Contacts of the helix formed by residues 363 - 383 (chain B) in PDB entry 6A5T
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 PHE 363 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B THR* 3.4 34.7 - - + +
360B GLU* 2.9 48.9 - - + +
361B GLU* 3.1 8.5 - - - +
362B GLY* 1.3 86.9 - - - +
364B GLU* 1.3 62.5 + - - +
365B THR* 3.3 6.7 - - - +
366B ARG* 2.9 48.1 + - + -
367B LYS* 3.8 13.4 - - - +
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 3.3 36.3 - - + +
282B GLY* 5.1 4.6 - - - -
361B GLU* 5.7 0.7 - - - +
362B GLY* 3.6 11.2 + - - -
363B PHE* 1.3 81.1 + - - +
365B THR* 1.3 76.5 + - + +
366B ARG 3.2 0.7 - - - -
367B LYS* 3.3 13.6 + - + +
368B THR* 2.9 28.5 + - + +
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Residues in contact with THR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLY 4.7 6.9 + - - +
363B PHE* 4.4 7.1 - - - -
364B GLU* 1.3 90.0 - - + +
366B ARG* 1.3 76.1 + - - +
368B THR* 2.2 27.2 + - - -
369B PHE* 3.0 28.7 + - - -
559B LEU* 5.8 0.7 - - - +
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Residues in contact with ARG 366 (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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357B ILE* 3.6 30.5 - - + -
358B THR* 4.7 5.7 - - + +
363B PHE* 2.9 48.2 + - + +
364B GLU 3.2 0.6 - - - -
365B THR* 1.3 83.9 + - - +
367B LYS* 1.3 67.4 + - - +
369B PHE* 3.4 1.7 + - - +
370B PHE* 3.0 25.0 + - + +
558B PRO* 5.9 1.4 - - - +
559B LEU* 3.4 44.4 - - + +
560B GLU* 4.9 7.7 + - - -
578B VAL* 4.7 4.9 - - - -
579B TRP 4.3 10.5 - - - +
580B THR* 4.4 11.7 + - - +
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Residues in contact with LYS 367 (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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281B LEU* 5.1 13.2 - - + -
349B LEU 3.5 17.9 + - - +
350B GLN* 2.9 31.1 + - - +
353B LEU 4.1 8.2 + - - +
354B LEU* 3.5 45.5 - - + +
357B ILE* 4.2 8.9 - - + +
358B THR* 3.4 26.9 + - + -
359B GLN* 5.3 0.6 - - - +
360B GLU 5.1 5.1 + - - -
361B GLU* 5.7 3.6 - - - +
363B PHE 3.8 15.5 - - - +
364B GLU* 3.3 13.6 + - + +
366B ARG* 1.3 78.3 - - - +
368B THR* 1.3 62.6 + - - +
370B PHE* 3.4 0.5 + - - -
371B LEU* 3.0 21.4 + - - +
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 4.4 10.6 - - + -
281B LEU* 4.2 30.7 - - + +
282B GLY 5.7 0.2 - - - -
283B VAL* 4.9 18.6 - - + +
292B HIS* 4.3 15.2 + - - -
364B GLU* 2.9 19.3 + - + +
365B THR* 2.2 34.6 + - - -
367B LYS* 1.3 72.8 - - - +
369B PHE* 1.3 72.1 + - - +
371B LEU* 2.8 22.8 + - - +
372B GLY* 2.9 10.0 + - - -
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Residues in contact with PHE 369 (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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292B HIS* 3.1 50.7 - + + -
295B TYR* 5.0 1.8 + - - -
365B THR* 3.0 31.8 + - - +
366B ARG 4.1 2.2 - - - +
368B THR* 1.3 83.3 + - - +
370B PHE* 1.3 57.6 + - - +
372B GLY* 3.0 3.9 + - - +
373B TYR 3.0 22.7 + - - -
559B LEU* 4.5 28.3 - - + -
560B GLU* 5.6 4.3 - - - -
562B TYR* 3.9 34.8 - + + -
564B PRO* 5.4 2.5 - - + -
579B TRP* 3.8 38.4 - + + -
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Residues in contact with PHE 370 (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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213B ILE* 6.2 0.2 - - - -
214B VAL* 3.9 27.6 - - + -
231B ILE* 4.1 14.6 - - + -
354B LEU* 4.2 13.0 - - + -
356B HIS* 5.5 1.6 - + - -
357B ILE* 3.8 25.4 - - + -
366B ARG* 3.0 16.2 + - + +
367B LYS 3.8 1.3 - - - +
368B THR 2.9 1.4 + - - -
