Contacts of the helix formed by residues 201 - 224 (chain B) in PDB entry 1BRR
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 LEU 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLN* 3.7 23.1 - - + +
4B ILE 5.5 0.2 - - - +
5B THR* 3.1 40.6 - - - +
9B GLU* 3.3 11.4 - - - +
77B PRO* 4.3 13.7 - - + +
78B ILE* 5.7 0.2 - - - -
79B TYR* 3.7 22.4 - - + -
193B SER* 3.5 30.4 - - - +
194B GLU* 5.3 4.7 - - + +
199B VAL 3.9 0.6 + - - -
200B PRO* 1.3 70.8 - - - +
202B ASN* 1.3 52.9 + - - +
204B GLU* 2.9 25.0 + - - +
205B THR* 2.7 43.9 + - - +
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Residues in contact with ASN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE 6.0 0.2 + - - -
8B PRO* 4.0 22.1 + - + +
9B GLU* 4.0 22.4 + - - +
12B TRP* 3.3 29.4 - - - +
200B PRO* 2.9 15.5 + - + +
201B LEU* 1.3 80.4 - - - +
203B ILE* 1.3 61.3 + - + +
205B THR* 3.1 4.2 + - - -
206B LEU 3.1 18.5 + - - -
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 6.0 2.2 - - + +
199B VAL* 3.2 28.3 - - + -
200B PRO* 3.0 18.0 + - + -
202B ASN* 1.3 80.0 - - + +
204B GLU* 1.3 58.9 + - - +
205B THR 3.1 0.2 - - - -
206B LEU* 3.7 15.7 - - + -
207B LEU* 2.9 49.6 + - + +
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 5.7 0.3 - - - -
82B ARG* 4.7 4.3 + - - -
188B VAL* 3.9 21.0 - - + +
189B TRP* 4.4 4.7 - - - -
192B GLY* 3.8 23.3 - - - -
193B SER 4.2 4.7 - - - -
194B GLU* 3.3 35.2 + - - +
199B VAL* 4.1 2.2 - - + +
200B PRO 3.0 11.2 + - - +
201B LEU* 2.9 31.7 + - - +
203B ILE* 1.3 78.2 - - - +
205B THR* 1.3 60.4 + - - +
207B LEU* 4.2 1.1 - - - -
208B PHE* 2.9 59.4 + - - +
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 3.5 31.3 - - + +
12B TRP* 3.9 8.7 - - + -
13B LEU* 3.5 33.4 - - + -
79B TYR* 4.2 2.6 - - - -
82B ARG* 3.6 18.4 + - - +
201B LEU* 2.7 26.6 + - - +
202B ASN 3.5 5.4 - - - -
204B GLU* 1.3 77.5 - - - +
206B LEU* 1.3 59.0 + - - +
208B PHE* 3.4 2.8 + - - +
209B MET* 2.9 31.4 + - + +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.3 64.8 - - + +
202B ASN 3.1 9.5 + - - +
203B ILE* 3.8 17.5 - - + +
205B THR* 1.3 77.1 - - - +
207B LEU* 1.3 73.4 + - + +
209B MET* 3.2 9.8 + - + +
210B VAL* 3.1 36.7 + - + +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 3.8 36.3 - - + -
191B ILE* 4.9 14.6 - - + -
199B VAL* 5.0 2.2 - - + -
203B ILE* 2.9 42.3 + - + +
204B GLU* 4.8 0.2 - - - -
206B LEU* 1.3 84.6 - - + +
208B PHE* 1.3 59.6 + - - +
210B VAL* 3.3 4.0 + - + +
211B LEU* 2.9 44.2 + - + +
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B TYR* 3.8 2.2 - - - -
82B ARG* 3.7 35.2 - - - +
86B TRP* 3.9 17.5 - + - -
185B TYR* 3.3 47.6 - + - -
188B VAL* 4.1 20.6 - - + -
189B TRP* 4.1 20.2 - + + -
194B GLU* 5.1 3.6 - - - -
204B GLU* 2.9 50.5 + - + +
205B THR 3.4 1.7 + - - +
206B LEU 3.3 0.2 - - - -
207B LEU* 1.3 79.1 - - - +
209B MET* 1.3 53.6 + - - +
211B LEU* 4.0 4.2 - - + +
212B ASP* 2.7 41.3 + - - +
999B RET 4.9 0.7 - - + -
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Residues in contact with MET 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.5 25.6 - - + +
