Contacts of the helix formed by residues 213 - 233 (chain O) in PDB entry 1UW9
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 213 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208O SER* 3.5 13.6 + - - +
209O GLN* 3.4 29.7 + - - +
210O PRO* 3.5 21.9 + - - +
212O MET* 1.3 75.8 - - - +
214O TRP* 1.3 67.5 + - + +
215O ARG* 3.3 2.8 + - + +
216O ASP* 3.3 24.6 + - - +
217O ARG* 3.2 18.5 + - - +
146R LYS* 5.1 0.2 - - - +
149R VAL 5.4 4.9 + - - -
152R PRO 5.6 1.1 - - - +
285R ARG* 3.7 45.8 - - - +
372R PRO* 6.0 6.9 - - - +
109V GLU* 5.4 0.8 - - - +
110V GLU* 2.8 43.0 + - - -
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Residues in contact with TRP 214 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207O ASN 3.4 18.8 - - - +
208O SER* 3.0 27.4 + - - -
212O MET 3.9 0.2 + - - -
213O ARG* 1.3 74.1 - - + +
215O ARG* 1.3 90.8 + - + +
217O ARG* 3.1 19.7 + - - +
218O PHE* 2.9 47.0 + + + -
249O GLU* 3.9 6.0 + - - -
252O LYS* 3.8 30.9 - - + +
253O ARG* 3.5 54.0 - - + +
256O SMC 3.5 39.3 - - + -
286R ASP* 5.3 10.2 + - - -
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Residues in contact with ARG 215 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M VAL* 3.7 37.0 + - - +
65M CYS* 4.9 2.8 + - - +
213O ARG* 3.3 2.0 - - + +
214O TRP* 1.3 111.7 - - + +
216O ASP* 1.3 67.8 + - - +
218O PHE* 3.4 2.2 + - - +
219O LEU* 3.1 49.4 + - + +
256O SMC 3.8 20.6 - - + +
161R LYS* 5.0 3.2 + - - +
258R LYS* 4.6 3.2 - - - +
285R ARG* 3.8 14.4 - - - +
286R ASP* 3.1 31.3 + - - +
287R ASN* 3.5 20.7 + - - +
288R GLY* 3.6 18.8 - - - +
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Residues in contact with ASP 216 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182O ALA* 3.6 20.0 - - + -
213O ARG* 3.3 25.7 + - - +
215O ARG* 1.3 78.9 - - - +
217O ARG* 1.3 61.6 + - - +
219O LEU* 3.3 3.6 + - - +
220O PHE* 3.1 29.7 + - + -
152R PRO 4.9 3.1 - - - +
153R HIS* 3.5 12.0 + - - -
157R VAL* 3.4 31.9 - - + +
161R LYS* 2.9 32.7 + - - +
285R ARG* 6.0 1.7 - - - -
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Residues in contact with ARG 217 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182O ALA* 3.6 11.2 - - - +
185O TYR* 3.7 13.7 - - + -
202O ASP* 2.8 41.3 + - - +
206O VAL* 3.4 20.4 + - - +
207O ASN* 2.7 32.7 + - - +
209O GLN* 5.5 0.2 + - - -
212O MET* 3.6 38.4 + - - +
213O ARG 3.2 3.8 + - - +
214O TRP* 3.1 18.4 + - - +
216O ASP* 1.3 77.3 - - - +
218O PHE* 1.3 76.8 + - - +
219O LEU 3.2 0.2 + - - -
220O PHE 3.3 0.9 + - - -
221O VAL* 2.8 50.4 + - + +
240O LEU* 4.6 2.0 - - + +
241O ASN 4.1 4.4 + - - -
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Residues in contact with PHE 218 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214O TRP* 2.9 49.6 + + + +
215O ARG 3.7 5.6 - - - +
216O ASP 3.4 0.2 - - - -
217O ARG* 1.3 94.4 - - - +
219O LEU* 1.3 57.8 + - - +
221O VAL* 3.9 1.2 - - - +
222O THR* 2.8 35.0 + - - -
240O LEU* 3.6 50.7 - - + +
241O ASN 3.5 20.0 - - - -
242O ALA* 5.1 0.2 - - - -
253O ARG* 3.3 30.1 - - + -
256O SMC 3.8 22.0 - - - -
257O ALA* 4.3 7.6 - - + -
260O LEU* 4.1 11.7 - - + -
265O ILE* 5.3 1.1 - - + -
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Residues in contact with LEU 219 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M VAL 4.8 3.1 - - - +
65M CYS 3.5 24.2 - - - +
66M LEU 3.9 16.4 - - - +
67M TYR* 4.0 21.8 - - + +
71M ARG* 5.5 2.7 - - - +
215O ARG* 3.1 49.6 + - - +
