7 + - - +
251D SER* 1.3 76.0 + - - +
253D LEU* 1.3 59.4 + - - +
255D LYS* 3.3 30.8 + - - +
256D ILE* 2.9 48.1 + - + +
259D GLU* 5.0 5.9 + - - -
260D TYR* 6.2 0.8 - - - -
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Residues in contact with LEU 253 (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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121D ILE* 3.6 16.2 - - + -
203D LEU* 4.4 14.8 - - + +
220D LEU* 3.7 29.6 - - + -
222D ILE* 3.7 26.0 - - + -
225D ILE* 4.0 18.2 - - + -
249D MET* 2.9 14.1 + - + +
250D LEU* 3.3 17.5 + - + +
252D ARG* 1.3 71.7 - - - +
254D GLN* 1.3 67.9 + - - +
256D ILE* 3.1 7.5 + - + +
257D SER* 2.8 23.9 + - - -
264D VAL* 4.1 21.1 - - + +
266D VAL* 4.6 3.6 - - + -
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Residues in contact with GLN 254 (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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163C ASN* 5.4 1.6 - - - +
192C ARG* 3.2 26.0 + - - +
194C TYR* 3.4 23.5 + - + +
121D ILE* 3.6 17.5 - - + -
250D LEU 3.1 13.9 + - - +
251D SER* 3.7 10.4 - - - +
252D ARG 3.3 0.2 - - - -
253D LEU* 1.3 78.0 - - - +
255D LYS* 1.3 61.3 + - - +
257D SER* 2.7 29.2 - - - -
258D GLU* 3.0 19.5 + - - +
295D HIS* 4.0 18.3 - - - +
296D ALA* 3.0 31.4 - - - +
298D THR* 4.8 5.6 - - + +
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Residues in contact with LYS 255 (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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194C TYR* 3.5 53.1 - - + +
195C THR* 5.6 4.6 - - - +
198C HIS* 6.0 1.2 - - - -
251D SER* 3.1 16.9 + - - +
252D ARG* 3.6 35.0 - - - +
253D LEU 3.2 0.2 - - - -
254D GLN* 1.3 79.1 - - - +
256D ILE* 1.3 56.4 + - - +
259D GLU* 2.8 51.3 + - + +
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Residues in contact with ILE 256 (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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203D LEU* 3.9 35.0 - - + +
206D VAL* 4.8 2.5 - - + -
207D ALA* 3.8 32.1 - - + +
210D PHE* 3.9 31.2 - - + -
220D LEU* 4.3 13.2 - - + -
252D ARG* 2.9 34.9 + - + +
253D LEU* 3.5 10.5 - - + +
255D LYS* 1.3 71.6 - - - +
257D SER* 1.3 65.2 + - - +
259D GLU* 5.1 0.4 - - - -
260D TYR* 3.1 34.5 + - + +
262D VAL* 4.1 4.9 - - + +
264D VAL* 5.4 0.7 - - + -
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Residues in contact with SER 257 (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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119D MET* 3.5 5.1 - - - -
120D ALA* 3.0 39.5 + - - -
121D ILE* 4.8 0.7 - - - -
253D LEU 2.8 15.3 + - - -
254D GLN* 2.7 22.2 - - - -
256D ILE* 1.3 73.3 - - - +
258D GLU* 1.3 60.5 + - - -
261D ASN* 3.3 7.8 + - - -
262D VAL* 3.2 37.4 + - - +
264D VAL* 3.3 10.5 - - - +
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Residues in contact with GLU 258 (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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163C ASN* 3.4 20.3 + - - +
192C ARG* 2.8 41.1 + - - +
194C TYR* 2.7 33.7 + - - +
91D TYR* 5.4 1.7 + - - -
94D LYS* 3.4 22.6 - - - +
119D MET* 3.6 39.9 - - + +
120D ALA* 5.5 0.3 - - - -
254D GLN* 3.0 22.6 + - - +
255D LYS 4.3 0.2 - - - +
257D SER* 1.3 80.1 - - - +
259D GLU* 1.3 66.1 + - - +
260D TYR 3.3 0.6 + - - -
261D ASN* 3.8 5.5 + - - +
298D THR* 5.3 0.7 - - - +
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Residues in contact with GLU 259 (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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94D LYS* 4.6 12.9 + - - +
211D HIS* 5.6 0.9 + - - -
252D ARG* 5.0 5.5 + - - -
255D LYS* 2.8 36.6 + - + +
256D ILE* 5.1 0.2 - - - -
258D GLU* 1.3 80.5 - - - +
260D TYR* 1.3 91.1 + - + +
261D ASN* 3.5 0.4 - - - +
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Residues in contact with TYR 260 (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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207D ALA* 3.7 30.9 + - + +
210D PHE* 3.6 38.8 - + + -
211D HIS* 3.1 46.3 + - - +
214D ALA* 6.3 1.8 - - - -
215D GLY* 5.5 5.2 + - - -
217D PHE 4.8 0.9 - - - +
252D ARG* 6.2 0.7 - - - -
256D ILE* 3.1 31.6 + - + +
259D GLU* 1.3 107.4 + - + +
261D ASN* 1.3 74.9 + - - +
262D VAL* 3.1 10.8 + - + +
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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