Contacts of the helix formed by residues 343 - 365 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A GLU 5.8 1.3 - - - -
238A LYS* 4.5 7.4 + - + +
340A ARG* 5.3 13.0 - - - +
341A GLU 3.8 8.3 - - - +
342A SER* 1.3 85.1 + - - +
344A PRO* 1.3 76.0 - - + +
345A TRP* 3.7 10.2 + - - +
346A TRP* 3.1 25.9 + - - +
347A GLN* 3.0 20.9 + - - +
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Residues in contact with PRO 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A THR* 1.3 89.4 - - + +
345A TRP* 1.3 56.6 + - - +
347A GLN* 3.3 2.5 + - + +
348A ALA* 2.9 31.9 + - - +
589A PHE* 3.4 37.6 - - + +
591A LEU* 3.8 25.8 - - + -
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Residues in contact with TRP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLU 3.7 13.7 - - - +
214A ARG* 3.4 42.3 - - + -
215A PRO* 2.8 43.4 + - + -
216A LEU* 4.0 17.7 - - + -
238A LYS 5.0 1.8 - - - -
240A PRO* 3.7 14.5 - - + +
273A ALA* 3.5 27.4 - - + -
276A GLN* 3.7 21.5 - - + -
277A ALA* 4.2 1.3 - - - -
343A THR* 3.3 8.7 - - - +
344A PRO* 1.3 74.6 - - - +
346A TRP* 1.3 68.0 + - - +
348A ALA* 3.8 1.4 - - - +
349A ASN* 2.9 53.8 + - - -
582A LEU* 4.9 2.2 - - + -
586A LEU* 4.0 19.7 - - + -
591A LEU* 3.7 11.0 - - + +
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Residues in contact with TRP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A SER* 3.8 8.7 - - - -
235A LYS* 4.7 4.5 - - + -
238A LYS* 3.1 58.4 - - + +
239A ILE 3.6 11.2 - - - -
240A PRO* 3.9 11.0 - - + -
255A TYR* 3.6 14.8 - + - -
257A ALA* 3.5 32.5 - - + -
342A SER* 3.6 16.7 - - - -
343A THR* 3.1 21.0 + - - +
345A TRP* 1.3 82.0 - - - +
347A GLN* 1.3 83.2 + - - +
349A ASN* 3.4 2.6 + - - +
350A LEU* 2.9 55.6 + - + +
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Residues in contact with GLN 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A SER* 2.9 33.3 + - - +
343A THR 3.0 13.8 + - - +
344A PRO* 3.8 1.3 - - + +
346A TRP* 1.3 90.4 - - - +
348A ALA* 1.3 66.3 + - - +
350A LEU* 3.3 16.8 + - - +
351A ALA* 3.0 25.3 + - - +
589A PHE* 3.6 38.7 - - + -
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A PRO 2.9 17.0 + - - +
345A TRP 3.8 4.3 - - - +
346A TRP 3.4 0.2 - - - -
347A GLN* 1.3 76.7 - - - +
349A ASN* 1.3 58.1 + - - +
351A ALA 3.4 0.3 + - - -
352A ASN* 3.0 25.3 + - - +
582A LEU* 3.9 3.5 - - + +
585A TYR* 3.5 35.5 - - + +
586A LEU* 3.7 32.1 - - + +
589A PHE* 3.8 7.2 - - + -
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Residues in contact with ASN 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PRO* 3.9 19.5 - - + +
257A ALA* 6.3 0.9 - - + -
259A LEU* 4.0 13.5 - - + +
269A PRO 4.7 1.0 - - - +
273A ALA* 3.4 26.2 - - - +
345A TRP* 2.9 62.1 + - - +
346A TRP 3.7 3.8 - - - +
348A ALA* 1.3 77.1 - - - +
350A LEU* 1.3 64.4 + - + +
352A ASN* 3.2 7.2 + - - +
353A VAL* 3.0 30.2 + - - +