216O ASP* 3.6 6.3 - - - +
218O PHE* 1.3 74.9 - - - +
220O PHE* 1.3 68.1 + - + +
222O THR* 3.2 7.5 + - - -
223O GLU* 3.1 18.9 + - - +
256O SMC 4.5 4.0 - - + -
260O LEU* 4.2 26.7 - - + -
161R LYS* 4.7 14.6 - - - +
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Residues in contact with PHE 220 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M ARG* 4.2 26.2 - - + -
72M TYR* 3.4 35.0 - + - +
182O ALA* 3.6 19.7 - - + +
183O LYS* 3.5 31.4 - - + -
186O GLY* 4.2 2.7 - - - -
216O ASP* 3.1 29.9 + - + +
217O ARG 4.0 0.9 - - - +
219O LEU* 1.3 73.9 - - + +
221O VAL* 1.3 66.9 + - - +
223O GLU* 3.2 7.0 + - - +
224O ALA* 3.0 18.2 + - - +
157R VAL* 5.2 3.1 - - + -
160R ASP* 3.5 45.1 - - + -
161R LYS* 3.7 19.5 - - + -
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Residues in contact with VAL 221 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185O TYR* 4.2 16.6 - - + -
186O GLY* 4.4 7.2 - - - +
189O VAL* 4.2 13.7 - - + -
217O ARG* 2.8 41.1 + - + +
218O PHE 4.0 0.4 - - - +
220O PHE* 1.3 73.0 - - - +
222O THR* 1.3 56.6 + - - +
224O ALA* 3.1 8.4 + - - +
225O ILE* 2.8 34.1 + - + +
238O HIS* 3.5 42.2 - - + +
240O LEU* 3.8 14.1 - - + -
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Residues in contact with THR 222 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M PHE* 4.2 12.1 - - + -
67M TYR* 4.1 10.8 - - + -
218O PHE 2.8 24.4 + - - -
219O LEU* 3.2 8.0 + - - -
221O VAL* 1.3 75.7 - - - +
223O GLU* 1.3 63.5 + - - +
225O ILE* 3.3 9.4 + - - +
226O TYR* 3.1 51.2 + - + -
240O LEU* 4.8 2.3 - - - +
260O LEU* 3.4 19.6 - - + +
262O VAL* 3.4 18.6 - - + +
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Residues in contact with GLU 223 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M TYR* 3.4 25.5 + - + +
68M TYR 3.2 18.2 - - - +
69M ASP* 4.4 6.4 - - - +
70M ASN 3.5 5.1 + - - +
71M ARG* 2.9 41.1 + - - +
72M TYR* 3.0 46.2 + - + +
1141M EDO 5.5 0.8 - - - -
219O LEU 3.1 10.5 + - - +
220O PHE* 3.5 10.3 - - - +
222O THR* 1.3 75.1 - - - +
224O ALA* 1.3 57.7 + - - +
226O TYR* 3.5 1.9 + - - +
227O LYS* 3.0 31.6 + - + +
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Residues in contact with ALA 224 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72M TYR* 4.3 5.1 - - + -
186O GLY 3.2 28.5 - - - +
189O VAL* 3.8 8.1 - - + -
190O TYR* 3.5 24.9 - - + +
193O LEU* 4.6 1.6 - - - -
220O PHE 3.0 11.7 + - - +
221O VAL 3.1 9.2 + - - +
223O GLU* 1.3 73.2 - - - +
225O ILE* 1.3 64.6 + - - +
227O LYS* 3.4 3.3 + - - +
228O ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 225 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189O VAL* 4.9 0.2 - - + -
193O LEU* 3.9 14.1 - - + -
221O VAL* 2.8 28.6 + - + +
222O THR* 3.3 4.7 + - - +
224O ALA* 1.3 72.0 - - - +
226O TYR* 1.3 76.1 + - + +
228O ALA* 3.4 1.7 + - - +
229O GLN* 2.9 30.0 + - - +
236O LYS* 3.5 30.4 - - + +
237O GLY* 4.3 1.3 - - - -
238O HIS* 3.8 41.5 - - + +
240O LEU* 5.3 1.6 - - + -
262O VAL* 4.0 27.4 - - + -
263O PRO* 4.7 4.0 - - + -
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Residues in contact with TYR 226 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M SER* 3.6 32.3 - - - +
59M ARG* 3.0 39.5 + - - -
60M PHE* 4.1 9.0 - + - -
67M TYR* 3.9 3.1 - - - +
69M ASP* 4.7 0.2 - - - +
1141M EDO 3.4 15.1 - - - -
222O THR* 3.1 36.7 + - + +
223O GLU 4.1 2.5 - - - +
225O ILE* 1.3 91.6 - - + +
227O LYS* 1.3 65.4 + - - +
