Contacts of the helix formed by residues 342 - 363 (chain A) in PDB entry 3A8X
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 PRO 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A LYS 4.2 4.3 - - - +
341A LEU* 1.3 93.4 - - + +
343A GLU* 1.3 65.9 + - - +
344A GLU* 4.3 4.9 - - + +
345A HIS* 3.0 50.4 + - + +
346A ALA* 3.1 10.6 + - - +
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Residues in contact with GLU 343 (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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341A LEU 3.6 1.6 + - - +
342A PRO* 1.3 71.3 - - - +
344A GLU* 1.3 58.6 + - - +
346A ALA* 3.2 2.3 + - - +
347A ARG* 2.8 43.8 + - - +
438A MET* 4.0 23.1 - - + -
475A SER 4.4 2.1 - - - +
476A LEU* 3.5 14.0 - - + +
477A SER* 2.6 54.6 + - - -
480A ALA* 3.8 12.8 - - - +
512A PHE* 4.2 7.4 - - + -
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PRO* 3.2 3.8 - - + +
343A GLU* 1.3 77.6 - - - +
345A HIS* 1.3 71.6 + - + +
347A ARG* 2.8 42.0 + - - +
348A PHE* 3.2 24.8 + - - +
515A ASN* 5.5 5.5 + - - +
529A PRO* 5.3 2.4 - - + +
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Residues in contact with HIS 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A HIS* 5.5 1.8 + - - -
341A LEU* 4.1 13.6 - - + +
342A PRO* 3.0 45.2 + - + +
344A GLU* 1.3 83.3 - - + +
346A ALA* 1.3 63.3 + - - +
348A PHE* 3.3 4.3 + - - +
349A TYR* 3.1 37.5 + - + -
529A PRO* 3.6 48.5 + - + +
530A PHE* 5.0 7.8 - + + +
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Residues in contact with ALA 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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341A LEU* 4.6 3.7 - - + +
342A PRO 3.1 8.1 + - - +
343A GLU 3.7 4.5 - - - +
345A HIS* 1.3 74.5 - - - +
347A ARG* 1.3 57.3 + - - +
349A TYR* 4.5 0.2 - - - -
350A SER* 2.4 40.0 + - - +
434A MET* 5.7 0.2 - - - -
437A MET* 3.8 31.3 - - + +
438A MET* 3.5 37.5 - - + -
512A PHE* 4.7 1.6 - - + -
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Residues in contact with ARG 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 GLU* 2.8 28.3 + - - +
344A GLU* 2.8 55.8 + - - +
346A ALA* 1.3 73.7 - - - +
348A PHE* 1.3 60.7 + - - +
350A SER* 3.7 1.0 - - - -
351A ALA* 2.8 33.3 + - - +
479A LYS* 5.7 4.6 - - - +
512A PHE* 2.6 64.5 + - + +
513A PHE* 3.8 10.5 - - + +
515A ASN* 5.4 12.2 - - - +
516A VAL* 4.0 28.7 - - + +
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Residues in contact with PHE 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 GLU* 3.2 17.1 + - - +
345A HIS 3.3 8.0 + - - +
347A ARG* 1.3 80.4 - - - +
349A TYR* 1.3 77.6 + + - +
351A ALA* 3.4 1.7 + - - +
352A GLU* 3.1 59.3 + - - +
381A GLY 3.8 16.8 - - - -
382A HIS* 3.6 9.9 - - - -
521A MET* 3.9 24.6 - - + +
526A VAL* 3.7 31.4 - - + -
527A VAL 4.4 0.9 - - - -
528A PRO* 3.6 18.2 - - + -
529A PRO* 3.4 26.7 - - + -
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Residues in contact with TYR 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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331A LEU* 4.3 16.6 - - + -
334A HIS* 3.8 10.7 + - - -
341A LEU* 3.9 18.4 - - + -
345A HIS* 3.1 28.3 + - + +
346A ALA 4.1 0.2 - - - +
348A PHE* 1.3 88.8 - + - +
