Contacts of the helix formed by residues 334 - 357 (chain A) in PDB entry 1HS6
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 334 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLY* 2.7 25.3 + - - -
331A ARG 4.5 0.6 + - - -
332A LEU 3.8 0.6 - - - -
333A PHE* 1.3 76.0 - - - +
335A GLU* 1.3 58.4 + - - -
336A LYS* 3.1 4.5 - - - -
337A PHE* 2.8 27.8 + - - +
338A ARG 3.1 4.9 + - - -
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Residues in contact with GLU 335 (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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327A HIS* 5.3 1.0 + - - -
330A GLY* 3.7 5.7 + - - -
334A GLY* 1.3 68.5 - - - -
336A LYS* 1.3 67.4 + - + +
338A ARG* 2.8 52.2 + - - +
339A HIS* 3.0 39.6 + - + +
400A PRO* 4.8 6.1 - - - +
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLY* 3.1 1.5 - - - -
335A GLU* 1.3 81.2 - - + +
337A PHE* 1.3 57.9 + - - +
339A HIS* 3.4 6.3 + - - +
340A PHE* 3.0 27.0 + - - +
461A ASP* 3.7 24.8 - - - +
463A THR* 3.7 30.8 + - + +
464A LEU* 3.8 17.4 + - + +
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Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ASN* 6.4 0.9 - - + -
329A CYS* 4.1 15.0 - - + -
333A PHE* 3.6 49.3 + + + +
334A GLY* 2.8 13.6 + - - +
336A LYS* 1.3 78.6 - - - +
338A ARG* 1.3 62.3 + - - +
340A PHE* 3.1 21.4 + + - +
341A ASN* 3.0 46.3 + - - -
464A LEU* 3.8 16.2 - - + +
497A HIS* 3.9 46.9 - + + -
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Residues in contact with ARG 338 (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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323A TYR* 4.4 4.0 - - - -
326A ARG* 3.4 42.3 - - + +
327A HIS* 3.3 31.4 + - - +
329A CYS 5.5 0.2 - - - -
330A GLY* 3.9 10.5 - - - +
334A GLY 3.1 5.9 + - - -
335A GLU* 2.8 47.6 + - - +
337A PHE* 1.3 76.7 - - - +
339A HIS* 1.3 62.5 + - + +
341A ASN* 3.3 7.3 + - - +
342A ALA* 2.9 29.3 + - + +
387A PHE* 5.4 4.1 - - + -
391A PHE* 3.6 22.6 - - + -
394A GLU* 3.0 40.6 + - - -
400A PRO* 4.1 9.1 - - - +
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Residues in contact with HIS 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU* 3.0 50.8 + - + +
336A LYS 3.7 5.8 - - - +
337A PHE 3.2 0.4 - - - -
338A ARG* 1.3 83.4 + - - +
340A PHE* 1.3 56.2 + - - +
342A ALA* 3.2 7.2 + - - +
343A LEU* 2.9 31.4 + - - +
391A PHE* 3.8 26.5 - + - -
394A GLU* 5.6 0.2 + - - -
395A GLN* 4.5 4.7 - - - -
459A ASN 4.1 7.0 - - - -
460A TYR* 3.6 7.5 - - - -
461A ASP* 2.8 52.9 + - + +
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LYS 3.0 14.8 + - - +
337A PHE* 3.1 17.9 + + - +
339A HIS* 1.3 77.2 - - - +
341A ASN* 1.3 75.2 + - - +
343A LEU* 3.4 3.2 + - - +
344A GLY* 2.9 25.7 + - - -
461A ASP 4.8 2.4 + - - -
464A LEU* 3.6 39.5 - - + +
465A THR* 3.4 25.2 + - - +
468A CYS* 4.2 1.6 - - - -
497A HIS* 3.4 42.0 - - + -
498A GLN* 4.1 9.6 - - + -
501A GLU* 3.6 29.0 - - + -
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Residues in contact with ASN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ASN* 5.7 4.0 - - - +
326A ARG* 3.4 31.7 + - + +
329A CYS* 4.5 9.5 - - - +
337A PHE* 3.0 46.6 + - - +
338A ARG* 3.7 5.2 - - - +
340A PHE* 1.3 94.6 - - - +
342A ALA* 1.3 65.7 + - - +
344A GLY* 3.4 1.9 + - - -
345A GLY 3.0 17.7 + - - -
497A HIS* 5.4 3.2 - - - -
