Contacts of the helix formed by residues 340 - 377 (chain A) in PDB entry 1USE
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 ASP 340 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A SER 3.4 3.8 + - - +
339A SER* 1.3 75.0 - - - +
341A TYR* 1.3 67.0 + - - +
342A SER* 3.1 19.1 + - - -
343A ASP* 2.9 39.9 + - - +
344A LEU* 3.2 16.8 + - - +
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Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASP* 1.3 77.3 - - - +
342A SER* 1.3 64.6 + - - +
344A LEU* 3.2 24.8 + - + +
345A GLN* 3.0 54.5 + - + +
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Residues in contact with SER 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASP* 3.1 18.4 + - - -
341A TYR* 1.3 79.7 - - - +
343A ASP* 1.3 59.0 + - - +
345A GLN* 3.2 9.3 + - - +
346A ARG* 2.9 29.3 + - - +
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Residues in contact with ASP 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A SER 4.2 2.8 - - - +
339A SER* 3.4 17.2 - - - -
340A ASP* 2.9 38.7 + - - +
342A SER* 1.3 76.7 - - - +
344A LEU* 1.3 64.6 + - - +
346A ARG* 3.2 12.1 + - - +
347A VAL* 3.0 32.7 + - + +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 5.0 13.2 - - - +
340A ASP 3.2 12.9 + - - +
341A TYR* 3.4 29.8 - - + +
343A ASP* 1.3 78.1 - - - +
345A GLN* 1.3 59.4 + - + +
347A VAL* 3.9 3.7 - - + +
348A LYS* 2.9 30.2 + - - +
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Residues in contact with GLN 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.0 53.3 + - + +
342A SER* 3.2 11.4 + - - +
344A LEU* 1.3 75.7 - - - +
346A ARG* 1.3 64.5 + - - +
348A LYS* 2.9 39.9 + - - +
349A GLN* 3.0 31.1 + - + +
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Residues in contact with ARG 346 (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 14.4 + - - +
343A ASP* 3.6 14.6 + - - +
345A GLN* 1.3 76.4 - - - +
347A VAL* 1.3 61.3 + - + +
349A GLN* 3.2 7.6 + - - +
350A GLU* 3.0 45.8 + - + +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ASP* 3.0 19.1 + - + +
344A LEU* 4.1 4.3 - - + +
346A ARG* 1.3 78.1 - - + +
348A LYS* 1.3 65.2 + - - +
350A GLU* 3.2 19.0 + - + +
351A LEU* 2.9 27.2 + - + +
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Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU 2.9 18.9 + - - +
345A GLN* 2.9 39.4 + - - +
346A ARG 3.3 0.2 - - - -
347A VAL* 1.3 75.2 - - - +
349A GLN* 1.3 82.3 + - - +
351A LEU* 3.4 7.3 + - - +
352A LEU* 2.9 33.2 + - + +
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Residues in contact with GLN 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLN* 3.0 22.1 + - + +
346A ARG* 3.6 6.7 - - - +
347A VAL 3.2 0.2 - - - -
348A LYS* 1.3 96.8 + - - +
350A GLU* 1.3 66.2 + - + +
352A LEU* 3.3 22.5 + - - +
353A GLU* 3.0 40.2 + - + +
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ARG* 3.0 38.0 + - + +
347A VAL* 3.2 22.8 + - + +
349A GLN* 1.3 77.1 - - + +
351A LEU* 1.3 62.8 + - - +
353A GLU* 3.4 5.8 + - - +
354A GLU* 3.1 36.1 + - - +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL* 2.9 20.3 + - + +
348A LYS* 3.6 7.6 - - - +
350A GLU* 1.3 75.8 - - - +
352A LEU* 1.3 58.2 + - - +
354A GLU* 3.2 15.3 + - + +
355A VAL* 2.8 48.9 + - + +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LYS* 2.9 24.1 + - + +
349A GLN* 3.3 25.5 + - - +
351A LEU* 1.3 76.6 - - - +
