Contacts of the helix formed by residues 244 - 268 (chain P) in PDB entry 1E33
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 ARG 244 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P ASP* 2.8 31.5 + - - +
41P HIS* 3.3 23.2 + - + -
43P SER* 3.1 29.8 - - - +
44P SER* 3.1 29.9 + - - +
242P SER* 3.1 4.1 + - - +
243P GLY* 1.3 75.7 - - - +
245P GLY* 1.3 65.2 + - - +
247P PHE* 3.5 39.6 + - - +
248P GLY* 3.6 18.3 + - - -
251P LEU* 4.4 1.4 - - - +
290P SER 5.0 6.5 + - - +
292P GLY 3.8 12.9 + - - -
293P GLY* 4.1 2.4 - - - -
294P CYS* 4.1 4.9 - - - +
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Residues in contact with GLY 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P GLU* 6.4 0.4 - - - -
242P SER* 4.0 3.8 + - - -
243P GLY 3.7 1.4 - - - -
244P ARG* 1.3 76.4 - - - +
246P PRO* 1.3 71.9 - - - +
248P GLY 2.8 17.5 + - - -
249P ASP* 2.8 22.9 + - - +
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Residues in contact with PRO 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P PHE* 3.7 23.2 - - + -
232P GLN* 3.8 10.7 - - + +
244P ARG 4.6 0.2 - - - +
245P GLY* 1.3 83.4 - - - +
247P PHE* 1.4 63.7 + - - +
249P ASP* 3.7 10.9 - - - +
250P SER* 3.0 24.6 + - - -
290P SER 5.9 1.1 - - - +
291P ARG* 3.7 46.0 - - + +
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Residues in contact with PHE 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P ASP 4.6 1.6 - - - -
31P LEU* 4.4 1.1 - - + -
35P ASP* 3.7 15.0 - - - -
228P THR* 3.5 39.1 - - + +
232P GLN* 3.9 15.6 - - - +
244P ARG* 3.5 39.0 + - - +
245P GLY 3.1 1.2 + - - -
246P PRO* 1.4 81.6 - - - +
248P GLY* 1.4 64.2 + - - +
250P SER* 3.7 3.3 + - - -
251P LEU* 3.1 27.9 + - + +
290P SER 3.9 19.2 + - - +
291P ARG* 3.3 23.8 - - - +
292P GLY* 3.4 8.5 - - - -
293P GLY* 3.3 28.9 - - - -
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Residues in contact with GLY 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P SER* 6.0 2.0 - - - -
45P THR 5.1 1.7 + - - +
242P SER* 3.0 24.8 - - - -
244P ARG* 3.6 19.4 + - - -
245P GLY 2.8 6.4 + - - -
247P PHE* 1.4 85.4 - - - +
249P ASP* 1.3 64.3 + - - -
250P SER 3.0 1.8 - - - -
251P LEU* 3.3 6.0 - - - +
252P MET* 2.9 19.9 + - - +
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Residues in contact with ASP 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P PHE* 3.9 18.0 - - + -
234P SER* 4.0 6.3 - - - +
238P PHE* 3.3 14.5 - - - +
239P ALA* 3.7 1.4 - - - -
240P GLU* 2.7 29.8 + - - +
241P ARG 3.4 1.7 + - - -
242P SER* 2.6 42.9 + - - +
245P GLY 2.8 21.1 + - - +
246P PRO* 3.7 10.1 - - - +
248P GLY* 1.3 75.1 - - - +
250P SER* 1.3 66.8 + - - +
252P MET* 3.3 3.4 + - - +
253P GLU* 2.9 23.6 + - - +
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Residues in contact with SER 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227P HIS* 2.8 47.8 + - - +
228P THR* 4.0 1.9 - - - +
232P GLN* 2.9 32.5 + - - -
233P PHE 3.3 23.7 + - - -
234P SER* 4.5 1.6 - - - -
246P PRO 3.0 10.6 + - - -
247P PHE 3.8 1.1 - - - -
249P ASP* 1.3 84.6 - - - +
251P LEU* 1.3 59.4 + - - +
253P GLU 3.6 0.5 + - - -
254P LEU 3.4 3.6 + - - -
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Residues in contact with LEU 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P LEU* 3.7 26.5 - - + -
35P ASP* 4.0 20.4 - - + +
36P LEU* 4.2 10.3 - - + -
44P SER* 4.0 12.1 - - - +
45P THR 5.0 0.7 - - - +
46P THR* 3.6 29.6 - - + -
49P LEU* 5.2 2.2 - - + -
228P THR* 3.9 13.9 - - + -
244P ARG* 4.4 0.7 - - - +
247P PHE* 3.1 30.3 + - + +
248P GLY* 3.0 8.3 + - - +
250P SER* 1.3 75.1 - - - +
252P MET* 1.3 54.7 + - - +
254P LEU* 3.0 17.3 + - + +