229O GLN* 3.9 17.3 - - - +
230O ALA* 3.0 18.7 + - - +
260O LEU 2.7 24.3 + - - -
261O GLY 3.2 11.9 + - - -
262O VAL* 3.6 8.2 + - + -
263O PRO* 5.8 0.9 - - + -
54T ASN* 5.8 2.2 - - - -
68T TYR* 5.4 4.0 - + - -
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Residues in contact with LYS 227 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M ALA* 5.7 1.6 - - - +
49M LYS* 4.2 29.5 + - - +
70M ASN* 4.9 5.4 + - - +
72M TYR* 3.3 39.6 + - + +
73M TRP* 4.2 7.1 - - - +
74M THR* 4.4 3.2 + - - -
1141M EDO 3.8 20.3 + - - +
190O TYR* 3.4 44.5 + - + -
223O GLU* 3.0 22.3 + - + +
224O ALA* 3.8 4.3 - - - +
225O ILE 3.3 0.2 - - - -
226O TYR* 1.3 77.6 - - - +
228O ALA* 1.3 57.4 + - - +
230O ALA* 3.3 3.3 + - - +
231O GLU* 2.9 33.2 + - - +
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Residues in contact with ALA 228 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O TYR* 3.9 12.1 - - + -
193O LEU* 3.5 32.1 - - + -
194O ARG* 3.8 14.1 - - - +
224O ALA 3.0 17.1 + - - +
225O ILE 3.9 2.7 - - - +
227O LYS* 1.3 77.4 - - - +
229O GLN* 1.3 57.1 + - - +
231O GLU* 3.7 4.9 - - - +
232O THR* 2.8 37.4 + - - +
236O LYS* 4.0 3.1 - - + -
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Residues in contact with GLN 229 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225O ILE* 2.9 22.0 + - - +
226O TYR* 3.9 15.9 - - - +
228O ALA* 1.3 77.2 - - - +
230O ALA* 1.3 56.3 + - - +
233O GLY* 2.8 30.0 + - - -
234O GLU 3.3 21.3 - - - +
235O VAL* 3.4 14.0 - - - +
236O LYS* 3.0 37.6 + - + +
52T VAL* 3.4 25.9 - - + +
54T ASN* 4.9 4.7 + - - +
68T TYR* 3.5 22.7 + - - -
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Residues in contact with ALA 230 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M LYS* 4.3 9.9 - - - +
1141M EDO 3.8 24.5 - - - +
226O TYR 3.0 18.7 + - - +
227O LYS 3.8 2.5 - - - +
229O GLN* 1.3 77.7 - - - +
231O GLU* 1.3 62.7 + - - +
233O GLY* 3.9 1.4 + - - -
10T LYS* 3.2 23.7 + - - -
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Residues in contact with GLU 231 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M LYS* 6.5 0.4 - - - +
74M THR* 4.2 0.2 + - - -
190O TYR* 2.5 29.3 + - - -
194O ARG* 3.0 44.2 + - - +
227O LYS* 2.9 20.9 + - + +
228O ALA* 3.7 5.6 - - - +
230O ALA* 1.3 79.4 - - - +
232O THR* 1.3 63.3 + - + +
4T TRP* 5.2 0.2 - - - -
5T THR 4.5 1.2 - - - +
6T PRO* 3.4 37.1 - - + +
9T ASN* 4.3 6.0 + - + +
10T LYS* 3.9 23.7 + - - +
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Residues in contact with THR 232 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193O LEU 4.3 0.2 - - - +
194O ARG* 3.5 36.6 - - - +
228O ALA 2.8 20.2 + - - +
231O GLU* 1.3 80.8 - - + +
233O GLY* 1.3 62.4 + - - +
234O GLU* 3.2 16.7 + - - -
236O LYS* 3.2 22.4 - - - +
9T ASN 4.7 3.4 - - - +
10T LYS* 3.6 7.0 - - - +
11T MET* 2.8 39.7 + - + +
17T TYR* 4.8 5.4 - - - +
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Residues in contact with GLY 233 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229O GLN 2.8 14.4 + - - -
230O ALA 3.9 2.7 + - - -
231O GLU 3.6 1.6 - - - -
232O THR* 1.3 76.4 - - - +
234O GLU* 1.3 61.5 + - - +
235O VAL 4.4 0.2 + - - -
10T LYS* 4.1 6.9 - - - +
11T MET 4.7 2.5 - - - +
12T PHE* 6.0 0.2 - - - -
13T GLU* 6.0 0.2 - - - +
51T TYR* 3.9 31.7 - - - -
52T VAL* 4.8 15.3 + - - +
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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