350A SER* 1.3 58.9 + - - +
352A GLU* 3.3 2.8 + - - +
353A ILE* 2.9 36.0 + - + +
377A LEU* 3.8 18.0 - - + +
381A GLY 3.7 20.9 + - - -
383A ILE* 3.5 25.3 - - + +
437A MET* 4.0 29.2 - - + -
529A PRO* 3.9 8.9 - - + +
530A PHE* 3.7 27.4 + - - +
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Residues in contact with SER 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 ALA 2.4 25.2 + - - -
347A ARG 3.7 2.9 - - - -
349A TYR* 1.3 75.6 - - - +
351A ALA* 1.3 54.5 + - - +
353A ILE* 3.9 2.7 - - - +
354A SER* 2.7 38.7 + - - -
430A LEU* 4.2 10.7 - - - +
434A MET* 3.1 47.5 - - - +
437A MET* 3.4 5.6 - - - +
513A PHE* 3.9 8.5 - - - -
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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 ARG 2.8 21.5 + - - +
348A PHE 3.7 4.0 - - - +
350A SER* 1.3 73.7 - - - +
352A GLU* 1.3 62.7 + - - +
354A SER* 3.4 2.4 + - - -
355A LEU* 3.1 29.3 + - - +
513A PHE* 4.0 5.6 - - + -
516A VAL* 4.4 6.7 - - + -
518A TRP* 3.5 29.6 - - + -
521A MET* 4.0 22.9 - - + -
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Residues in contact with GLU 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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305A PHE* 3.2 43.7 - - + -
348A PHE* 3.1 36.8 + - - +
349A TYR 3.8 1.6 - - - +
351A ALA* 1.3 75.5 - - - +
353A ILE* 1.3 63.1 + - - +
355A LEU* 3.3 2.2 + - - -
356A ALA* 3.1 19.6 + - - +
382A HIS* 2.7 29.0 + - - -
383A ILE* 2.9 43.7 + - + +
521A MET* 3.7 17.6 - - - +
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Residues in contact with ILE 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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331A LEU* 4.4 4.5 - - + -
349A TYR* 2.9 27.3 + - + +
350A SER* 3.9 6.3 - - - +
352A GLU* 1.3 72.5 - - - +
354A SER* 1.3 62.1 + - - +
356A ALA* 3.1 3.8 + - - +
357A LEU* 2.8 49.9 + - + +
370A LEU* 4.0 16.2 - - + -
375A VAL* 4.0 20.4 - - + -
383A ILE* 3.6 23.1 - - + -
385A LEU* 4.1 8.5 - - + -
430A LEU* 4.1 12.1 - - + -
433A LEU* 3.9 28.0 - - + -
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Residues in contact with SER 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 SER 2.7 25.4 + - - -
351A ALA* 3.5 8.8 - - - -
352A GLU 3.3 0.2 - - - -
353A ILE* 1.3 77.1 - - - +
355A LEU* 1.3 56.0 + - - +
358A ASN* 2.9 31.5 + - - +
427A TRP* 3.4 23.9 - - - -
430A LEU* 3.3 17.5 - - - +
504A PHE* 3.6 12.5 - - - -
507A ILE* 4.2 10.6 - - - +
513A PHE* 4.7 2.9 - - - -
518A TRP* 4.3 7.6 - - - -
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Residues in contact with LEU 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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303A HIS* 3.8 7.6 + - + +
305A PHE* 3.9 13.9 - - + -
351A ALA 3.1 18.8 + - - +
352A GLU 3.5 5.8 - - - +
353A ILE 3.2 0.2 - - - -
354A SER* 1.3 77.8 - - - +
356A ALA* 1.3 60.7 + - - +
358A ASN* 3.9 2.9 + - - +
359A TYR* 3.1 25.1 + - - +
504A PHE* 3.7 25.8 - - + -
508A GLN* 5.2 0.4 - - - +
518A TRP* 3.9 19.3 - - + +
521A MET* 3.7 28.3 - - + -
522A GLU* 3.8 41.1 - - + +
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Residues in contact with ALA 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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303A HIS* 3.9 11.6 - - - -
