Contacts of the helix formed by residues 358 - 378 (chain B) in PDB entry 3BRW
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 GLY 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B PHE* 3.8 11.6 - - - -
356B ARG 4.4 0.2 - - - -
357B LYS* 1.3 82.8 - - - +
359B PRO* 1.4 77.7 - - - -
360B GLU* 2.7 8.7 + - - +
361B PHE* 3.0 13.5 + - - -
362B GLN* 3.6 6.5 + - - -
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Residues in contact with PRO 359 (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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358B GLY* 1.4 80.5 - - - +
360B GLU* 1.3 65.7 + - - +
361B PHE 3.2 1.0 + - - -
362B GLN* 3.6 14.9 + - + +
363B GLU* 3.3 22.7 + - - +
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Residues in contact with GLU 360 (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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355B PHE* 4.9 14.4 - - + -
356B ARG 5.1 5.8 - - - +
357B LYS 6.1 0.2 - - - +
358B GLY* 2.7 7.8 + - - +
359B PRO* 1.3 78.8 - - - +
361B PHE* 1.3 63.5 + - + +
363B GLU* 3.8 13.1 - - - +
364B PHE* 4.0 5.4 + - - +
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Residues in contact with PHE 361 (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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223B PHE* 4.8 1.8 - + - -
226B PHE* 3.2 41.7 - + - -
320B VAL* 4.6 6.7 - - + -
332B TYR* 4.0 23.1 - + + -
334B VAL* 3.9 21.3 - - + -
355B PHE* 3.2 55.4 - + + -
356B ARG 3.5 20.9 - - - +
358B GLY 3.0 5.8 + - - +
360B GLU* 1.3 73.6 - - + +
362B GLN* 1.3 66.4 + - - +
363B GLU 3.1 2.2 - - - -
364B PHE* 2.9 21.6 + + - +
365B LEU* 3.1 36.0 + - + +
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Residues in contact with GLN 362 (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 PHE* 3.6 38.5 - - + +
227B LEU* 3.6 27.7 - - + +
228B GLY* 5.0 2.1 - - - -
257B CYS* 5.7 2.4 - - - +
259B PHE* 5.4 3.0 - - - -
358B GLY 3.6 4.8 + - - +
359B PRO* 3.8 17.8 + - + +
361B PHE* 1.3 78.3 - - - +
363B GLU* 1.3 78.6 + - - +
365B LEU* 3.3 5.3 + - - +
366B LEU* 3.1 39.0 + - + +
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Residues in contact with GLU 363 (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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79B VAL* 5.5 6.4 - - - +
259B PHE* 3.5 32.7 - - + -
260B ARG* 4.5 9.9 + - - -
359B PRO 3.3 14.8 + - - +
360B GLU* 3.8 7.1 - - - +
361B PHE 3.1 0.4 - - - -
362B GLN* 1.3 87.5 - - - +
364B PHE* 1.3 60.6 + - - +
366B LEU* 3.6 0.6 + - - -
367B THR* 3.1 33.3 + - - +
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Residues in contact with PHE 364 (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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318B VAL* 6.4 0.2 - - + -
334B VAL* 5.0 9.9 - - + -
347B PRO* 3.2 48.7 - - + -
348B PRO 3.7 12.3 - - - -
349B LEU* 4.5 16.4 - - + -
350B PRO* 5.0 0.2 - - + -
355B PHE* 4.1 37.7 - + + -
360B GLU* 4.0 3.9 + - - +
361B PHE* 2.9 21.8 + + - +
363B GLU* 1.3 76.5 - - - +
365B LEU* 1.3 73.7 + - + +
367B THR* 3.0 9.4 + - - -
368B LYS* 2.8 48.8 + - + +
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Residues in contact with LEU 365 (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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223B PHE* 4.4 18.6 - - + -
226B PHE* 4.7 5.6 - - + -
227B LEU* 3.8 33.7 - - + -
295B VAL* 4.9 6.5 - - + -
318B VAL* 3.6 33.2 - - + -
320B VAL* 4.1 13.0 - - + -
334B VAL* 5.3 2.2 - - + -
361B PHE* 3.1 25.4 + - + +