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Residues in contact with ALA 342 (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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326A ARG* 3.9 13.6 + - - +
338A ARG* 2.9 18.1 + - + +
339A HIS* 3.5 7.0 - - - +
341A ASN* 1.3 78.8 - - - +
343A LEU* 1.3 61.2 + - - +
345A GLY* 3.2 3.3 + - - -
346A TRP* 3.1 17.8 + - - +
387A PHE* 3.4 30.9 - - + -
391A PHE* 4.1 8.5 - - + -
460A TYR* 3.6 20.1 + - + -
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A HIS 2.9 16.5 + - - +
340A PHE 3.9 4.0 - - - +
342A ALA* 1.3 76.1 - - - +
344A GLY* 1.3 63.2 + - - +
346A TRP* 3.2 9.1 + - + +
347A GLY* 3.2 16.1 + - - -
457A LYS* 4.1 18.8 - - - +
460A TYR* 3.6 40.8 - - + -
461A ASP 5.0 1.1 - - - +
462A MET* 3.6 33.2 - - + -
465A THR* 3.9 25.1 - - + +
501A GLU* 6.1 0.9 - - - +
1001A IMD 5.2 0.2 + - - -
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Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 2.9 17.0 + - - -
341A ASN* 3.9 2.7 - - - -
342A ALA 3.3 0.2 - - - -
343A LEU* 1.3 79.0 - - - +
345A GLY* 1.4 55.6 + - - +
347A GLY 3.0 13.9 + - - -
348A GLU* 3.0 13.9 + - - +
501A GLU* 3.9 24.4 - - - -
1001A IMD 3.2 14.7 - - - -
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Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 3.8 7.8 - - - +
341A ASN 3.0 10.1 + - - -
342A ALA 3.2 3.8 + - - -
344A GLY* 1.4 72.0 - - - +
346A TRP* 1.4 58.7 + - - +
348A GLU* 3.0 9.8 + - - +
349A LEU 2.8 24.8 + - - -
384A GLU* 3.2 40.5 - - - +
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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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342A ALA 3.1 7.7 + - - +
343A LEU* 3.2 14.8 + - + +
345A GLY* 1.4 74.7 - - - +
347A GLY* 1.3 58.8 + - - +
349A LEU* 3.1 13.5 + - + +
350A GLN* 2.8 54.2 + - - +
384A GLU* 4.2 1.3 + - - -
388A ALA* 4.2 12.1 - - + -
453A LEU* 4.2 23.5 - - + +
454A PRO* 3.5 41.3 - - + -
456A ILE 4.0 3.4 - - - -
457A LYS* 3.6 50.6 - - + +
458A PRO* 3.9 17.9 - - + -
460A TYR* 3.6 27.6 - - + +
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Residues in contact with GLY 347 (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 LEU 3.2 7.6 + - - -
344A GLY 3.0 10.0 + - - -
346A TRP* 1.3 79.9 - - - +
348A GLU* 1.3 60.1 + - - +
350A GLN* 3.2 20.4 + - - +
351A ASN* 3.1 26.7 + - - +
508A GLN* 3.5 1.0 + - - -
1001A IMD 3.5 21.3 - - - -
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Residues in contact with GLU 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 GLY 3.0 12.0 + - - +
345A GLY* 3.0 13.1 + - - +
347A GLY* 1.3 74.0 - - - +
349A LEU* 1.4 57.6 + - - +
351A ASN* 3.1 18.1 + - - +
352A SER* 2.9 30.9 + - - -
380A SER* 4.6 12.7 + - - +
384A GLU* 4.6 9.6 - - + +
504A ALA* 4.6 0.3 - - - +
537A ARG* 3.9 29.8 + - - +
565A LYS* 5.9 1.2 - - - -
1001A IMD 2.7 25.6 + - + +
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Residues in contact with LEU 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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345A GLY 2.8 13.1 + - - +
346A TRP* 3.4 20.0 - - + +
348A GLU* 1.4 75.1 - - - +
350A GLN* 1.3 65.1 + - - +
352A SER* 3.2 4.5 + - - +
353A VAL* 3.0 33.6 + - + +
380A SER* 4.6 0.7 - - - +
381A VAL* 4.1 22.9 - - + +
384A GLU* 3.7 13.6 - - + +
385A LYS* 3.8 38.4 - - + +
