Contacts of the helix formed by residues 245 - 272 (chain B) in PDB entry 6DWM
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 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ALA* 4.7 9.7 - - - +
240B LEU* 3.5 23.7 + - - +
241B ARG 5.5 0.9 - - - +
243B LEU 2.9 10.5 + - - +
244B PRO* 1.3 73.0 - - - +
246B PRO* 1.3 69.4 - - - +
247B SER* 3.4 12.5 + - - -
248B LEU* 3.2 40.5 + - + +
249B ASN* 3.1 32.3 + - - +
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Residues in contact with PRO 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PRO* 3.8 7.6 - - + +
245B ASN* 1.3 87.1 - - - +
247B SER* 1.3 68.1 + - - +
249B ASN* 3.4 7.4 + - + +
250B ALA* 3.1 24.3 + - - +
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Residues in contact with SER 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ASN* 2.9 32.7 + - - +
227B VAL* 4.0 9.8 - - - +
245B ASN* 3.3 10.2 + - - -
246B PRO* 1.3 82.2 - - - +
248B LEU* 1.3 61.5 + - - +
250B ALA* 3.5 0.8 + - - -
251B PHE* 3.1 10.7 + - - +
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 3.8 25.8 - - + -
111B THR* 4.0 27.8 - - + -
114B LEU* 4.7 8.7 - - + -
227B VAL* 4.0 14.1 - - + -
232B ASN* 4.9 1.6 - - - +
234B ALA* 4.6 11.9 - - + -
241B ARG* 4.2 22.2 - - + +
245B ASN* 3.2 32.1 + - + +
247B SER* 1.3 76.8 - - - +
249B ASN* 1.3 63.2 + - - +
251B PHE* 3.2 5.4 + - + +
252B LYS* 3.0 43.4 + - - +
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Residues in contact with ASN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PRO* 5.8 0.8 - - - +
245B ASN* 3.1 30.1 + - - +
246B PRO* 4.0 6.2 - - + +
248B LEU* 1.3 74.8 - - - +
250B ALA* 1.3 65.4 + - - +
252B LYS* 3.1 25.0 + - - +
253B ASP* 3.0 32.9 + - - +
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ASN* 5.0 15.7 - - + +
223B ASN* 3.9 16.0 - - - +
246B PRO 3.1 17.0 + - - +
247B SER* 3.8 5.2 - - - +
249B ASN* 1.3 76.9 - - - +
251B PHE* 1.3 57.1 + - - +
253B ASP* 3.9 7.7 - - - +
254B LEU* 2.9 29.6 + - - +
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Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B THR 3.6 20.9 - - - -
114B LEU* 3.8 24.2 - - + -
115B ILE* 3.8 13.2 - - + -
223B ASN* 4.0 6.3 + - - +
224B PHE* 3.6 36.8 - + - -
227B VAL* 3.7 33.9 - - + -
228B VAL* 3.7 26.7 - - + -
247B SER 3.1 14.4 + - - +
248B LEU* 3.4 10.8 - - + +
249B ASN 3.1 0.8 - - - -
250B ALA* 1.3 76.0 - - - +
252B LYS* 1.3 63.0 + - - +
254B LEU* 3.4 5.0 + - + +
255B ASN* 2.8 46.0 + - - +
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 3.6 24.8 + - - -
114B LEU* 4.1 25.6 - - + -
241B ARG 5.0 7.5 + - - -
248B LEU* 3.0 32.6 + - - +
249B ASN* 3.1 23.8 + - - +
251B PHE* 1.3 77.3 - - - +
253B ASP* 1.3 65.1 + - - +
254B LEU 3.4 0.2 + - - -
255B ASN* 3.4 4.5 + - - +
256B GLU* 3.2 33.3 + - - +
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Residues in contact with ASP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASN* 3.0 24.8 + - - +
250B ALA* 4.0 6.8 - - - +
252B LYS* 1.3 77.9 - - - +
254B LEU* 1.3 63.1 + - - +
256B GLU* 3.4 17.2 + - - +
257B LYS* 3.0 25.7 + - - +
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Residues in contact with LEU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B SER 5.9 0.4 - - - +
217B LEU* 4.4 3.1 - - - +
220B LEU 4.7 4.0 - - - +
221B ASN 4.0 10.1 - - - +
222B ASN* 3.4 26.7 - - - +
223B ASN* 4.1 8.7 - - - +
224B PHE* 3.9 31.9 - - + +
250B ALA 2.9 19.2 + - - +
251B PHE* 3.7 7.9 - - + +
252B LYS 3.2 0.4 - - - -
253B ASP* 1.3 76.4 - - - +
255B ASN* 1.3 58.2 + - - +
257B LYS* 3.2 16.1 + - + +
