Contacts of the helix formed by residues 355 - 376 (chain A) in PDB entry 1UA4
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 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LYS* 1.3 76.7 - - - +
356A GLU* 1.3 63.1 + - - -
357A HIS* 3.0 19.5 + - - -
358A VAL* 3.2 10.6 + - - +
359A ARG 4.3 0.2 + - - -
413A ILE* 4.8 0.4 - - - -
420A GLN* 3.0 30.2 + - - -
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Residues in contact with GLU 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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355A GLY* 1.3 70.3 - - - -
357A HIS* 1.3 63.8 + - - +
358A VAL 3.0 0.4 - - - -
359A ARG* 3.1 31.4 + - - +
360A ASP* 3.0 28.3 + - - +
411A GLU* 5.1 4.9 - - - +
413A ILE* 3.7 23.5 - - + +
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Residues in contact with HIS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 5.2 5.6 - - - +
353A TYR* 4.4 7.9 - + - -
354A LYS 3.6 9.9 - - - -
355A GLY* 3.4 25.5 - - - -
356A GLU* 1.3 80.5 + - - +
358A VAL* 1.3 68.4 + - + +
360A ASP* 3.8 6.7 - - - -
361A ALA* 3.0 24.6 + - - +
450A GLU* 3.5 42.5 + - + +
453A PHE* 3.6 30.6 - - + +
454A THR* 3.9 18.2 - - + +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 5.2 1.3 + - - +
349A ALA* 3.7 29.6 - - + +
351A THR* 4.2 12.1 - - + +
353A TYR* 3.7 30.3 - - + -
355A GLY* 3.5 14.6 - - - +
356A GLU 3.0 0.8 - - - -
357A HIS* 1.3 86.0 - - + +
359A ARG* 1.3 62.9 + - - +
361A ALA* 3.4 3.3 + - - +
362A LEU* 3.2 25.2 + - + +
420A GLN* 3.8 12.8 - - - +
422A ALA* 4.1 8.5 - - + -
450A GLU* 3.8 23.6 - - - +
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Residues in contact with ARG 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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4A TRP* 4.2 12.8 - - - -
7A LEU* 3.8 25.5 - - - +
355A GLY 4.3 0.6 + - - -
356A GLU* 3.1 29.9 + - - +
358A VAL* 1.3 80.6 - - - +
360A ASP* 1.3 89.6 + - - +
362A LEU* 3.0 15.0 + - - +
363A LEU* 3.0 26.1 + - + +
411A GLU* 3.0 43.7 + - - +
412A GLY 4.8 0.2 - - - +
413A ILE* 3.9 32.2 - - + +
422A ALA* 4.4 7.0 - - + +
423A PHE 4.2 4.9 - - - +
424A ILE* 3.7 19.1 - - + -
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Residues in contact with ASP 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.9 2.8 - - - +
10A ASN* 6.5 0.7 - - - -
11A ALA* 3.6 19.5 - - + +
14A LYS* 4.7 14.5 + - + +
356A GLU* 3.0 24.6 + - - +
357A HIS* 4.1 4.1 - - - +
359A ARG* 1.3 106.5 + - - +
361A ALA* 1.3 58.5 + - - +
363A LEU* 3.2 15.7 + - - +
364A PHE* 3.0 25.1 + - - +
453A PHE* 3.7 18.7 - - + -
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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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338A ARG* 5.4 0.4 - - - +
357A HIS 3.0 18.8 + - - +
358A VAL 3.7 4.0 - - - +
359A ARG 3.2 0.4 - - - -
360A ASP* 1.3 74.4 - - - +
362A LEU* 1.3 65.1 + - + +
364A PHE* 3.3 6.9 + - - +
365A ALA* 3.0 23.7 + - - +
446A ALA* 3.4 20.2 - - + +
449A GLY* 4.0 2.2 - - - -
450A GLU* 3.4 34.8 - - + +
453A PHE* 3.6 7.8 - - + -
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 4.7 3.6 - - - +
340A HIS* 3.3 44.0 - - + +
347A TYR* 3.8 5.9 - - + +
348A LEU 4.4 2.7 - - - -
349A ALA* 3.8 28.3 - - + +
358A VAL 3.2 15.7 + - - +
359A ARG* 3.0 8.6 + - - +
361A ALA* 1.3 77.0 - - - +
363A LEU* 1.3 56.3 + - - +
365A ALA* 3.2 6.2 + - - +
366A ALA 2.9 25.1 + - - -
422A ALA* 4.0 22.0 - - + +
424A ILE* 3.2 36.0 - - + +
446A ALA* 4.3 4.7 - - + -