369B PHE* 1.3 75.8 - - - +
371B LEU* 1.3 72.1 + - - +
373B TYR* 3.2 15.1 + + + +
374B MET* 3.0 42.6 + - + +
574B PHE* 5.1 7.4 - + - -
577B GLY* 4.1 25.1 - - - -
578B VAL* 5.3 0.4 - - - -
579B TRP* 4.7 22.0 - - + -
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Residues in contact with LEU 371 (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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245B MET* 3.6 31.6 - - + -
247B ILE* 4.7 10.1 - - + -
274B ILE* 6.3 1.3 - - + -
277B VAL* 4.8 11.9 - - + -
278B PHE* 3.4 36.3 - - + -
281B LEU* 4.4 19.7 - - + -
353B LEU* 6.4 2.0 - - + -
354B LEU* 4.0 15.3 - - + -
367B LYS 3.0 18.0 + - - +
368B THR* 2.8 10.3 + - + +
370B PHE* 1.3 76.5 - - - +
372B GLY* 1.3 54.4 + - - +
374B MET* 2.4 30.7 + - - +
375B VAL* 2.9 12.2 + - + +
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Residues in contact with GLY 372 (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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278B PHE* 4.5 3.3 - - - -
292B HIS* 4.6 11.0 - - - -
293B ILE* 4.1 24.3 - - - +
295B TYR* 4.7 6.3 - - - -
368B THR 2.9 12.7 + - - -
369B PHE* 3.0 6.9 + - - -
371B LEU* 1.3 74.7 - - - +
373B TYR* 1.3 62.8 + - - +
375B VAL* 3.4 2.7 + - - +
376B ASN* 2.9 24.8 + - - +
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Residues in contact with TYR 373 (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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214B VAL* 3.6 38.3 - - + +
295B TYR* 4.8 6.1 + + - +
369B PHE 3.0 10.8 + - - +
370B PHE* 3.5 19.7 - + + +
371B LEU 3.0 0.2 - - - -
372B GLY* 1.3 78.5 - - - +
374B MET* 1.3 67.1 + - - +
376B ASN* 3.2 9.6 + - + +
377B ARG* 2.2 68.2 + - + +
572B ARG* 4.3 31.0 - - - -
574B PHE* 4.6 15.7 - + - -
579B TRP* 5.1 11.2 - + + -
614B GLU* 5.6 0.2 + - - -
616B GLU* 2.8 20.3 + - - -
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Residues in contact with MET 374 (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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214B VAL* 3.9 22.7 - - + -
229B ALA* 4.3 15.5 - - + +
230B GLU 5.2 0.4 - - - -
231B ILE* 3.4 40.6 - - + +
245B MET* 3.5 31.4 - - + +
247B ILE* 4.3 16.4 - - + -
354B LEU* 4.9 1.3 - - + -
370B PHE* 3.0 41.1 + - + +
371B LEU* 2.4 25.7 + - - +
373B TYR* 1.3 73.8 - - - +
375B VAL* 1.3 57.0 + - - +
377B ARG* 3.2 2.6 + - - +
378B LEU* 2.9 28.1 + - - +
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Residues in contact with VAL 375 (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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247B ILE* 4.9 13.7 - - + -
261B ILE* 4.8 20.0 - - + -
274B ILE* 4.8 7.9 - - + -
278B PHE* 4.1 25.4 - - + -
293B ILE* 3.5 33.9 - - + -
306B LEU* 5.5 2.2 - - + -
371B LEU* 2.9 12.1 + - + +
372B GLY 3.9 3.4 - - - +
374B MET* 1.3 74.1 - - - +
376B ASN* 1.3 66.6 + - - +
378B LEU* 2.9 7.9 + - + +
379B LEU* 2.9 36.3 + - + +
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Residues in contact with ASN 376 (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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293B ILE* 4.5 15.2 - - + +
295B TYR* 3.1 38.5 - - + +
302B MET* 4.0 15.8 - - - +
372B GLY 2.9 18.3 + - - +
373B TYR* 3.6 10.8 - - + +
375B VAL* 1.3 77.7 - - - +
377B ARG* 1.3 58.3 + - - +
379B LEU* 3.4 4.6 + - - +
380B LEU* 2.9 44.2 + - - +
572B ARG* 4.5 9.7 - - - +
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Residues in contact with ARG 377 (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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214B VAL* 3.1 33.2 + - + -