15B LEU* 3.4 46.7 - - + -
16B GLY* 3.6 16.2 - - - +
19B LEU* 4.7 5.2 - - + -
57B TYR* 3.3 19.0 + - + +
205B THR* 2.9 19.5 + - + +
206B LEU* 3.2 17.2 + - + +
208B PHE* 1.3 76.7 - - - +
210B VAL* 1.3 67.3 + - + +
212B ASP* 4.0 0.8 - - - +
213B VAL* 3.1 32.3 + - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 3.1 30.9 + - + +
207B LEU* 3.8 4.9 - - + +
209B MET* 1.3 85.0 - - + +
211B LEU* 1.3 66.9 + - + +
212B ASP 3.2 1.3 - - - -
213B VAL* 4.3 2.9 - - - +
214B SER* 2.7 38.4 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.1 20.0 - - + +
184B ALA* 3.6 28.9 - - + -
185B TYR* 3.4 34.1 - - + +
188B VAL* 4.2 17.7 - - + -
207B LEU* 2.9 36.5 + - + +
208B PHE* 4.0 4.3 - - + +
210B VAL* 1.3 85.6 - - + +
212B ASP* 1.3 58.0 + - - +
214B SER* 3.5 5.9 + - - -
215B ALA* 2.9 33.6 + - - +
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Residues in contact with ASP 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 3.6 15.0 - - + -
57B TYR* 2.7 34.2 + - + +
82B ARG* 4.3 6.4 + - - +
85B ASP* 5.6 1.1 - - - +
86B TRP* 3.6 16.3 + - - -
185B TYR* 2.6 26.3 + - - -
208B PHE 2.7 21.8 + - - +
209B MET 4.1 2.0 - - - +
211B LEU* 1.3 72.7 - - - +
213B VAL* 1.3 67.6 + - - +
215B ALA* 2.8 14.8 + - - +
216B LYS* 2.9 22.4 + - - +
999B RET 3.4 14.0 - - - +
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLY* 4.7 6.7 - - - -
19B LEU* 3.4 49.1 - - + -
20B MET* 3.6 16.8 - - + +
57B TYR* 6.2 0.4 - - + -
209B MET* 3.1 23.6 + - - +
210B VAL* 4.3 3.8 - - - +
212B ASP* 1.3 76.6 - - - +
214B SER* 1.3 58.8 + - - +
217B VAL* 2.8 43.8 + - + -
218B GLY 3.1 4.0 + - - -
1004B OCT 4.7 14.8 - - + -
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 4.5 3.6 - - - +
181B LEU* 3.3 28.0 - - - +
210B VAL* 2.7 25.4 + - - +
211B LEU* 3.5 4.7 + - - -
212B ASP 3.2 0.2 - - - -
213B VAL* 1.3 76.2 - - - +
215B ALA* 1.3 57.0 + - - +
216B LYS 3.1 4.9 - - - -
218B GLY* 3.3 9.9 - - - +
219B PHE* 3.1 21.8 + - - +
1004B OCT 6.3 1.1 - - - -
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 4.0 11.6 - - - +
177B VAL* 5.4 0.9 - - - -
178B THR* 5.9 1.0 - - + +
181B LEU* 3.6 21.5 - - + -
182B TRP* 4.9 6.7 + - + +
185B TYR* 4.2 9.9 - - - +
211B LEU 2.9 20.3 + - - +
212B ASP* 2.8 8.4 + - - +
214B SER* 1.3 72.6 + - - +
216B LYS* 1.3 61.3 + - - +
219B PHE* 3.1 22.9 - - - +
999B RET 4.4 17.0 - - + -
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 3.3 32.5 - - + -
27B PHE* 4.7 0.7 - - - -
46B THR* 5.4 0.7 - - - +
49B VAL* 3.4 26.5 - - + +
50B PRO* 4.7 8.7 - - + +
53B ALA* 4.0 7.9 - - + -
85B ASP* 4.0 8.4 + - - -
86B TRP* 4.3 3.0 - - - -
89B THR* 3.2 21.3 - - - +
93B LEU* 4.4 0.9 - - + -
212B ASP* 2.9 19.8 + - - +
213B VAL 4.0 0.4 - - - +
214B SER 3.1 0.8 - - - -
215B ALA* 1.3 79.5 - - - +
217B VAL* 1.3 58.9 + - - +
218B GLY 3.0 0.4 + - - -
219B PHE* 3.1 2.3 + - - +
220B GLY* 2.7 34.8 + - - -
999B RET 1.3 73.6 - - + +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.2 17.9 - - + +