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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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4A TRP* 4.0 9.0 - - + -
7A LEU* 3.6 39.0 - - + +
8A TYR* 3.5 48.7 - - + -
11A ALA* 3.7 9.6 - - + -
359A ARG* 3.0 21.6 + - - +
360A ASP* 3.2 23.8 + - - +
362A LEU* 1.3 75.1 - - - +
364A PHE* 1.3 65.3 + - - +
366A ALA 3.3 0.7 + - - -
367A LEU* 3.2 21.1 + - - +
424A ILE* 3.6 26.9 - - + -
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Residues in contact with PHE 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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11A ALA* 4.4 6.4 - - - +
12A ILE* 3.7 23.3 - - + -
15A ALA* 3.6 28.7 - - + -
19A VAL* 3.9 22.7 - - + -
125A TYR* 3.7 29.8 - + - -
360A ASP 3.0 12.3 + - - +
361A ALA* 3.5 9.4 - - - +
362A LEU 3.3 0.2 - - - -
363A LEU* 1.3 75.8 - - - +
365A ALA* 1.3 64.0 + - - +
367A LEU* 3.2 10.8 + - - +
368A ALA* 3.1 18.7 + - - +
381A LEU* 4.4 8.1 - - + -
384A ILE* 4.3 15.0 - - + -
445A SER* 3.5 36.8 - - - -
448A ILE* 5.9 0.4 - - + -
449A GLY* 4.4 7.2 - - - -
453A PHE* 5.1 1.1 - + + -
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Residues in contact with ALA 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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340A HIS* 4.7 0.4 - - + -
347A TYR* 4.2 3.1 - - + -
361A ALA 3.0 13.4 + - - +
362A LEU* 3.5 8.5 - - - +
364A PHE* 1.3 79.1 - - - +
366A ALA* 1.3 57.0 + - - +
368A ALA* 3.2 2.8 + - - +
369A ALA* 2.8 28.9 + - - +
442A ILE* 3.3 38.7 - - + +
445A SER* 3.9 12.6 - - - -
446A ALA* 3.8 13.7 - - + +
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Residues in contact with ALA 366 (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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8A TYR* 3.5 26.0 - - + +
347A TYR* 3.5 24.1 - - + +
362A LEU 2.9 14.5 + - - +
363A LEU 3.5 8.1 - - - +
364A PHE 3.3 0.2 - - - -
365A ALA* 1.3 75.8 - - - +
367A LEU* 1.3 58.8 + - - +
369A ALA* 3.3 2.9 + - - +
370A ALA* 3.0 27.2 + - - +
424A ILE* 3.8 5.2 - - + -
426A THR* 4.3 8.0 - - + -
427A LYS* 4.7 7.3 + - - +
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Residues in contact with LEU 367 (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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8A TYR* 3.7 16.6 - - + +
12A ILE* 3.5 38.6 - - + +
363A LEU 3.2 18.4 + - - +
364A PHE* 3.2 8.7 + - - +
366A ALA* 1.3 73.0 - - - +
368A ALA* 1.3 66.3 + - - +
370A ALA* 3.2 2.2 + - - -
371A ALA* 3.0 20.8 + - - +
384A ILE* 3.6 16.6 - - + +
387A ALA* 3.5 13.9 - - - +
388A THR* 3.8 36.1 - - + +
427A LYS* 3.7 28.5 - - + -
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Residues in contact with ALA 368 (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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125A TYR* 3.6 20.4 - - - +
364A PHE* 3.1 12.3 + - + +
365A ALA* 3.2 8.0 + - - +
367A LEU* 1.3 76.6 - - - +
369A ALA* 1.3 63.9 + - - +
371A ALA 3.3 1.0 + - - -
372A LYS* 2.9 24.9 + - - +
378A ILE* 3.4 5.8 - - + +
384A ILE* 3.7 19.7 - - + +
441A THR* 3.6 19.7 - - + -
445A SER* 3.8 6.7 - - - +
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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
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347A TYR* 3.3 26.5 - - - +
365A ALA 2.8 9.0 + - - +
366A ALA 3.5 6.1 - - - +
367A LEU 3.2 0.2 - - - -
368A ALA* 1.3 78.0 - - - +
370A ALA* 1.3 56.9 + - - +
372A LYS* 3.3 5.2 + - - +
373A ALA* 2.9 31.0 + - - +
438A ILE* 3.8 19.2 - - + +
441A THR* 4.2 3.8 - - - +
442A ILE* 3.6 13.9 - - + -
1456A AMP 4.5 8.7 - - + +