216B VAL* 3.4 25.5 - - + +
229B ALA* 5.9 0.2 - - + -
373B TYR* 2.2 58.7 + - + +
374B MET 3.6 4.3 - - - +
376B ASN* 1.3 76.7 - - - +
378B LEU* 1.3 67.3 + - - +
380B LEU* 3.1 8.7 + - + +
381B CYS* 3.0 22.5 + - + +
386B LYS* 3.2 33.0 - - + +
389B ASP* 2.7 24.5 + - - -
614B GLU* 5.2 4.9 + - - +
616B GLU* 3.8 8.5 + - - -
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Residues in contact with LEU 378 (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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216B VAL* 4.4 8.1 - - + -
227B HIS* 3.4 44.6 - - + +
228B VAL 4.1 1.6 - - - +
229B ALA* 4.0 20.1 - - + +
247B ILE* 3.7 28.7 - - + -
249B LEU* 4.1 20.4 - - + +
261B ILE* 4.4 10.1 - - + -
374B MET 2.9 16.4 + - - +
375B VAL* 2.9 7.6 + - + +
377B ARG* 1.3 76.4 - - - +
379B LEU* 1.3 61.0 + - + +
381B CYS* 3.3 1.4 + - - -
382B ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 379 (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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249B LEU* 5.4 6.5 - - + -
261B ILE* 4.9 13.7 - - + -
293B ILE* 4.8 4.9 - - + -
302B MET* 3.8 40.4 - - + +
305B MET* 4.8 25.6 - - + -
306B LEU* 4.7 16.6 - - + -
375B VAL* 2.9 34.0 + - + +
376B ASN* 3.8 4.3 - - - +
378B LEU* 1.3 77.5 - - + +
380B LEU* 1.3 62.0 + - - +
381B CYS 3.0 5.7 + - - -
382B ALA* 4.3 4.9 - - + +
383B LEU* 3.3 37.5 + - + +
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Residues in contact with LEU 380 (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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299B ASP* 5.1 0.7 - - - +
302B MET* 4.6 13.0 - - + -
376B ASN* 2.9 40.8 + - - +
377B ARG* 3.1 7.8 + - + +
379B LEU* 1.3 77.0 - - - +
381B CYS* 1.3 57.1 + - - +
383B LEU* 4.5 1.3 - - + -
385B ARG* 3.5 34.9 + - + +
386B LYS* 3.2 44.7 + - + +
572B ARG* 6.4 0.4 - - - +
614B GLU* 4.9 11.9 - - - +
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Residues in contact with CYS 381 (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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216B VAL* 3.4 31.4 - - + -
227B HIS* 2.7 36.9 + - + -
377B ARG* 3.0 10.2 + - + +
378B LEU 4.1 1.1 - - - +
379B LEU 3.0 0.8 - - - -
380B LEU* 1.3 79.2 - - - +
382B ALA* 1.3 64.1 + - - +
383B LEU 3.3 1.3 - - - -
384B GLU* 3.5 10.0 + - - +
386B LYS* 3.7 14.8 - - + +
387B ASP 4.2 2.2 - - - +
388B GLN* 3.7 29.2 - - - -
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Residues in contact with ALA 382 (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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226B SER* 4.3 1.1 - - - +
227B HIS* 3.3 29.7 - - + +
249B LEU* 3.7 24.9 - - + -
305B MET* 5.2 6.5 - - + -
378B LEU 2.9 16.9 + - - +
379B LEU* 3.4 6.5 + - + +
381B CYS* 1.3 79.9 - - - +
383B LEU* 1.3 62.9 + - + +
384B GLU* 3.1 9.3 + - - +
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Residues in contact with LEU 383 (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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301B GLN* 4.6 17.3 - - + +
302B MET* 4.7 11.2 - - + +
305B MET* 4.3 27.6 - - + -
379B LEU* 3.3 26.3 + - + +
380B LEU* 5.5 0.9 - - + -
382B ALA* 1.3 78.0 - - + +
384B GLU* 1.3 67.2 + - - +
385B ARG* 3.0 59.2 + - + +
90I GLN* 4.8 4.7 + - - -
92I ARG* 5.9 0.3 - - - +
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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
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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