255P ASP* 2.9 34.2 + - - +
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Residues in contact with MET 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P THR* 3.7 36.9 + - + +
47P PRO* 5.7 1.6 - - + -
238P PHE* 3.3 45.1 - - + +
241P ARG* 3.4 15.3 - - + +
242P SER* 3.0 42.0 - - - +
248P GLY 2.9 14.1 + - - +
249P ASP* 3.6 1.3 - - - +
251P LEU* 1.3 73.0 - - - +
253P GLU* 1.3 58.2 + - - +
255P ASP* 3.2 4.7 + - + +
256P ALA* 2.7 29.9 + - + +
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Residues in contact with GLU 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P LEU 5.4 1.0 - - - +
195P PRO 5.5 0.7 - - - +
198P GLU* 3.6 34.2 + - + +
227P HIS* 3.0 28.4 + - - +
233P PHE* 4.2 6.2 - - - -
234P SER* 3.6 14.4 - - - -
235P GLY* 2.6 30.1 + - - -
238P PHE* 3.1 35.7 - - + -
249P ASP 2.9 15.5 + - - +
250P SER 3.8 0.4 - - - +
251P LEU 3.2 0.2 - - - -
252P MET* 1.3 76.6 - - - +
254P LEU* 1.4 55.6 + - - +
256P ALA* 3.0 2.3 + - - +
257P ALA* 2.8 27.5 + - - +
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Residues in contact with LEU 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ILE* 4.4 11.7 - - + -
28P ALA* 3.6 29.2 - - + -
31P LEU* 4.7 0.4 - - + -
49P LEU* 5.0 2.5 - - + -
223P TYR* 4.0 17.9 - - + +
225P SER* 3.9 29.6 - - - +
227P HIS* 3.8 18.7 - - + +
228P THR* 5.5 0.7 - - + -
250P SER 3.4 7.8 + - - +
251P LEU* 3.0 26.1 + - + +
253P GLU* 1.4 77.3 - - - +
255P ASP* 1.3 62.8 + - - +
257P ALA* 3.4 4.6 + - - +
258P VAL* 3.1 21.1 + - + +
278P PHE* 3.8 17.7 - - + -
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Residues in contact with ASP 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P THR* 3.1 27.5 - - + -
47P PRO* 3.0 14.0 - - - +
48P ASN* 2.9 40.1 + - - +
49P LEU* 2.7 45.4 + - + +
251P LEU 2.9 14.6 + - - +
252P MET* 3.4 8.1 - - - +
254P LEU* 1.3 80.4 - - - +
256P ALA* 1.3 58.1 + - - +
258P VAL* 3.1 5.1 + - - +
259P GLY 3.1 16.1 + - - -
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Residues in contact with ALA 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P ASN* 4.0 8.3 - - - +
198P GLU* 4.1 3.8 - - - +
238P PHE* 3.4 35.9 - - + -
252P MET* 2.7 12.8 + - + +
253P GLU 3.0 1.3 + - - +
255P ASP* 1.3 74.1 + - - +
257P ALA* 1.3 65.1 + - - +
258P VAL 3.0 1.4 + - - -
259P GLY* 3.0 3.1 + - - -
260P THR* 3.0 23.2 + - - +
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Residues in contact with ALA 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198P GLU* 3.2 27.6 + - + +
202P MET* 3.5 17.7 - - + +
223P TYR* 3.5 28.0 - - + +
253P GLU 2.8 15.9 + - - +
254P LEU* 3.7 9.9 - - - +
256P ALA* 1.3 72.5 - - - +
258P VAL* 1.4 59.0 + - - +
260P THR* 3.3 2.7 + - - -
261P LEU* 3.0 23.5 + - - +
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Residues in contact with VAL 258 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ILE* 3.9 34.5 - - + -
48P ASN* 4.4 10.3 - - + -
49P LEU* 4.0 33.2 - - + +
52P LEU* 4.7 18.2 - - + -
223P TYR* 5.6 0.2 - - + -
254P LEU* 3.1 22.6 + - + +
255P ASP* 3.1 9.3 + - - +
257P ALA* 1.4 72.4 - - - +
259P GLY* 1.3 66.8 + - - +
261P LEU* 3.4 9.5 + - + +
262P MET* 3.0 27.9 + - + +
276P VAL* 6.1 1.3 - - + -
278P PHE* 4.8 0.7 - - + -
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Residues in contact with GLY 259 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P ASN* 3.6 27.6 - - - +
255P ASP 3.1 4.8 + - - -
256P ALA 3.0 7.0 + - - -
258P VAL* 1.3 80.0 - - - +
260P THR* 1.3 55.1 + - - +
262P MET* 3.1 9.2 + - - +
263P THR* 3.0 30.6 + - - -
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Residues in contact with THR 260 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198P GLU* 4.5 2.3 + - - -