362B GLN* 3.3 8.5 + - - +
364B PHE* 1.3 85.6 - - + +
366B LEU* 1.3 52.8 + - - +
368B LYS* 3.1 4.3 + - + +
369B LEU* 2.7 49.4 + - + +
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Residues in contact with LEU 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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227B LEU* 4.1 12.1 - - + +
257B CYS* 4.1 15.0 - - + -
259B PHE* 3.6 47.6 - - + -
264B ILE* 3.9 13.5 - - + -
266B PHE* 3.9 28.9 - - + -
362B GLN* 3.1 39.1 + - + +
363B GLU 4.0 1.3 - - - +
365B LEU* 1.3 75.2 - - - +
367B THR* 1.3 65.9 + - - +
369B LEU* 3.1 11.1 + - + +
370B ILE* 3.0 26.7 + - - +
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Residues in contact with THR 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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80B LYS 5.8 1.6 - - - -
81B LEU* 4.9 8.1 - - + -
259B PHE* 3.1 32.1 - - + -
260B ARG* 4.3 19.3 - - - +
347B PRO* 3.4 19.3 - - - +
363B GLU* 3.1 15.5 + - - +
364B PHE* 3.0 12.5 + - - -
366B LEU* 1.3 74.0 - - - +
368B LYS* 1.3 60.4 + - - +
370B ILE* 3.2 5.9 + - - +
371B ASN* 2.8 43.2 + - - +
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Residues in contact with LYS 368 (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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318B VAL* 4.7 9.8 - - + +
336B VAL* 3.7 35.9 - - + +
344B PHE* 5.0 4.6 - - - -
345B PHE* 3.6 37.3 + - + -
346B GLY* 3.6 16.6 - - - -
347B PRO* 3.5 28.5 + - + +
348B PRO* 4.9 2.6 - - - +
349B LEU* 4.7 11.8 - - - +
364B PHE* 2.8 37.1 + - + +
365B LEU* 3.4 6.3 - - + +
367B THR* 1.3 76.8 + - - +
369B LEU* 1.3 57.2 + - - +
371B ASN 3.8 0.3 - - - -
372B ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 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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195B PHE* 3.5 33.2 - - + -
266B PHE* 4.0 22.9 - - + -
293B VAL* 3.7 23.3 - - + +
294B ALA 4.3 1.3 - - - +
295B VAL* 3.8 32.1 - - + -
318B VAL* 3.7 19.7 - - + -
365B LEU* 2.7 33.6 + - + +
366B LEU* 3.1 15.5 + - + +
368B LYS* 1.3 74.7 - - - +
370B ILE* 1.3 61.7 + - - +
372B ALA* 3.1 18.8 - - - +
373B GLU 3.2 5.4 + - - -
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Residues in contact with ILE 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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81B LEU* 3.8 14.6 - - + -
193B PHE* 3.6 31.0 - - + -
195B PHE* 4.1 20.0 - - + -
259B PHE* 4.1 23.8 - - + -
262B LYS* 4.4 15.9 - - + -
264B ILE* 4.2 11.0 - - + -
366B LEU 3.0 14.3 + - - +
367B THR 3.7 5.6 - - - +
369B LEU* 1.3 71.9 - - - +
371B ASN* 1.3 56.8 + - - +
372B ALA 3.0 4.0 - - - -
373B GLU* 2.9 21.6 + - - +
374B TYR* 3.0 39.9 + - + +
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Residues in contact with ASN 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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80B LYS 5.3 4.0 + - - -
81B LEU* 3.1 24.8 - - - +
82B GLU* 3.2 35.0 + - - +
345B PHE* 3.4 12.7 - - - +
346B GLY* 3.2 40.8 - - - +
347B PRO* 3.8 7.1 - - - +
367B THR* 2.8 27.5 + - - +
368B LYS 3.8 1.1 - - - +
370B ILE* 1.3 71.5 - - - +
372B ALA* 1.3 57.7 + - - +
374B TYR* 3.7 8.6 + - - +
375B ALA 3.0 20.6 + - - -
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Residues in contact with ALA 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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293B VAL* 3.7 24.2 - - + -
316B ALA* 4.7 4.3 - - + -
318B VAL* 5.6 1.8 - - + -
345B PHE* 3.4 30.0 - - + -
368B LYS 3.0 14.4 + - - +