582A LEU* 4.4 9.3 - - - +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PRO* 3.7 33.5 - - + +
257A ALA* 3.8 21.3 - - + -
346A TRP* 2.9 55.4 + - + +
347A GLN* 3.6 25.1 - - - +
349A ASN* 1.3 75.1 - - - +
351A ALA* 1.3 62.0 + - - +
353A VAL* 3.5 3.1 + - - +
354A LYS* 3.1 29.3 + - + +
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLN 3.0 16.2 + - - +
348A ALA 3.7 2.9 - - - +
350A LEU* 1.3 74.8 - - - +
352A ASN* 1.3 64.6 + - - +
354A LYS* 3.3 12.0 + - + +
355A ASN* 3.1 23.2 + - - +
585A TYR* 3.6 31.7 - - + -
588A GLN* 5.1 0.9 - - - +
589A PHE* 4.6 9.2 - - + -
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Residues in contact with ASN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LYS* 3.0 22.3 + - - -
269A PRO* 3.5 26.4 + - + +
272A GLU* 2.8 24.8 + - - +
348A ALA 3.0 16.8 + - - +
349A ASN* 3.2 8.3 + - - +
351A ALA* 1.3 76.9 - - - +
353A VAL* 1.3 56.6 + - - +
355A ASN* 3.3 5.0 + - - +
356A TRP* 3.0 28.4 + - - +
580A GLN 3.8 0.7 - - - +
582A LEU* 3.7 26.3 - - + +
585A TYR* 3.7 18.9 - - + -
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Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 3.4 26.7 - - + +
257A ALA* 5.1 0.7 - - - -
258A TYR 4.0 9.2 - - - +
259A LEU* 3.4 26.9 - - + -
269A PRO* 4.0 16.4 - - + -
349A ASN 3.0 16.8 + - - +
350A LEU 3.7 2.7 - - - +
352A ASN* 1.3 73.2 - - - +
354A LYS* 1.3 66.2 + - + +
356A TRP* 3.1 3.1 + - + +
357A ARG* 2.9 64.3 + - + +
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Residues in contact with LYS 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PRO* 6.4 2.2 - - + -
350A LEU* 3.1 20.7 + - + +
351A ALA* 3.3 14.1 + - - +
353A VAL* 1.3 77.1 - - + +
355A ASN* 1.3 62.3 + - - +
357A ARG* 4.0 5.3 - - - +
358A ALA* 3.1 25.0 + - - +
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Residues in contact with ASN 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LYS* 4.6 1.4 + - - -
351A ALA 3.1 6.4 + - - +
352A ASN 3.4 10.1 - - - +
354A LYS* 1.3 78.7 - - - +
356A TRP* 1.3 62.6 + - - +
358A ALA* 3.5 6.7 + - - +
359A TYR* 3.2 16.8 + - - +
578A ASP* 2.8 26.5 + - - +
579A LEU* 3.4 17.4 - - - +
580A GLN* 2.8 31.9 + - - +
585A TYR* 3.2 28.6 + - + +
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Residues in contact with TRP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU 5.1 1.1 - - - -
267A GLN* 2.8 33.7 + - + +
268A LYS* 3.6 41.1 - - + +
269A PRO* 3.5 26.5 - - + -
352A ASN* 3.0 17.5 + - - +
353A VAL* 3.1 4.9 + - + +
355A ASN* 1.3 74.6 - - - +
357A ARG* 1.3 74.5 + - + +
359A TYR* 3.1 30.1 + + - +
360A LEU* 3.1 41.1 + - + +
403A ARG* 3.5 46.9 - - + -
550A LEU* 4.2 12.8 - - + -
579A LEU* 4.0 11.2 - - + -
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Residues in contact with ARG 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ASP 2.8 21.0 + - - -
254A ARG* 3.2 24.6 + - - +
255A TYR 2.7 23.6 + - - -
256A PRO* 3.8 9.5 - - - +
258A TYR* 3.3 22.6 + - - +
