Contacts of the helix formed by residues 260 - 285 (chain G) in PDB entry 5MGX
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 THR 260 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258G ASP 6.0 0.2 - - - +
259G MET* 1.3 76.1 - - - +
261G PHE* 1.3 64.1 + - - +
262G GLU* 3.8 16.4 + - - +
263G GLU* 2.8 42.9 + - - +
264G GLU* 3.1 22.2 + - - +
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Residues in contact with PHE 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260G THR* 1.3 73.7 - - - +
262G GLU* 1.3 78.0 + - + +
264G GLU* 3.2 13.1 + - + +
265G ALA* 3.0 42.7 + - + +
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Residues in contact with GLU 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G THR* 3.8 13.9 - - - +
261G PHE* 1.3 99.6 + - + +
263G GLU* 1.3 56.6 + - + +
265G ALA* 3.7 5.4 + - - +
266G GLN* 3.1 29.5 + - - +
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Residues in contact with GLU 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G GLY* 3.8 21.4 + - - -
215G GLN* 3.7 19.3 + - - +
218G VAL* 5.0 1.7 - - + +
259G MET* 3.3 17.9 - - + +
260G THR* 2.8 46.5 + - - +
261G PHE 3.2 0.6 - - - -
262G GLU* 1.3 76.7 - - + +
264G GLU* 1.3 58.3 + - - +
266G GLN* 3.4 13.4 + - - +
267G LEU* 3.0 37.4 + - + +
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Residues in contact with GLU 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254G SER* 5.0 2.3 + - - -
257G VAL 5.4 0.7 - - - +
259G MET* 3.1 40.9 + - + +
260G THR 3.1 20.4 + - - +
261G PHE* 3.2 14.6 + - + +
263G GLU* 1.3 75.5 - - - +
265G ALA* 1.4 55.0 + - - +
267G LEU* 3.3 9.6 + - - +
268G LEU* 2.9 38.4 + - + +
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Residues in contact with ALA 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G PHE* 3.0 33.6 + - + +
262G GLU* 3.9 7.2 - - - +
264G GLU* 1.4 71.2 - - - +
266G GLN* 1.4 60.3 + - - +
268G LEU* 3.2 13.4 + - - +
269G GLN* 3.0 34.3 + - + +
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Residues in contact with GLN 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G VAL* 3.9 36.0 - - + +
262G GLU 3.1 19.6 + - - +
263G GLU* 3.4 13.0 + - - +
265G ALA* 1.4 74.3 - - - +
267G LEU* 1.3 61.7 + - - +
269G GLN* 3.5 10.1 + - - +
270G LEU* 3.3 22.0 + - - +
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Residues in contact with LEU 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G GLY* 4.2 8.1 - - - +
217G ARG* 3.9 38.8 - - + +
218G VAL* 3.9 14.4 - - + -
251G ILE* 3.6 42.8 - - + +
259G MET* 3.7 30.7 - - + -
263G GLU 3.0 21.9 + - - +
264G GLU* 3.7 6.1 - - - +
266G GLN* 1.3 73.4 - - - +
268G LEU* 1.4 59.9 + - - +
269G GLN 3.4 0.2 - - - -
270G LEU* 3.4 9.8 + - + +
271G LYS* 3.0 28.2 + - - +
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Residues in contact with LEU 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264G GLU* 2.9 21.0 + - + +
265G ALA* 3.2 15.9 + - - +
267G LEU* 1.4 72.5 - - - +
269G GLN* 1.3 70.6 + - - +
271G LYS* 3.3 21.1 + - - +
272G VAL* 3.2 31.2 + - + +
301G HIS* 3.6 33.9 - - + +
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Residues in contact with GLN 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G ALA* 3.0 19.3 + - + +
266G GLN* 3.6 11.2 - - - +
268G LEU* 1.3 80.4 - - - +
270G LEU* 1.3 59.0 + - - +
272G VAL* 3.8 6.5 + - - +
273G LYS* 3.3 32.8 + - - +
302G GLN* 3.6 26.4 + - - +
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Residues in contact with LEU 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G VAL* 3.8 15.9 - - + +