369B LEU* 3.1 12.3 - - - +
370B ILE 3.0 0.4 - - - -
371B ASN* 1.3 74.3 - - - +
373B GLU* 1.3 55.3 + - - +
375B ALA* 3.2 3.3 + - - +
376B CYS* 2.7 38.2 + - - -
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Residues in contact with GLU 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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192B ASN 4.8 2.6 - - - +
193B PHE* 3.3 30.2 - - + +
194B LYS* 4.2 8.3 + - - +
195B PHE* 3.5 19.6 - - - -
292B ILE* 3.7 25.5 - - + +
293B VAL* 3.5 11.9 - - + +
369B LEU 3.2 4.9 + - - +
370B ILE 2.9 9.4 + - - +
372B ALA* 1.3 78.3 - - - +
374B TYR* 1.3 64.1 + - - +
376B CYS* 3.1 6.7 + - - +
377B TYR* 2.9 59.1 + - + +
63D GLN* 3.6 12.6 + - - -
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Residues in contact with TYR 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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81B LEU* 4.0 11.2 - - + -
82B GLU 3.4 32.8 - - - +
83B CYS* 3.6 32.8 - - + +
84B ASN 5.6 0.2 - - - -
88B ARG* 5.8 0.5 + - - -
190B SER 4.7 4.1 + - - -
193B PHE* 3.4 25.0 - + - -
262B LYS* 3.9 19.8 + - - -
370B ILE* 3.0 41.2 + - + +
371B ASN* 3.8 10.3 - - - +
373B GLU* 1.3 75.4 - - - +
375B ALA* 1.3 62.9 + - - +
377B TYR* 3.0 43.9 + + - +
378B LYS* 3.8 11.7 + - - +
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Residues in contact with ALA 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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342B VAL* 4.6 2.5 - - + -
343B PRO* 3.2 49.5 - - + +
344B PHE 4.6 2.0 - - - +
345B PHE* 3.6 17.7 - - + -
371B ASN 3.0 19.0 + - - +
372B ALA 3.5 3.6 - - - +
374B TYR* 1.3 75.1 - - - +
376B CYS* 1.3 61.7 + - - +
378B LYS* 3.1 23.7 + - - +
379B ALA 3.8 0.9 + - - -
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Residues in contact with CYS 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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292B ILE* 3.5 26.0 - - + -
293B VAL* 4.6 0.9 - - - -
315B HIS* 3.6 28.0 - - + -
316B ALA* 3.8 19.5 - - - -
342B VAL* 3.7 18.2 - - + -
372B ALA 2.7 23.5 + - - +
373B GLU* 3.3 9.2 - - - +
375B ALA* 1.3 69.1 - - - +
377B TYR* 1.3 57.3 + - + +
378B LYS 2.9 2.9 - - - -
379B ALA* 2.7 31.9 + - - +
382B PHE* 3.4 9.1 - - + -
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Residues in contact with TYR 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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188B VAL* 5.8 11.4 - - + -
190B SER* 5.6 6.1 + - - -
192B ASN 5.6 0.3 + - - -
193B PHE* 4.1 6.6 - - - -
292B ILE* 4.0 15.7 - - + -
373B GLU* 2.9 51.2 + - + +
374B TYR* 3.0 42.6 + + - +
376B CYS* 1.3 75.5 - - - +
378B LYS* 1.3 59.3 + - + +
379B ALA 3.2 0.2 - - - -
382B PHE* 3.6 12.1 - + + +
383B ALA* 3.4 25.6 + - - +
386B GLU* 5.3 10.4 - - + +
63D GLN* 4.2 4.2 + - - -
64D PHE* 4.1 22.9 - + - -
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Residues in contact with LYS 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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82B GLU 5.5 3.8 + - - -
341B ASP 4.4 5.9 - - - +
343B PRO* 4.1 23.5 - - + +
344B PHE 5.7 1.4 + - - -
374B TYR* 4.0 8.5 + - - +
375B ALA* 3.1 28.3 + - - +
376B CYS 2.9 1.4 - - - -
377B TYR* 1.3 77.4 - - + +
379B ALA* 1.3 64.3 + - - +
380B GLU* 3.7 0.9 + - - -
383B ALA* 4.1 10.7 - - - +
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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
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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