Contacts of the helix formed by residues 343 - 365 (chain B) in PDB entry 2EZT
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 343 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B GLU 5.9 0.9 - - - -
237B LEU 5.5 1.6 - - - +
238B LYS* 4.5 10.7 + - + +
340B ARG* 5.6 9.4 - - + +
341B GLU 3.5 14.8 - - - +
342B SER* 1.3 78.5 + - - +
344B PRO* 1.4 76.2 - - - +
345B TRP* 3.5 10.9 + - - +
346B TRP* 3.2 24.6 + - - +
347B GLN* 3.0 21.6 + - - +
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Residues in contact with PRO 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B SER 4.8 1.3 - - - +
343B THR* 1.4 86.5 - - + +
345B TRP* 1.3 51.2 + - - +
347B GLN* 3.2 4.0 + - + +
348B ALA* 2.8 36.4 + - - +
589B PHE* 3.2 37.7 - - + +
590B GLY 5.9 0.2 - - - -
591B LEU* 3.9 23.6 - - + -
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Residues in contact with TRP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLU 3.8 13.9 - - - +
214B ARG* 3.5 41.1 - - + -
215B PRO* 2.9 38.3 + - + -
216B LEU* 4.0 20.9 - - + -
238B LYS 4.7 3.4 - - - -
240B PRO* 3.6 16.0 - - + +
273B ALA* 3.6 26.7 - - + -
276B GLN* 3.7 23.1 - - + -
277B ALA* 4.1 1.6 - - - -
343B THR* 3.2 8.2 + - - +
344B PRO* 1.3 77.6 - - - +
346B TRP* 1.3 55.5 + - - +
348B ALA* 3.6 1.9 + - - +
349B ASN* 2.7 60.2 + - - -
582B LEU* 4.7 2.5 - - + -
586B LEU* 4.0 21.3 - - + -
591B LEU* 3.7 12.6 - - + +
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Residues in contact with TRP 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B SER* 3.7 23.8 - - - -
235B LYS* 4.4 5.6 - - + -
238B LYS* 3.3 57.6 - - + +
239B ILE 3.6 4.3 - - - -
240B PRO* 4.1 9.2 - - + -
255B TYR* 3.5 22.9 - + - -
257B ALA* 3.3 26.9 - - + -
342B SER* 3.6 23.3 - - - -
343B THR* 3.2 16.9 + - - +
345B TRP* 1.3 79.3 - - - +
347B GLN* 1.3 66.7 + - - +
349B ASN* 3.4 5.3 + - - +
350B LEU* 3.0 57.3 + - + +
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Residues in contact with GLN 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B SER* 3.0 33.6 + - - +
343B THR 3.0 14.1 + - - +
344B PRO* 3.8 4.0 - - + +
346B TRP* 1.3 86.0 - - - +
348B ALA* 1.3 62.6 + - - +
350B LEU* 3.5 19.2 + - - +
351B ALA* 3.1 26.2 + - - +
589B PHE* 3.6 35.9 - - + -
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B PRO 2.8 22.1 + - - +
345B TRP 3.8 4.3 - - - +
347B GLN* 1.3 73.5 - - - +
349B ASN* 1.3 57.4 + - - +
351B ALA* 3.4 2.9 + - - +
352B ASN* 2.9 28.9 + - - +
582B LEU* 4.3 3.4 - - + -
585B TYR* 3.6 33.1 - - + +
586B LEU* 3.8 23.3 - - + +
589B PHE* 3.6 9.9 - - + -
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Residues in contact with ASN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PRO* 3.8 21.5 - - + +
257B ALA* 6.2 2.2 - - + -
259B LEU* 4.0 12.8 - - + +
269B PRO 4.7 1.0 - - - +
273B ALA* 3.4 26.2 - - - +
345B TRP* 2.7 61.3 + - - +
346B TRP 3.8 3.8 - - - +
347B GLN 3.4 0.2 - - - -
348B ALA* 1.3 76.8 - - - +
350B LEU* 1.3 56.8 + - + +
352B ASN* 3.2 7.8 + - - +
353B VAL* 2.9 35.4 + - - +
582B LEU* 4.4 10.7 - - - +
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Residues in contact with LEU 350 (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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256B PRO* 3.5 39.9 - - + +
257B ALA* 3.9 16.4 - - + +
346B TRP* 3.0 55.0 + - + +
347B GLN* 3.8 25.4 - - - +
