Contacts of the helix formed by residues 219 - 243 (chain B) in PDB entry 3LRB
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 ASN 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B VAL* 4.4 2.2 - - - +
218B LYS* 1.3 83.3 - - - +
220B PRO* 1.3 63.6 - - + +
221B LYS* 4.6 2.0 - - + +
222B ARG* 4.2 24.0 - - + +
223B ASN* 2.7 56.2 + - - +
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Residues in contact with PRO 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER 5.0 0.5 - - - +
68B PRO* 3.6 40.1 - - + +
214B ALA* 4.0 19.1 - - - +
215B GLY* 5.7 0.4 - - - -
217B VAL* 4.1 2.2 - - + +
218B LYS 3.5 10.5 - - - +
219B ASN* 1.3 81.5 - - + +
221B LYS* 1.3 59.4 + - + +
222B ARG 2.8 7.8 + - - -
224B VAL* 3.1 40.6 + - + +
225B PRO* 3.3 2.8 - - - +
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Residues in contact with LYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER 4.8 3.1 - - - -
65B PHE* 3.4 47.6 - - + +
66B LEU* 3.5 21.9 + - - +
68B PRO* 4.2 16.6 - - + -
219B ASN* 3.4 2.3 - - + +
220B PRO* 1.3 79.3 - - + +
222B ARG* 1.3 65.4 + - + +
225B PRO* 4.4 3.7 - - - +
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 6.2 0.2 - - + -
219B ASN* 3.5 19.0 + - + +
220B PRO 2.8 1.2 + - - -
221B LYS* 1.3 87.9 - - + +
223B ASN* 1.3 65.0 + - - +
224B VAL 3.5 0.7 - - - -
225B PRO* 3.5 7.0 - - - +
226B ILE* 3.0 33.5 - - + +
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Residues in contact with ASN 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.2 47.3 + - + +
217B VAL* 3.6 16.6 - - + -
218B LYS* 3.1 14.8 - - - +
219B ASN* 2.7 59.1 + - - +
222B ARG* 1.3 77.6 - - - +
224B VAL* 1.3 55.0 + - - +
226B ILE* 3.5 3.6 - - - +
227B ALA* 2.9 27.6 + - - +
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 5.9 0.2 - - - -
64B SER* 3.1 33.0 - - - +
68B PRO* 5.0 2.5 - - + -
210B ALA* 3.4 31.8 - - + +
211B SER* 4.1 1.8 - - - +
214B ALA* 4.6 7.6 - - - -
217B VAL* 4.6 17.7 - - + -
220B PRO* 3.1 36.1 + - + +
223B ASN* 1.3 73.2 - - - +
225B PRO* 1.3 73.0 - - + +
227B ALA* 3.1 9.1 + - - +
228B THR* 3.0 19.0 + - + +
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Residues in contact with PRO 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA* 3.1 33.0 - - + +
62B LYS* 4.1 15.9 - - - +
64B SER* 4.2 3.6 - - - +
65B PHE* 4.1 21.3 - - + -
220B PRO 3.3 10.1 - - - +
221B LYS 4.5 4.9 - - - +
222B ARG* 3.5 12.6 - - - +
224B VAL* 1.3 89.3 - - + +
226B ILE* 1.3 68.3 + - + +
227B ALA 2.8 1.6 - - - -
228B THR* 2.5 24.6 + - + -
229B ILE* 2.9 15.1 + - - +
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.5 35.2 - - + -
16B THR* 4.4 3.3 - - + +
62B LYS* 5.6 0.2 - - - +
222B ARG* 3.0 27.4 - - + +
223B ASN* 3.5 9.6 - - - +
225B PRO* 1.3 78.3 - - + +
227B ALA* 1.3 57.0 + - - +
229B ILE* 3.8 6.5 - - - +
230B GLY* 2.8 30.1 + - - -
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.1 9.6 - - + -
16B THR* 3.3 28.4 - - + +
19B VAL* 3.8 13.0 - - + +
210B ALA* 3.7 13.2 - - + -
223B ASN 2.9 15.0 + - - +
224B VAL* 3.1 11.2 - - - +
225B PRO 2.6 4.2 + - - -
226B ILE* 1.3 71.0 - - - +
228B THR* 1.3 68.1 + - - +
231B GLY* 2.8 24.8 + - - -