221G ALA* 3.7 26.2 - - + -
222G ASN* 3.5 40.6 - - - +
225G ARG* 4.1 15.3 - - - +
251G ILE* 4.0 10.1 - - + -
266G GLN* 3.3 10.4 + - + +
267G LEU* 3.5 14.1 - - + +
268G LEU 3.2 0.2 - - - -
269G GLN* 1.3 79.1 - - - +
271G LYS* 1.3 58.9 + - - +
273G LYS* 3.3 12.5 + - + +
274G CYS* 3.0 36.5 + - - -
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Residues in contact with LYS 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G ILE* 4.9 9.0 - - + -
251G ILE* 3.7 23.1 - - + +
252G THR* 3.9 29.4 - - + +
267G LEU 3.0 17.7 + - - +
268G LEU* 3.3 27.6 + - + +
270G LEU* 1.3 75.7 - - - +
272G VAL* 1.4 52.2 + - + +
274G CYS* 3.3 4.7 + - - +
275G LEU* 2.8 54.1 + - + +
301G HIS* 4.6 14.8 + - - -
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Residues in contact with VAL 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G LEU 3.2 18.1 + - - +
269G GLN* 4.0 7.0 - - - +
270G LEU 3.4 0.2 - - - -
271G LYS* 1.4 72.6 - - + +
273G LYS* 1.3 61.9 + - + +
275G LEU* 3.4 7.1 + - + -
276G ASN* 3.0 32.0 + - - +
298G VAL* 3.5 34.3 - - + +
301G HIS* 3.8 34.3 - - + +
302G GLN* 3.8 31.9 - - - +
305G ASN* 4.5 2.2 - - - +
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Residues in contact with LYS 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B ASP* 3.8 41.4 + - + +
225G ARG* 4.7 11.0 - - - +
269G GLN* 3.3 20.1 + - - +
270G LEU* 3.3 20.7 + - + +
272G VAL* 1.3 79.0 - - + +
274G CYS* 1.4 56.1 + - - +
276G ASN* 3.5 5.4 + - - +
277G ASN* 3.0 36.7 + - - +
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Residues in contact with CYS 274 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G ALA 4.7 0.4 - - - -
225G ARG* 3.9 25.8 - - - -
244G TYR* 3.8 12.0 - - + +
247G ALA* 3.8 24.0 - - - -
248G ILE* 3.8 20.6 - - + -
251G ILE* 4.5 7.4 - - - -
270G LEU* 3.0 30.3 + - - +
271G LYS* 3.7 5.2 - - - +
273G LYS* 1.4 73.0 - - - +
275G LEU* 1.4 54.6 + - - +
277G ASN* 3.4 9.2 + - - +
278G LEU* 2.8 33.1 + - - +
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Residues in contact with LEU 275 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G ILE* 3.9 24.0 - - + -
271G LYS* 2.8 43.3 + - + +
272G VAL* 3.4 2.9 + - + -
274G CYS* 1.4 69.4 - - - +
276G ASN* 1.3 60.5 + - - +
278G LEU* 3.4 8.5 + - + +
279G ALA* 3.0 21.5 + - - +
294G SER* 3.5 27.9 - - - +
297G LEU* 4.0 39.5 - - + +
298G VAL* 3.6 18.4 - - + +
301G HIS* 5.7 4.5 - - + +
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Residues in contact with ASN 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B ASP* 4.4 11.5 + - - +
272G VAL* 3.0 17.8 + - - +
273G LYS* 3.8 7.0 - - - +
275G LEU* 1.3 75.4 - - - +
277G ASN* 1.4 58.2 + - - +
279G ALA* 3.3 8.2 - - - +
280G ALA 3.1 16.3 + - - -
295G CYS* 6.0 0.2 - - - -
298G VAL* 3.6 14.3 - - + +
305G ASN* 2.9 40.8 + - - +
307G LYS* 3.9 5.1 - - - +
308G ALA* 3.6 18.2 + - - +
311G ARG* 2.9 44.0 + - - +
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Residues in contact with ASN 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B VAL* 3.4 15.7 - - - +
709B ASP* 2.8 48.8 + - - +
225G ARG* 4.1 7.7 - - - +
229G ASN* 3.1 17.0 + - - -
244G TYR* 3.4 25.0 - - + -
273G LYS 3.0 23.4 + - - +
274G CYS 3.5 5.4 - - - +
276G ASN* 1.4 74.1 - - - +
278G LEU* 1.4 61.2 + - - +
280G ALA* 3.4 5.4 + - - +
281G SER* 3.0 27.5 + - - -
311G ARG* 5.0 2.4 + - - -
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Residues in contact with LEU 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G ALA* 3.4 41.1 - - + +