353A VAL* 2.9 35.2 + - + +
354A LYS* 4.0 5.6 - - - +
356A TRP* 1.3 87.8 - - + +
358A ALA* 1.3 52.1 + - - +
360A LEU* 3.2 10.5 + - + +
361A ALA* 2.8 36.2 + - - +
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LYS 3.1 19.6 + - - +
355A ASN* 3.7 8.1 - - - +
357A ARG* 1.3 74.5 - - - +
359A TYR* 1.3 57.8 + - - +
361A ALA* 3.8 6.6 - - - +
362A SER* 3.0 28.8 + - - -
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Residues in contact with TYR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ASN 3.2 5.4 + - - +
356A TRP* 3.1 39.0 + + - +
358A ALA* 1.3 76.8 - - - +
360A LEU* 1.3 69.7 + - + +
362A SER* 2.6 26.6 + - - -
363A LEU* 3.2 34.7 + - + +
374A TYR* 5.4 1.9 + - - -
403A ARG* 5.7 0.9 - - - -
550A LEU* 3.6 30.7 + - + +
574A TYR* 2.5 32.6 + - - +
575A GLU 3.3 21.8 - - - -
576A ALA* 3.7 7.2 - - + -
578A ASP* 6.1 5.4 - - + -
579A LEU* 3.4 30.5 - - + +
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLN* 4.1 2.7 - - - +
356A TRP* 3.1 54.1 + - + +
357A ARG* 3.8 10.1 - - + +
359A TYR* 1.3 91.2 - - + +
361A ALA* 1.3 60.1 + - - +
363A LEU* 3.2 8.9 + - + +
364A GLU* 3.0 36.9 + - - +
403A ARG* 3.6 39.9 - - + +
404A HIS* 3.9 25.6 - - + +
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ARG 2.8 18.0 + - - +
358A ALA* 3.8 8.5 - - - +
360A LEU* 1.3 75.7 - - - +
362A SER* 1.3 56.3 + - - +
364A GLU* 3.2 13.8 + - - +
365A ASP* 2.8 48.5 + - - +
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ALA 3.0 17.5 + - - -
359A TYR* 2.6 26.0 + - - -
361A ALA* 1.3 76.5 - - - +
363A LEU* 1.3 66.3 + - - +
365A ASP* 3.7 9.7 + - - +
366A LYS* 3.7 16.7 + - - +
575A GLU 4.9 3.8 + - - -
578A ASP* 6.1 1.6 - - - -
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A TYR* 3.2 41.0 + - + +
360A LEU* 3.4 10.1 - - + +
361A ALA 3.2 0.2 - - - -
362A SER* 1.3 85.5 + - - +
364A GLU* 1.3 59.4 + - - +
365A ASP 3.5 0.3 + - - -
366A LYS* 3.7 10.2 - - - +
374A TYR* 3.8 51.4 - - + -
375A GLN* 2.7 30.3 + - - +
404A HIS* 4.5 9.0 - - + +
574A TYR 4.5 5.2 - - - +
575A GLU* 4.1 34.5 - - + +
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Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A LEU* 3.0 24.8 + - - +
361A ALA* 3.6 10.7 - - - +
363A LEU* 1.3 76.0 - - - +
365A ASP* 1.3 63.7 + - - +
366A LYS 3.3 1.2 + - - -
374A TYR 3.8 19.5 - - - +
375A GLN* 3.7 3.8 - - - +
378A ARG* 2.9 51.6 + - + +
381A ASN* 4.7 6.5 + - - -
403A ARG 5.0 0.3 - - - +
404A HIS* 2.7 44.4 + - + +
406A LYS* 4.3 18.7 + - - -
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Residues in contact with ASP 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A ALA* 2.8 39.9 + - - +
362A SER* 3.7 6.2 + - - +
363A LEU 3.3 0.4 - - - -
364A GLU* 1.3 78.4 - - - +
366A LYS* 1.3 61.7 + - - +
367A GLN* 2.8 32.9 + - - +
378A ARG* 4.9 5.1 + - - +
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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