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Residues in contact with THR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.7 11.6 - - - +
57B SER 3.3 22.0 + - - -
60B TYR* 5.0 2.7 - - + -
61B ALA* 3.4 17.0 - - - +
64B SER* 4.9 0.7 - - - +
207B VAL 3.9 18.2 - - - +
210B ALA* 3.3 16.2 - - + -
211B SER 4.4 2.9 - - - +
224B VAL* 3.0 21.5 + - + +
225B PRO* 2.5 17.6 + - + +
227B ALA* 1.3 71.3 - - - +
229B ILE* 1.3 56.7 + - - +
231B GLY* 3.8 0.5 - - - -
232B VAL* 2.7 41.9 + - - +
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER* 3.9 16.8 - - - +
58B MET* 4.5 13.9 - - + -
61B ALA* 3.3 28.3 - - + -
62B LYS* 3.9 17.9 - - - +
225B PRO 2.9 10.3 + - - +
226B ILE* 4.0 6.3 - - - +
228B THR* 1.3 81.8 + - - +
230B GLY* 1.3 61.7 + - - +
232B VAL* 3.9 0.6 - - - +
233B LEU* 2.8 57.2 + - + +
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Residues in contact with GLY 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B THR* 5.0 5.2 - - - -
226B ILE* 2.8 20.4 + - - -
227B ALA 3.9 0.2 - - - -
229B ILE* 1.3 77.3 - - - +
231B GLY* 1.3 64.3 + - - +
233B LEU* 3.9 5.6 - - - +
234B ILE* 2.9 37.3 + - - +
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Residues in contact with GLY 231 (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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16B THR* 3.8 7.2 + - - -
19B VAL* 4.2 3.4 - - - -
20B SER* 3.5 34.8 + - - -
23B ILE* 6.0 0.2 - - - -
227B ALA 2.8 20.8 + - - -
228B THR 3.8 0.4 - - - -
230B GLY* 1.3 74.1 - - - +
232B VAL* 1.3 57.3 + - - +
234B ILE* 3.3 3.3 - - - +
235B ALA* 2.8 29.0 + - - +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 4.9 2.5 - - + -
23B ILE* 5.5 2.7 - - + -
53B ALA 4.5 3.6 - - - +
54B LEU* 4.4 14.8 - - + -
57B SER* 3.3 24.7 - - - +
204B PHE* 3.3 30.7 - - + -
207B VAL* 3.2 31.0 - - + -
228B THR* 2.7 32.7 + - - +
229B ILE* 4.0 2.5 - - - +
231B GLY* 1.3 70.2 - - - +
233B LEU* 1.3 56.8 + - - +
235B ALA* 2.8 8.3 + - - +
236B ALA* 2.6 34.1 + - - +
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Residues in contact with LEU 233 (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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54B LEU* 3.4 33.4 - - + -
229B ILE* 2.8 46.0 + - + +
230B GLY* 3.9 5.4 - - - +
232B VAL* 1.3 72.2 - - - +
234B ILE* 1.3 63.4 + - + +
236B ALA* 3.8 5.2 - - + +
237B VAL* 2.9 30.2 + - + +
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Residues in contact with ILE 234 (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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16B THR* 5.0 9.4 - - - +
17B LEU* 5.7 6.3 - - + -
20B SER* 2.9 28.9 - - - +
24B MET* 5.0 2.0 - - + -
159B LEU* 5.1 12.6 - - + -
230B GLY* 2.9 31.1 + - - +
231B GLY* 3.3 4.3 - - - +
233B LEU* 1.3 75.8 - - + +
235B ALA* 1.3 58.0 + - - +
237B VAL* 3.9 3.5 - - - -
238B CYS* 2.9 52.0 + - - -
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Residues in contact with ALA 235 (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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20B SER* 4.5 3.4 - - - +
23B ILE* 3.3 35.0 - - + -
24B MET* 4.2 17.5 - - - +
204B PHE* 4.7 1.8 - - + -
231B GLY 2.8 13.7 + - - +
232B VAL* 2.8 11.7 + - - +
234B ILE* 1.3 76.7 - - - +
236B ALA* 1.3 57.1 + - - +