353A GLU* 1.3 58.0 + - - +
355A VAL* 4.0 10.0 - - + +
356A LYS* 3.1 63.2 + - + +
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Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLN* 3.0 31.7 + - + +
350A GLU* 3.7 6.7 - - - +
352A LEU* 1.3 76.9 - - - +
354A GLU* 1.3 63.3 + - + +
356A LYS* 3.3 35.9 + - - +
357A LYS* 3.1 22.9 + - - +
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A GLU* 3.1 26.0 + - - +
351A LEU* 3.7 17.2 - - + +
353A GLU* 1.3 75.2 - - + +
355A VAL* 1.3 63.3 + - + +
357A LYS* 3.3 8.2 + - - +
358A GLU* 3.0 31.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 2.8 38.3 + - + +
352A LEU* 4.1 11.7 - - + +
354A GLU* 1.3 75.7 - - + +
356A LYS* 1.3 58.2 + - + +
358A GLU* 3.2 8.5 + - + +
359A LEU* 2.9 48.5 + - + +
----------------------------------------------------------
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Residues in contact with LYS 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLN* 6.0 0.2 - - - +
352A LEU* 3.1 48.0 + - + +
353A GLU* 3.3 34.5 + - - +
355A VAL* 1.3 77.7 - - - +
357A LYS* 1.3 57.2 + - - +
359A LEU* 3.3 12.3 + - + +
360A GLN* 3.0 34.4 + - + +
----------------------------------------------------------
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLU 3.1 13.7 + - - +
354A GLU* 3.5 11.2 - - - +
355A VAL 3.3 0.2 - - - -
356A LYS* 1.3 77.4 - - - +
358A GLU* 1.3 60.5 + - + +
360A GLN* 3.4 7.4 + - - +
361A LYS* 3.1 27.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLU* 3.0 20.9 + - + +
355A VAL* 3.2 7.6 + - + +
357A LYS* 1.3 77.4 - - - +
359A LEU* 1.3 59.0 + - + +
361A LYS* 3.4 11.1 + - - +
362A VAL* 3.0 29.7 + - - +
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A VAL* 2.9 38.1 + - + +
356A LYS* 3.6 11.9 - - + +
358A GLU* 1.3 75.4 - - + +
360A GLN* 1.3 63.2 + - - +
362A VAL* 3.2 17.0 - - + +
363A LYS* 2.9 29.8 + - - +
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Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.0 21.2 + - + +
357A LYS* 3.6 7.6 - - - +
358A GLU 3.3 0.2 - - - -
359A LEU* 1.3 78.3 - - - +
361A LYS* 1.3 64.9 + - - +
363A LYS* 2.5 43.2 + - - +
364A GLU* 3.0 40.8 + - - +
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Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LYS 3.1 14.3 + - - +
358A GLU* 3.6 17.3 - - - +
359A LEU 3.3 0.2 - - - -
360A GLN* 1.3 77.2 - - - +
362A VAL* 1.3 60.9 + - - +
364A GLU* 3.3 13.0 + - - +
365A GLU* 3.1 32.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLU 3.0 15.4 + - - +
359A LEU* 3.2 26.2 - - + +
361A LYS* 1.3 72.5 - - - +
363A LYS* 1.3 70.5 + - + +
365A GLU* 3.3 17.9 + - + +
366A ILE* 2.9 46.4 + - + +
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Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU 2.9 18.3 + - - +
360A GLN* 2.5 43.4 + - - +
362A VAL* 1.3 78.8 - - - +
364A GLU* 1.3 74.2 + - - +
366A ILE* 3.3 8.7 + - - +
367A ILE* 3.0 48.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLN* 3.0 26.3 + - - +
361A LYS* 3.6 12.8 - - - +
363A LYS* 1.3 87.5 + - - +
365A GLU* 1.3 58.9 + - + +
367A ILE* 3.4 7.8 + - - +
368A GLU* 2.9 31.1 - - - +
----------------------------------------------------------
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Residues in contact with GLU 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LYS* 3.1 19.5 + - + +
362A VAL* 3.7 25.2 - - + +
363A LYS 3.3 0.2 - - - -