305A PHE* 3.7 24.2 - - + +
306A LEU* 3.8 8.1 - - + +
352A GLU 3.1 13.5 + - - +
353A ILE* 3.5 9.4 - - - +
355A LEU* 1.3 76.3 - - - +
357A LEU* 1.3 62.0 + - - +
359A TYR* 3.3 3.1 + - - +
360A LEU* 3.1 25.5 + - - +
385A LEU* 3.6 23.3 - - + -
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Residues in contact with LEU 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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353A ILE* 2.8 40.1 + - + +
356A ALA* 1.3 73.9 - - - +
358A ASN* 1.3 57.9 + - - +
360A LEU* 3.4 4.8 + - + +
361A HIS* 2.9 43.1 + - + -
367A TYR* 3.9 29.8 - - + -
370A LEU* 4.0 15.3 - - + -
385A LEU* 3.7 20.4 - - + -
426A ASP* 4.2 20.2 - - + +
427A TRP* 3.9 31.9 - - + -
430A LEU* 4.5 2.9 - - + -
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Residues in contact with ASN 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 SER 2.9 19.4 + - - +
355A LEU* 3.9 4.1 + - - +
357A LEU* 1.3 76.9 - - - +
359A TYR* 1.3 60.3 + - - +
361A HIS* 3.3 11.5 + - - +
362A GLU* 2.9 54.9 + - - +
427A TRP* 4.2 4.8 - - + -
504A PHE* 3.4 55.3 - - + +
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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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299A GLN* 3.1 32.5 + - - -
301A SER* 3.3 16.0 + - - -
303A HIS* 3.4 35.9 - + + +
306A LEU* 3.8 17.9 - - + -
355A LEU 3.1 17.7 + - - +
356A ALA 3.7 3.4 - - - +
358A ASN* 1.3 79.7 - - - +
360A LEU* 1.3 66.7 + - + +
362A GLU* 3.2 3.5 + - - -
363A ARG* 2.6 82.2 + - + +
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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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296A VAL* 4.7 9.4 - - + -
299A GLN* 5.5 0.7 - - + -
300A ALA* 5.0 4.5 - - - +
306A LEU* 3.5 44.4 - - + -
356A ALA 3.1 11.8 + - - +
357A LEU* 3.4 9.9 - - - +
359A TYR* 1.3 82.7 - - + +
361A HIS* 1.3 59.4 - - + +
363A ARG* 2.8 21.9 + - + +
364A GLY 3.2 0.2 + - - -
365A ILE* 3.0 54.6 + - + +
367A TYR* 4.4 27.6 - - + +
385A LEU* 4.5 8.3 - - + -
388A TYR* 5.1 5.4 - - + -
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Residues in contact with HIS 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 LEU* 2.9 29.6 + - + +
358A ASN* 3.7 8.3 + - - +
360A LEU* 1.3 73.4 - - + +
362A GLU* 1.3 64.9 + - + +
363A ARG 3.0 0.2 - - - -
364A GLY 3.0 11.3 + - - -
365A ILE 3.2 20.9 - - - -
423A PHE* 3.3 58.5 - + + +
426A ASP* 2.7 32.8 + - + +
427A TRP* 3.4 42.3 + + - -
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Residues in contact with GLU 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 ASN* 2.9 42.1 + - - +
359A TYR* 3.7 1.3 - - - -
360A LEU 3.2 0.4 - - - -
361A HIS* 1.3 77.5 - - - +
363A ARG* 1.3 81.6 + - - +
364A GLY 3.4 0.4 + - - -
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Residues in contact with ARG 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLN* 3.7 41.8 - - + +
359A TYR* 2.6 75.9 + - + +
360A LEU* 2.8 10.8 + - + +
362A GLU* 1.3 99.5 + - - +
364A GLY* 1.3 60.4 + - - +
365A ILE* 3.5 12.8 + - + +
394A GLY* 5.0 3.5 + - - -
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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