238B CYS* 3.7 1.4 - - - +
239B TYR* 2.9 40.3 + - + -
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.6 38.4 - - + -
54B LEU* 5.1 3.8 - - + -
204B PHE* 3.8 10.3 - - + -
232B VAL 2.6 18.3 + - - +
233B LEU* 3.8 8.3 - - + +
235B ALA* 1.3 72.1 - - - +
237B VAL* 1.3 64.3 + - - +
239B TYR* 2.9 28.1 - - - +
240B VAL* 2.9 11.8 + - - +
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Residues in contact with VAL 237 (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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163B VAL* 6.4 2.2 - - + -
166B ALA* 5.9 1.1 - - + -
233B LEU 2.9 18.1 + - - +
234B ILE* 3.9 4.5 - - - +
236B ALA* 1.3 74.8 - - - +
238B CYS* 1.3 72.6 + - - +
240B VAL* 3.0 15.3 + - - -
241B LEU* 3.0 38.0 + - + +
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Residues in contact with CYS 238 (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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24B MET* 3.2 37.2 - - + -
159B LEU* 4.6 2.0 - - - -
162B ILE* 3.9 10.5 - - + +
163B VAL* 4.1 22.9 - - - -
234B ILE* 2.9 38.3 + - - +
235B ALA 3.7 2.7 - - - +
237B VAL* 1.3 82.9 - - - +
239B TYR* 1.3 54.2 + - - +
241B LEU* 4.0 2.4 - - - +
242B SER* 2.5 39.4 + - - -
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Residues in contact with TYR 239 (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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23B ILE* 3.0 20.8 + - + -
24B MET* 3.1 21.4 + - - -
27B GLY* 5.7 1.0 - - - -
28B VAL* 3.9 12.1 + - + -
31B LEU* 3.2 33.2 - - + -
46B TRP* 3.8 19.3 - + + -
203B SER* 2.6 25.3 + - - -
204B PHE* 3.6 42.5 - + - -
235B ALA* 2.9 29.3 + - + -
236B ALA* 2.9 11.9 - - - +
238B CYS* 1.3 75.2 - - - +
240B VAL* 1.3 55.4 + - - +
242B SER* 2.7 18.2 + - - -
243B THR* 3.0 22.8 + - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 5.7 6.5 - - + -
46B TRP* 4.4 21.8 - - + -
50B ILE* 3.4 31.9 - - + -
236B ALA 2.9 8.4 + - - +
237B VAL* 3.0 6.9 + - - +
239B TYR* 1.3 73.2 - - - +
241B LEU* 1.3 73.7 + - + +
242B SER 2.9 5.9 + - - -
243B THR* 3.4 3.8 + - - -
244B THR* 3.0 42.1 + - + +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ILE* 4.1 15.4 - - - +
166B ALA* 3.7 45.8 - - + +
237B VAL* 3.0 32.7 + - + +
238B CYS 4.6 0.9 - - - +
240B VAL* 1.3 86.8 - - + +
242B SER* 1.3 58.4 + - - +
244B THR* 3.3 15.9 + - - +
245B ALA 4.3 1.9 + - - -
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.4 12.3 - - - +
32B PRO* 5.5 1.8 - - - +
162B ILE* 4.2 26.2 - - - -
165B ILE* 4.9 9.1 - - - +
238B CYS 2.5 23.8 + - - -
239B TYR* 2.7 17.7 + - - -
240B VAL 2.9 1.4 - - - -
241B LEU* 1.3 78.3 - - - +
243B THR* 1.3 63.9 + - - +
244B THR 3.1 8.0 + - - -
245B ALA* 3.4 20.8 + - - +
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 5.8 2.0 - - + -
31B LEU* 4.2 11.9 - - + -
32B PRO* 3.4 42.4 - - + -
35B LEU* 4.5 10.9 - - + +
41B ILE* 6.0 1.2 - - - +
43B ILE* 6.0 1.4 - - - +
46B TRP* 3.2 33.5 + - + -
239B TYR 3.0 18.4 + - - +
240B VAL* 3.7 3.1 + - - -
242B SER* 1.3 78.3 - - - +
244B THR* 1.3 61.9 + - - +
245B ALA 3.5 1.6 - - - -
246B ILE* 3.4 19.5 - - - +
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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