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Residues in contact with ALA 370 (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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366A ALA 3.0 13.8 + - - +
367A LEU* 3.2 9.6 + - - +
369A ALA* 1.3 76.3 - - - +
371A ALA* 1.3 62.5 - - - +
373A ALA* 3.2 2.7 + - - -
374A MET* 3.1 29.1 + - - +
387A ALA* 3.8 14.1 - - + -
390A VAL* 4.3 9.0 - - + -
427A LYS* 3.8 23.1 - - + +
429A VAL* 3.4 16.6 - - + +
1456A AMP 4.6 2.0 - - - -
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Residues in contact with ALA 371 (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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367A LEU 3.0 13.4 + - - +
368A ALA 3.6 7.9 - - - +
370A ALA* 1.3 75.7 - - - +
372A LYS* 1.3 62.8 + - - +
374A MET* 3.2 16.7 + - + +
375A LYS* 3.2 29.2 + - + +
378A ILE* 4.3 14.2 - - + +
383A GLU* 3.7 35.4 - - + +
384A ILE* 4.1 4.3 - - + -
387A ALA* 4.4 0.2 - - + -
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Residues in contact with LYS 372 (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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109A ARG* 4.2 8.6 - - - +
116A ILE* 5.1 11.1 - - - +
368A ALA 2.9 17.6 + - - +
369A ALA* 3.5 6.5 - - - +
371A ALA* 1.3 77.5 - - - +
373A ALA* 1.3 58.4 + - - +
376A GLY* 2.7 63.8 + - - +
377A ASN* 4.0 13.0 - - - +
378A ILE* 3.9 17.6 - - + +
434A SER 4.9 2.1 - - - +
436A VAL 3.8 20.5 + - - -
437A GLY* 4.2 12.3 - - - -
438A ILE* 3.8 18.6 - - + -
441A THR* 3.9 18.4 - - - +
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Residues in contact with ALA 373 (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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369A ALA 2.9 17.3 + - - +
370A ALA 3.2 5.4 + - - +
372A LYS* 1.3 77.8 - - - +
374A MET* 1.3 59.0 + - - +
429A VAL* 3.9 8.3 - - + -
432A PRO* 3.2 9.3 - - + +
433A LYS* 2.9 30.0 + - - +
434A SER 4.4 4.3 + - - -
438A ILE* 3.9 19.7 - - + -
1456A AMP 3.8 28.5 - - + +
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Residues in contact with MET 374 (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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370A ALA 3.1 21.4 + - - +
371A ALA* 3.6 18.2 - - + +
372A LYS 3.2 0.2 - - - -
373A ALA* 1.3 79.9 - - - +
375A LYS* 1.3 80.5 + - + +
376A GLY 4.0 0.2 + - - -
383A GLU 5.0 2.0 - - - +
386A GLU* 5.4 1.3 - - + -
387A ALA* 3.9 22.7 - - + +
390A VAL* 4.0 18.6 - - + -
429A VAL* 3.5 24.0 - - + -
431A LYS 5.3 2.3 - - - +
432A PRO* 5.1 0.4 - - - -
433A LYS* 4.1 11.3 + - - +
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Residues in contact with LYS 375 (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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371A ALA* 3.2 11.9 + - - +
374A MET* 1.3 99.0 - - + +
376A GLY* 1.3 56.5 - - - +
377A ASN* 2.8 37.0 + - - +
379A THR* 5.9 0.2 - - - +
383A GLU* 3.7 42.2 + - + +
386A GLU* 4.6 10.4 + - - -
433A LYS* 3.9 14.3 - - - +
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Residues in contact with GLY 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 3.1 33.1 + - - -
372A LYS* 2.7 54.9 + - - -
373A ALA 5.2 0.2 - - - -
374A MET 3.6 1.6 - - - -
375A LYS* 1.3 70.0 - - - +
377A ASN* 1.3 52.6 + - - +
433A LYS* 4.0 9.3 - - - +
434A SER* 4.2 6.3 - - - -
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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
------------------------------------------------------------
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