202P MET* 3.4 38.7 - - + +
256P ALA* 3.0 13.5 + - - +
257P ALA* 3.4 8.3 - - - -
259P GLY* 1.3 70.7 - - - +
261P LEU* 1.3 67.7 + - + +
262P MET 2.8 0.9 + - - -
263P THR* 3.0 15.9 + - - +
264P ALA* 3.0 16.8 + - + +
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Residues in contact with LEU 261 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P VAL* 4.4 10.1 - - + -
26P ILE* 3.5 33.0 - - + -
202P MET* 3.3 35.2 - - + -
205P ALA* 3.9 20.2 - - + -
209P MET* 4.8 7.0 - - + -
221P LEU* 4.4 10.8 - - + -
223P TYR* 3.9 19.3 - - + -
257P ALA 3.0 17.7 + - - +
258P VAL* 3.4 7.8 + - - +
260P THR* 1.3 75.6 - - + +
262P MET* 1.3 61.0 + - - +
264P ALA* 3.6 8.0 - - - +
265P ILE* 2.8 39.8 + - + +
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Residues in contact with MET 262 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P VAL* 5.8 0.4 - - - -
26P ILE* 6.4 0.7 - - - -
48P ASN* 6.4 0.7 - - + -
52P LEU* 3.9 20.4 - - + -
258P VAL* 3.0 24.1 + - + +
259P GLY* 3.3 9.4 - - - +
260P THR 2.8 0.8 + - - -
261P LEU* 1.3 82.4 - - - +
263P THR* 1.3 56.0 + - - +
265P ILE* 3.2 11.2 + - + +
266P GLY* 3.1 20.8 + - - -
271P LEU* 4.1 22.6 - - + +
276P VAL* 3.8 24.9 - - + -
317P PHE* 3.4 38.4 - - + -
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Residues in contact with THR 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259P GLY 3.0 12.8 + - - -
260P THR* 3.0 10.8 + - - -
262P MET* 1.3 70.1 - - - +
264P ALA* 1.3 69.7 + - - +
265P ILE 3.1 0.4 - - - -
266P GLY* 2.7 4.9 + - - -
267P ASP* 2.7 43.6 + - - +
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Residues in contact with ALA 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206P HIS* 4.2 21.5 - - + -
209P MET* 3.4 28.1 - - + +
260P THR* 3.0 12.7 + - + +
261P LEU* 3.6 6.1 - - - +
263P THR* 1.3 79.5 - - - +
265P ILE* 1.3 62.9 + - - +
267P ASP* 3.8 10.4 - - - +
268P LEU* 3.3 25.6 + - - +
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Residues in contact with ILE 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P VAL* 4.0 17.7 - - + -
209P MET* 4.0 23.8 - - - -
219P PHE* 5.0 1.1 - - + -
261P LEU* 2.8 29.1 + - + +
262P MET* 3.2 12.9 + - + +
263P THR 2.8 2.2 + - - -
264P ALA* 1.3 73.2 - - - +
266P GLY* 1.3 66.7 + - - +
268P LEU* 3.4 1.1 + - - -
269P GLY 3.3 2.1 + - - -
270P LEU* 3.0 55.8 + - + +
271P LEU* 3.7 14.6 - - + -
274P THR* 3.7 32.3 - - + +
276P VAL* 4.3 8.1 - - + -
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Residues in contact with GLY 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262P MET 3.1 10.9 + - - -
263P THR* 2.7 6.6 + - - -
265P ILE* 1.3 74.7 - - - +
267P ASP* 1.3 52.9 + - - +
269P GLY* 2.5 34.5 + - - -
270P LEU 5.1 0.2 - - - -
271P LEU* 4.1 18.9 - - - +
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Residues in contact with ASP 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206P HIS* 5.8 4.1 + - - +
263P THR* 2.7 40.5 + - - +
264P ALA* 3.8 8.5 - - - +
266P GLY* 1.3 69.7 - - - +
268P LEU* 1.3 65.5 + - + +
269P GLY 3.0 3.6 + - - -
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Residues in contact with LEU 268 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206P HIS* 4.6 13.9 - - + +
209P MET* 4.0 15.9 - - + +
210P ALA* 3.7 35.4 - - + +
213P GLN* 2.7 46.6 + - - +
264P ALA* 3.3 19.3 + - + +
265P ILE* 4.1 0.4 - - - +
266P GLY 3.0 1.0 + - - -
267P ASP* 1.3 76.4 - - + +
269P GLY* 1.3 60.1 + - - +
270P LEU* 3.2 27.2 + - + +
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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