349B ASN* 1.3 75.8 - - - +
351B ALA* 1.3 57.5 + - - +
353B VAL* 3.4 2.9 + - - +
354B LYS* 3.0 33.9 + - - +
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Residues in contact with ALA 351 (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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347B GLN 3.1 15.7 + - - +
348B ALA 3.5 4.5 - - - +
350B LEU* 1.3 79.5 - - - +
352B ASN* 1.3 61.3 + - - +
354B LYS* 3.4 10.7 + - - +
355B ASN* 3.1 24.1 + - - +
585B TYR* 3.6 27.4 - - + -
588B GLN* 5.1 0.7 - - - +
589B PHE* 4.2 12.1 - - + -
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Residues in contact with ASN 352 (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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268B LYS* 2.8 23.6 + - - +
269B PRO* 3.5 27.1 + - + +
272B GLU* 2.8 24.1 + - - +
348B ALA 2.9 17.2 + - - +
349B ASN* 3.2 7.2 + - - +
351B ALA* 1.3 73.4 - - - +
353B VAL* 1.3 64.5 + - - +
355B ASN* 3.5 2.9 + - - +
356B TRP* 3.0 22.2 + - - +
580B GLN 3.7 0.5 - - - +
582B LEU* 3.8 23.9 - - + +
585B TYR* 3.5 24.1 - - + -
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Residues in contact with VAL 353 (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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256B PRO* 3.5 20.0 - - + +
258B TYR 3.7 10.5 - - - +
259B LEU* 3.5 28.5 - - + -
269B PRO* 4.0 16.4 - - + -
349B ASN 2.9 20.0 + - - +
350B LEU 3.7 4.9 - - - +
352B ASN* 1.3 73.6 - - - +
354B LYS* 1.3 52.2 + - + +
356B TRP* 3.1 4.5 + - + +
357B ARG* 2.8 74.1 + - + +
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Residues in contact with LYS 354 (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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256B PRO* 6.6 0.4 - - + -
350B LEU* 3.0 17.6 + - + +
351B ALA* 3.4 14.6 - - - +
353B VAL* 1.3 76.6 - - + +
355B ASN* 1.3 62.6 + - - +
357B ARG* 3.4 5.9 + - - +
358B ALA* 3.0 24.1 + - - +
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Residues in contact with ASN 355 (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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268B LYS* 4.4 2.4 + - - -
351B ALA 3.1 10.1 + - - +
352B ASN 3.6 4.3 - - - +
354B LYS* 1.3 77.8 - - - +
356B TRP* 1.3 63.1 + - - +
358B ALA* 3.4 6.8 + - - +
359B TYR* 3.2 17.5 + - - +
578B ASP* 2.9 26.0 + - - +
579B LEU* 3.3 18.9 - - - +
580B GLN* 3.0 29.5 + - - +
585B TYR* 3.0 30.1 + - + +
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Residues in contact with TRP 356 (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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259B LEU 5.3 0.9 - - - -
267B GLN* 2.8 29.2 + - + +
268B LYS* 3.5 45.8 - - + -
269B PRO* 3.6 25.1 - - + -
352B ASN 3.0 13.8 + - - +
353B VAL* 3.3 8.7 - - + +
355B ASN* 1.3 77.2 + - - +
357B ARG* 1.3 72.0 + - + +
359B TYR* 3.2 29.7 + + - +
360B LEU* 3.1 41.6 + - + +
403B ARG* 3.7 44.2 - - - -
550B LEU* 4.1 15.5 - - + -
579B LEU* 3.9 12.3 - - + -
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Residues in contact with ARG 357 (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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253B ASP 2.8 25.1 + - - -
254B ARG* 3.1 25.6 + - - +
255B TYR 2.8 17.8 + - - -
256B PRO* 3.7 9.3 - - - +
258B TYR* 3.3 24.7 + - - +
353B VAL* 2.8 31.7 + - + +
354B LYS* 3.9 6.5 - - - +
355B ASN 3.3 0.2 - - - -