364A GLU* 1.3 73.9 - - + +
366A ILE* 1.3 67.3 + - + +
368A GLU* 4.0 4.9 + - - +
369A ALA* 3.0 24.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A VAL* 2.9 40.5 + - + +
363A LYS* 3.7 6.5 - - - +
365A GLU* 1.3 78.9 - - + +
367A ILE* 1.3 66.8 + - + +
369A ALA* 3.2 6.5 + - - +
370A PHE* 3.0 23.8 + - + +
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Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LYS* 3.0 42.8 + - + +
364A GLU* 3.9 6.3 - - - +
366A ILE* 1.3 80.2 - - + +
368A GLU* 1.3 62.7 + - - +
370A PHE* 3.2 8.8 + - + +
371A VAL* 3.0 34.5 + - + +
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLU 2.9 18.2 - - - +
365A GLU* 4.1 5.6 - - - +
367A ILE* 1.3 77.3 + - - +
369A ALA* 1.3 57.8 - - - +
371A VAL* 3.4 8.4 - - - +
372A GLN* 2.9 57.7 + - + +
375A ARG* 4.6 7.7 + - - -
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU 3.0 19.0 + - - +
366A ILE* 3.6 5.8 - - - +
368A GLU* 1.3 76.0 + - - +
370A PHE* 1.3 63.1 + - - +
372A GLN* 3.4 6.3 + - - +
373A GLU* 3.0 29.9 + - + +
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Residues in contact with PHE 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ILE* 3.0 18.1 + - + +
367A ILE* 3.2 9.4 + - + +
369A ALA* 1.3 75.2 - - - +
371A VAL* 1.3 74.5 + - + +
373A GLU* 3.2 9.0 + - + +
374A LEU* 2.9 64.1 + - + +
----------------------------------------------------------
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 3.0 32.4 + - + +
368A GLU* 3.8 11.0 - - - +
370A PHE* 1.3 86.6 - - + +
372A GLN* 1.3 63.5 + - - +
374A LEU* 3.1 10.2 + - + +
375A ARG* 2.9 60.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 2.9 41.6 + - + +
369A ALA* 3.8 7.2 - - - +
371A VAL* 1.3 77.4 - - - +
373A GLU* 1.3 62.8 + - - +
375A ARG* 3.2 40.9 + - - +
376A LYS* 3.1 36.8 + - + +
----------------------------------------------------------
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA* 3.0 18.9 + - + +
370A PHE* 3.6 12.6 - - + +
372A GLN* 1.3 77.9 - - - +
374A LEU* 1.3 58.1 + - + +
376A LYS* 2.7 33.5 + - - +
377A ARG* 2.9 67.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 2.9 59.9 + - + +
371A VAL* 3.1 10.5 + - + +
373A GLU* 1.3 75.7 - - + +
375A ARG* 1.3 61.4 + - + +
377A ARG* 2.9 26.3 - - + +
----------------------------------------------------------
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Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLU* 4.6 5.1 + - - -
371A VAL* 2.9 38.9 + - + +
372A GLN* 3.2 44.0 + - - +
374A LEU* 1.3 77.8 - - + +
376A LYS* 1.3 63.1 + - + +
377A ARG 4.2 1.9 - - - +
----------------------------------------------------------
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN* 3.1 21.7 + - + +
373A GLU* 2.7 42.1 + - - +
375A ARG* 1.3 81.4 - - + +
377A ARG* 1.3 64.4 + - + +
----------------------------------------------------------
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Residues in contact with ARG 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU* 2.9 44.4 + - - +
374A LEU* 2.9 20.2 - - + +
375A ARG 4.2 1.4 - - - +
376A LYS* 1.3 85.7 - - + +
----------------------------------------------------------
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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
------------------------------------------------------------
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