244G TYR* 3.8 10.9 - - + -
245G ASP* 4.4 11.7 - - + +
248G ILE* 3.8 23.1 - - + -
274G CYS 2.8 16.4 + - - +
275G LEU* 3.5 12.3 - - + +
277G ASN* 1.4 74.5 - - - +
279G ALA* 1.4 57.5 + - - +
281G SER* 3.1 3.6 + - - -
282G GLN* 2.9 55.8 + - - +
294G SER* 3.9 11.2 - - - +
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Residues in contact with ALA 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G LEU 3.0 14.3 + - - +
276G ASN* 3.3 17.7 - - - +
277G ASN 3.3 0.4 - - - -
278G LEU* 1.4 73.4 - - - +
280G ALA* 1.3 63.7 + - - +
282G GLN* 3.5 9.7 + - - -
283G LEU* 3.1 27.6 + - - +
291G ALA* 4.0 6.2 - - - +
294G SER* 3.9 8.7 - - - -
295G CYS* 3.8 29.8 - - - +
311G ARG* 4.6 5.3 - - - +
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Residues in contact with ALA 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708B VAL* 4.9 2.2 - - + -
232G TYR* 3.6 27.3 + - + +
276G ASN 3.1 7.6 + - - +
277G ASN* 3.6 11.2 - - - +
278G LEU 3.4 0.2 - - - -
279G ALA* 1.3 76.7 - - - +
281G SER* 1.3 57.6 + - - +
283G LEU* 4.1 5.7 - - - +
284G LYS* 3.3 30.1 + - - +
311G ARG* 3.5 37.6 - - - +
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Residues in contact with SER 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232G TYR* 3.5 16.8 - - - -
237G PHE* 3.8 22.7 - - - +
240G ALA* 3.7 4.2 - - - +
241G ALA* 4.0 13.5 - - - -
244G TYR* 3.4 16.5 - - - -
277G ASN 3.0 13.2 + - - -
278G LEU* 3.1 8.7 + - - -
280G ALA* 1.3 74.8 - - - +
282G GLN* 1.3 63.9 + - - +
284G LYS* 3.3 13.5 + - - +
285G LEU* 3.4 18.8 + - - +
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Residues in contact with GLN 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G ALA* 5.0 5.8 - - + -
278G LEU* 2.9 48.2 + - + +
281G SER* 1.3 68.6 - - - +
283G LEU* 1.3 58.6 + - - +
285G LEU* 3.0 20.3 + - + +
287G HIS* 2.9 39.1 + - + +
290G ALA* 3.4 24.9 + - + +
291G ALA* 3.5 23.3 - - + -
294G SER* 2.7 27.6 + - - -
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Residues in contact with LEU 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B GLU* 5.6 0.9 - - - +
279G ALA 3.1 18.4 + - - +
280G ALA* 4.1 6.3 - - - +
282G GLN* 1.3 73.6 - - - +
284G LYS* 1.3 73.7 + - - +
286G ASP* 3.2 18.5 + - - +
287G HIS 4.9 1.3 - - - +
288G TYR* 4.2 5.6 - - + -
291G ALA* 3.9 5.7 - - - +
310G PHE* 5.9 0.2 - - + -
311G ARG* 4.1 33.0 - - + +
314G LYS* 4.0 24.7 - - + +
315G VAL* 3.5 28.9 - - + +
318G GLN* 3.6 29.3 - - - +
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Residues in contact with LYS 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B GLU* 3.0 38.1 + - - +
352E LYS* 3.8 15.8 + - - -
232G TYR* 4.5 7.9 + - - +
237G PHE* 3.6 47.5 - - + -
280G ALA 3.3 15.0 + - - +
281G SER 3.3 11.6 + - - +
282G GLN 3.3 0.4 - - - -
283G LEU* 1.3 86.5 - - - +
285G LEU* 1.3 59.2 + - - +
286G ASP* 3.3 3.4 + - - +
314G LYS* 4.5 7.3 - - - +
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Residues in contact with LEU 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E TYR* 4.3 1.6 + - - -
351E LYS* 4.8 3.8 - - + +
352E LYS* 3.6 45.2 - - + +
355E ALA* 4.5 13.7 - - + -
237G PHE* 3.7 38.6 - - + +
238G VAL* 3.7 28.9 - - + +
241G ALA* 4.9 6.5 - - + -
281G SER 3.4 13.2 + - - +
282G GLN* 3.0 13.4 + - + +
284G LYS* 1.3 76.7 - - - +
286G ASP* 1.3 69.3 + - - +
287G HIS* 3.1 8.4 + - + +
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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