356B TRP* 1.3 85.5 - - + +
358B ALA* 1.3 58.6 + - - +
360B LEU* 3.5 11.7 + - + +
361B ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 358 (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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354B LYS 3.0 17.6 + - - +
355B ASN* 3.8 7.9 - - - +
356B TRP 3.3 0.2 - - - -
357B ARG* 1.3 72.8 - - - +
359B TYR* 1.3 59.0 + - - +
361B ALA* 3.4 6.1 + - - +
362B SER* 2.9 30.9 + - - -
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Residues in contact with TYR 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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355B ASN 3.2 5.6 + - - +
356B TRP* 3.2 32.1 + + - +
358B ALA* 1.3 76.1 - - - +
360B LEU* 1.3 72.2 + - + +
362B SER* 2.6 26.3 + - - -
363B LEU* 3.2 38.8 + - + +
374B TYR* 5.2 2.6 + - - -
403B ARG* 5.5 1.6 - - - -
550B LEU* 3.7 34.6 + - + +
574B TYR* 2.5 31.1 + - - +
575B GLU 3.3 20.4 - - - -
576B ALA* 3.9 5.8 - - + -
578B ASP* 6.1 1.8 - - + -
579B LEU* 3.5 30.5 - - + +
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Residues in contact with LEU 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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267B GLN* 4.1 4.3 - - - +
356B TRP* 3.1 48.3 + - + +
357B ARG* 3.8 12.1 - - + +
358B ALA 3.4 0.2 - - - -
359B TYR* 1.3 94.0 - - + +
361B ALA* 1.3 57.5 + - - +
363B LEU* 3.3 9.4 + - + +
364B GLU* 3.0 36.2 + - - +
403B ARG* 3.7 37.0 - - + +
404B HIS* 3.9 24.2 - - + +
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG 2.9 19.3 + - - +
358B ALA* 3.7 8.1 - - - +
359B TYR 3.3 0.2 - - - -
360B LEU* 1.3 77.9 - - - +
362B SER* 1.3 56.9 + - - +
364B GLU* 3.2 13.1 + - - +
365B ASP* 2.8 48.1 + - - +
406B LYS* 6.4 0.4 - - - +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ALA 2.9 13.8 + - - -
359B TYR* 2.6 27.9 + - - -
361B ALA* 1.3 77.4 - - - +
363B LEU* 1.3 66.1 + - - +
365B ASP* 3.6 9.9 + - - +
366B LYS* 3.6 17.1 + - - +
575B GLU 5.1 2.8 + - - -
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Residues in contact with LEU 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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359B TYR* 3.2 48.1 + - + +
360B LEU* 3.5 15.3 - - + +
362B SER* 1.3 83.3 + - - +
364B GLU* 1.3 64.3 + - - +
365B ASP 3.4 0.5 + - - -
366B LYS* 3.6 10.0 - - - +
374B TYR* 3.6 49.8 - - + -
375B GLN* 2.9 26.5 + - - +
404B HIS* 4.6 0.9 - - + -
575B GLU* 4.0 39.0 - - + +
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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
----------------------------------------------------------
360B LEU* 3.0 25.8 + - - +
361B ALA* 3.2 10.8 + - - +
363B LEU* 1.3 76.5 - - - +
365B ASP* 1.3 68.0 + - - +
366B LYS 3.4 1.2 + - - -
374B TYR 3.6 19.3 - - - +
375B GLN* 3.7 4.9 - - - +
378B ARG* 3.2 45.9 + - + +
381B ASN* 4.7 5.8 + - - -
403B ARG 5.1 0.3 - - - +
404B HIS* 2.7 44.6 + - + +
406B LYS* 3.6 23.0 + - - -
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Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ALA* 2.8 38.5 + - - +
362B SER* 3.6 5.1 + - - +
363B LEU 3.2 0.6 - - - -
364B GLU* 1.3 80.0 - - - +
366B LYS* 1.3 66.0 + - - +
367B GLN* 3.3 23.6 + - - +
378B ARG* 5.0 6.6 + - - +
382B LYS* 5.8 1.9 + - - -
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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