258B PHE* 3.0 42.7 + - + -
602B HJJ 3.7 25.1 - - + +
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Residues in contact with ASN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 3.3 21.9 - - - +
115B ILE* 3.5 26.5 - - - +
116B SER 4.2 4.7 + - - +
224B PHE* 4.0 5.5 - - - -
251B PHE* 2.8 47.5 + - - +
252B LYS* 4.0 4.0 - - - +
253B ASP 3.3 0.2 - - - -
254B LEU* 1.3 76.0 - - - +
256B GLU* 1.3 61.0 + - + +
258B PHE* 3.3 5.0 + - - +
259B TYR* 2.9 31.9 + - - +
312B LEU* 5.5 0.3 - - - +
602B HJJ 3.6 25.6 + - - +
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Residues in contact with GLU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LYS* 3.2 22.4 + - - +
253B ASP* 3.8 17.8 - - - +
254B LEU 3.4 0.2 - - - -
255B ASN* 1.3 77.1 - - + +
257B LYS* 1.3 56.4 + - - +
259B TYR* 4.0 4.4 - - - +
260B SER* 2.9 37.1 + - - +
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Residues in contact with LYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B SER* 3.3 40.7 + - - +
217B LEU* 3.9 17.7 - - + +
220B LEU* 5.1 7.5 - - - +
253B ASP 3.0 14.4 + - - +
254B LEU* 3.2 17.2 + - + +
256B GLU* 1.3 75.9 - - - +
258B PHE* 1.3 58.8 + - + +
260B SER* 3.4 4.2 + - - -
261B PHE* 2.9 29.6 + - - +
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Residues in contact with PHE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 3.3 46.2 - - + -
218B VAL* 4.6 0.7 - - + -
254B LEU* 3.0 35.9 + - + +
255B ASN 3.3 4.0 + - - +
257B LYS* 1.3 77.2 - - - +
259B TYR* 1.3 58.4 + - - +
261B PHE* 3.4 3.1 + + - +
262B MET* 3.0 27.4 + - - +
312B LEU* 3.8 31.9 - - + +
315B PHE* 3.7 28.0 - + - -
316B GLY* 4.7 2.2 - - - -
319B PHE* 3.6 22.2 - + - -
602B HJJ 3.1 47.1 - + + +
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Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B SER* 3.5 32.1 + - - -
117B ASN* 3.6 21.8 - - + -
255B ASN 2.9 18.3 + - - +
256B GLU* 4.0 4.9 - - - +
258B PHE* 1.3 73.6 - - - +
260B SER* 1.3 65.8 + - - +
262B MET* 3.3 24.3 + - + +
263B GLN* 3.0 49.8 + - + +
305B GLU* 2.6 40.9 + - + +
309B ASN* 3.4 18.6 + - + +
312B LEU* 3.5 19.3 - - + +
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Residues in contact with SER 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B GLU* 2.9 22.9 + - - +
257B LYS* 3.8 5.2 - - - -
259B TYR* 1.3 73.3 - - - +
261B PHE* 1.3 65.1 + - - +
263B GLN* 3.2 14.4 + - - +
264B LYS* 3.0 23.4 + - - +
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Residues in contact with PHE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B CYS* 5.2 0.4 - - - -
203B PHE* 4.1 21.8 - + - -
207B TYR* 3.4 33.0 - + - -
213B GLU* 3.9 31.2 - - + -
214B LEU* 5.3 4.0 - - + -
217B LEU* 3.6 35.2 - - + -
257B LYS 2.9 18.0 + - - +
258B PHE* 3.7 6.5 - + - +
260B SER* 1.3 76.8 - - - +
262B MET* 1.3 65.7 + - - +
264B LYS* 3.3 10.5 + - + +
265B MET* 3.1 53.6 + - + +
312B LEU* 5.9 1.8 - - + -
315B PHE* 4.3 13.9 - + - -
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Residues in contact with MET 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE* 5.2 5.8 - - + -
258B PHE 3.0 14.6 + - - +
259B TYR* 3.5 45.5 - - + +
260B SER 3.2 0.2 - - - -
261B PHE* 1.3 81.5 - - - +
263B GLN* 1.3 76.1 + - + +
265B MET* 3.1 7.1 + - - +
266B VAL* 2.9 38.2 + - + +
305B GLU* 6.0 1.3 - - + -
308B ILE* 4.4 11.4 - - + +
309B ASN* 3.5 34.3 - - + +
311B VAL* 4.2 13.0 - - + -
312B LEU* 4.2 19.3 - - + -
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Residues in contact with GLN 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 3.0 40.4 + - + +