388A ALA* 5.0 0.2 - - + -
453A LEU* 4.1 10.1 - - + -
454A PRO* 3.6 35.9 - - + -
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Residues in contact with GLN 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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346A TRP* 2.8 43.7 + - - +
347A GLY* 3.2 16.8 + - - +
349A LEU* 1.3 72.1 - - - +
351A ASN* 1.3 58.9 + - - +
353A VAL* 3.5 2.2 + - - +
354A LYS* 2.9 29.8 + - - +
453A LEU* 4.1 22.4 - - + +
457A LYS* 5.2 2.6 + - - -
508A GLN* 3.2 28.0 + - - +
1001A IMD 5.1 0.6 - - - -
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Residues in contact with ASN 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 GLY 3.1 8.0 + - - -
348A GLU* 3.4 32.8 + - - +
349A LEU 3.1 0.2 - - - -
350A GLN* 1.3 77.9 - - - +
352A SER* 1.3 57.6 + - - +
354A LYS* 3.2 7.4 + - - +
355A THR* 2.9 35.3 + - - +
504A ALA* 5.3 1.4 + - - +
507A LEU* 6.0 3.8 - - - +
508A GLN* 2.8 36.6 + - - +
1001A IMD 3.8 7.5 - - - -
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLU 2.9 10.7 + - - -
349A LEU* 3.2 8.7 + - - -
351A ASN* 1.3 77.9 - - - +
353A VAL* 1.3 57.3 + - - +
355A THR* 3.3 7.3 + - - -
356A PHE* 2.9 41.3 + - - -
363A THR* 5.0 0.4 - - - -
379A SER* 4.6 1.9 - - - -
380A SER* 3.3 31.7 + - - -
381A VAL* 4.2 21.8 - - - -
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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
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349A LEU* 3.0 31.4 + - + +
350A GLN 3.9 3.1 - - - +
352A SER* 1.3 74.9 - - - +
354A LYS* 1.3 62.7 + - - +
357A GLY* 2.8 29.4 + - - +
358A GLU* 3.6 29.5 + - + -
363A THR* 4.2 17.3 - - + +
381A VAL* 5.3 1.3 - - + -
452A GLY* 4.0 27.6 - - - +
453A LEU* 4.2 20.9 - - + +
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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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350A GLN 2.9 18.9 + - - +
351A ASN* 3.7 7.6 - - - +
353A VAL* 1.3 81.3 - - - +
355A THR* 1.3 65.6 + - - +
357A GLY* 3.5 7.0 + - - -
508A GLN 4.4 15.2 + - - -
510A ALA 6.0 0.6 + - - -
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Residues in contact with THR 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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351A ASN* 2.9 20.0 + - - +
352A SER* 3.6 9.0 - - - +
354A LYS* 1.3 81.2 - - - +
356A PHE* 1.3 75.3 + - + +
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Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A SER* 2.9 29.7 + - - +
355A THR* 1.3 83.5 - - + +
357A GLY* 1.3 57.2 + - - +
360A HIS* 3.4 48.5 + + + +
362A PHE* 3.7 36.3 - + + -
363A THR* 3.6 20.6 - - + -
376A VAL 5.5 2.5 - - - -
377A ALA 4.2 5.2 - - - -
378A TYR 4.9 2.0 - - - -
379A SER* 3.5 36.8 - - - -
381A VAL* 4.3 2.9 - - + -
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Residues in contact with GLY 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A VAL 2.8 15.4 + - - +
354A LYS 4.1 5.2 - - - -
355A THR 3.3 2.6 - - - -
356A PHE* 1.3 77.4 - - - +
358A GLU* 1.3 57.4 + - - -
359A THR* 3.1 6.1 - - - -
360A HIS* 3.1 25.0 + - - +
363A THR* 3.7 7.3 - - - +
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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
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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