20B MET* 4.4 19.5 - - - -
23B GLY* 4.0 23.6 - - - -
26B TYR* 6.5 0.4 - - + -
27B PHE* 3.6 17.0 - - + -
50B PRO* 4.8 5.6 - - + +
213B VAL* 2.8 29.4 + - + +
216B LYS* 1.3 74.8 - - - +
218B GLY* 1.3 63.4 + - - +
220B GLY 3.3 0.2 + - - -
221B LEU* 2.9 34.5 + - + +
1004B OCT 4.6 16.4 - - + -
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Residues in contact with GLY 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 5.9 0.7 - - - -
213B VAL 3.1 8.9 + - - -
214B SER* 3.3 15.7 - - - +
216B LYS 3.0 0.6 - - - -
217B VAL* 1.3 76.8 - - - +
219B PHE* 1.3 54.4 + - - +
221B LEU* 2.8 30.3 + - - +
222B ILE* 3.2 17.5 + - - +
1004B OCT 5.3 7.1 - - - +
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Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 5.2 2.0 - - + -
93B LEU* 3.9 34.5 - - + -
96B ASP* 3.6 24.5 - - + -
97B LEU* 3.2 33.9 - - + -
174B LEU* 3.6 29.3 - - + +
177B VAL* 5.1 7.4 - - + +
178B THR* 3.5 34.3 - - + -
214B SER 3.1 8.2 + - - +
215B ALA* 3.1 26.0 - - - +
216B LYS 3.1 1.7 + - - +
218B GLY* 1.3 74.5 - - - +
220B GLY* 1.3 66.9 + - - +
222B ILE* 3.4 6.6 + - - -
223B LEU* 3.2 24.3 + - + +
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Residues in contact with GLY 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 3.7 9.6 - - - -
46B THR* 3.5 27.8 - - - -
216B LYS 2.7 20.4 + - - -
217B VAL 3.7 1.8 - - - -
219B PHE* 1.3 76.5 - - - +
221B LEU* 1.3 56.0 + - - +
223B LEU* 4.6 1.1 - - - -
224B LEU* 2.9 35.3 + - - +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.8 19.5 - - + +
27B PHE* 3.4 24.5 - - + -
30B LYS* 5.3 1.6 - - - +
217B VAL* 2.9 29.0 + - + +
218B GLY* 2.8 17.0 + - - +
220B GLY* 1.3 68.2 - - - +
222B ILE* 1.3 65.3 + - + +
224B LEU* 5.3 0.4 - - - -
225B ARG* 3.3 47.6 + - + +
1004B OCT 5.0 16.4 - - + -
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B THR* 4.5 6.4 - - + +
173B VAL* 3.6 29.8 - - + -
174B LEU* 3.6 29.6 - - + -
177B VAL* 3.7 32.1 - - + -
218B GLY 3.2 14.1 + - - +
219B PHE* 3.7 3.8 - - - +
220B GLY 3.4 0.2 - - - -
221B LEU* 1.3 77.6 - - + +
223B LEU* 1.3 63.3 + - - +
225B ARG* 4.4 1.6 - - - +
226B SER* 3.7 18.5 + - - -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 4.2 18.4 - - + -
46B THR* 3.6 9.4 - - - +
96B ASP* 3.1 42.2 - - + +
97B LEU* 5.8 0.2 - - + -
100B LEU* 3.9 22.9 - - + -
170B THR* 4.4 5.4 - - + -
174B LEU* 3.6 26.4 - - + +
219B PHE* 3.2 19.7 + - + +
220B GLY* 3.8 3.8 - - - +
222B ILE* 1.3 76.5 - - - +
224B LEU* 1.3 64.5 + - + +
225B ARG 3.2 4.0 - - - -
226B SER* 2.9 24.6 + - - +
228B ALA* 4.7 11.2 - - + +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 3.8 34.8 - - + -
30B LYS* 3.1 26.0 + - - +
42B PHE* 3.9 28.0 - - + +
43B TYR* 3.7 49.7 + - + -
46B THR* 3.6 28.5 - - + +
220B GLY 2.9 19.3 + - - +
221B LEU* 4.9 0.7 - - - +
223B LEU* 1.3 73.4 - - + +
225B ARG* 1.3 57.8 + - - +
226B SER 3.4 4.5 - - - +
228B ALA* 6.0 1.3 - - - -
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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