260B SER* 3.2 13.8 + - - +
262B MET* 1.3 86.4 - - + +
264B LYS* 1.3 63.5 + - - +
266B VAL* 3.1 6.1 + - - +
267B LYS* 2.9 52.3 + - - +
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Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ARG* 4.7 13.8 - - - +
213B GLU* 2.9 41.2 + - - +
260B SER 3.0 12.5 + - - +
261B PHE* 3.6 15.7 - - + +
262B MET 3.3 0.2 - - - -
263B GLN* 1.3 76.2 - - - +
265B MET* 1.3 60.9 + - - +
267B LYS* 3.9 7.5 - - - +
268B GLU* 3.1 56.8 + - + +
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Residues in contact with MET 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B CYS* 5.3 0.4 - - - -
203B PHE* 3.2 56.8 - - + +
205B ARG* 3.8 41.7 - - + +
207B TYR* 4.0 3.1 - - - +
261B PHE* 3.1 48.2 + - + +
262B MET 3.1 3.3 + - - +
264B LYS* 1.3 80.9 - - - +
266B VAL* 1.3 58.2 + - - +
268B GLU* 3.7 10.6 + - - +
269B HIS* 2.5 43.7 + - + -
282B THR* 5.1 0.7 - - - -
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Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE* 5.6 1.1 - - + -
262B MET* 2.9 31.4 + - + +
263B GLN* 3.8 5.6 - - - +
265B MET* 1.3 77.2 - - + +
267B LYS* 1.3 65.9 + - + +
269B HIS* 3.2 3.2 + - - +
270B TYR* 3.0 22.8 + - + +
282B THR* 4.3 16.4 - - + +
286B ILE* 4.1 14.6 - - + +
308B ILE* 3.6 37.9 - - + -
311B VAL* 5.1 4.5 - - + -
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Residues in contact with LYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLN* 2.9 46.9 + - - +
264B LYS* 3.9 5.8 - - - +
266B VAL* 1.3 77.0 - - + +
268B GLU* 1.3 62.2 + - + +
270B TYR* 3.1 8.0 + - - +
271B LYS* 3.1 23.8 + - - +
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Residues in contact with GLU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ARG* 3.4 22.5 + - - -
264B LYS* 3.1 48.8 + - + +
265B MET* 3.9 14.3 - - - +
267B LYS* 1.3 76.2 - - + +
269B HIS* 1.3 64.4 + - + +
271B LYS* 3.6 6.0 + - - +
272B THR* 3.0 31.9 + - + +
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Residues in contact with HIS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE* 3.3 32.4 + + + -
265B MET* 2.5 39.2 + - + +
266B VAL 3.7 4.7 - - - +
267B LYS 3.1 0.8 - - - -
268B GLU* 1.3 79.5 - - + +
270B TYR* 1.3 65.7 + - - +
272B THR* 3.4 2.4 + - - -
273B PHE* 3.0 26.7 + - - +
279B ARG* 3.5 16.7 + - - +
280B ASP* 2.7 32.8 + - - -
282B THR* 3.6 10.2 - - + -
283B ASP* 3.3 20.9 - - - +
286B ILE* 3.7 17.0 - - + -
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Residues in contact with TYR 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B VAL* 3.0 13.9 + - + +
267B LYS* 3.1 9.8 + - - +
269B HIS* 1.3 78.1 - - - +
271B LYS* 1.3 64.4 + - - +
272B THR 3.2 0.7 + - - -
273B PHE* 3.3 18.4 + + + +
286B ILE* 4.1 23.9 - - + +
290B GLN* 3.7 26.9 + - + +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LYS 3.1 15.0 + - - +
268B GLU* 3.9 8.1 - - - +
269B HIS 3.3 0.2 - - - -
270B TYR* 1.3 77.6 - - - +
272B THR* 1.3 67.0 + - + +
273B PHE 3.8 0.9 + - - +
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Residues in contact with THR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLU* 3.0 19.0 + - + +
269B HIS* 3.4 1.6 + - - -
270B TYR 3.2 0.6 - - - -
271B LYS* 1.3 90.1 - - + +
273B PHE* 1.3 62.5 + - - +
274B GLU* 3.5 5.0 + - - +
279B ARG* 3.1 34.8 + - - -
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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
------------------------------------------------------------
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