Contacts of the helix formed by residues 375 - 396 (chain A) in PDB entry 6FD3
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 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A CYS 3.8 1.2 + - - +
374A MET* 1.3 76.0 - - - +
376A GLU* 1.3 60.0 + - - +
377A GLY* 3.1 6.3 + - - -
378A GLN* 2.8 55.0 + - - +
379A ILE* 2.9 26.3 + - - +
538A LYS* 2.7 31.2 + - - +
605A EDO 3.9 9.9 - - - +
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Residues in contact with GLU 376 (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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375A ASP* 1.3 76.7 - - - +
377A GLY* 1.3 57.0 + - - +
379A ILE* 4.3 5.4 - - - -
380A ALA* 2.8 31.2 + - - +
502A ARG 4.3 1.9 - - - +
503A LEU* 3.4 12.3 - - - +
504A SER* 2.6 52.5 + - - -
507A PHE* 3.5 23.4 - - + +
533A PHE* 3.6 9.1 - - + -
536A LEU* 3.9 14.9 - - + +
605A EDO 3.8 18.2 + - - +
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Residues in contact with GLY 377 (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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375A ASP* 3.1 7.1 + - - -
376A GLU* 1.3 78.1 - - - +
378A GLN* 1.3 56.5 + - - +
381A ALA* 3.1 22.5 + - - +
536A LEU* 3.2 25.9 - - - +
537A ASP* 3.5 1.0 - - - -
538A LYS* 3.1 29.8 + - - -
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Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A CYS 4.3 1.4 - - - +
374A MET* 3.4 15.7 - - + -
375A ASP* 2.8 51.9 + - - +
377A GLY* 1.3 74.7 - - - +
379A ILE* 1.3 64.9 + - - +
381A ALA* 3.3 5.8 + - - +
382A VAL* 3.1 28.2 + - - +
538A LYS* 4.2 5.3 - - + +
542A SER* 3.0 48.0 + - - +
543A LEU* 3.7 15.6 - - + +
546A LEU* 3.5 21.7 - - - +
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Residues in contact with ILE 379 (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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374A MET* 3.8 17.7 - - + +
375A ASP 2.9 18.6 + - - +
376A GLU* 3.8 5.6 - - - +
378A GLN* 1.3 76.8 - - - +
380A ALA* 1.3 57.0 + - - +
382A VAL* 3.2 2.8 + - - +
383A CYS* 2.8 40.4 + - - -
467A ALA* 4.9 1.6 - - + -
470A MET* 3.8 46.7 - - + +
471A VAL* 4.1 7.2 - - + -
507A PHE* 3.8 25.1 - - + -
533A PHE* 4.0 3.4 - - + -
605A EDO 3.8 30.5 - - - -
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Residues in contact with ALA 380 (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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376A GLU 2.8 18.6 + - - +
377A GLY 3.8 4.7 - - - +
379A ILE* 1.3 77.4 - - - +
381A ALA* 1.3 57.3 + - - +
383A CYS* 3.3 1.1 + - - -
384A ARG* 2.9 30.3 + - - +
533A PHE* 3.5 43.0 - - + +
534A LEU* 3.6 7.5 - - - +
536A LEU 4.2 1.1 - - - -
537A ASP* 3.8 17.5 - - + +
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Residues in contact with ALA 381 (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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377A GLY 3.1 14.8 + - - +
378A GLN* 3.6 7.6 - - - +
379A ILE 3.3 0.2 - - - -
380A ALA* 1.3 77.2 - - - +
382A VAL* 1.3 61.0 + - + +
384A ARG* 3.3 5.9 + - - +
385A GLU* 3.2 26.9 + - - +
537A ASP* 3.7 10.4 - - + +
538A LYS 3.3 26.7 - - - +
539A PRO 5.0 0.7 - - - +
540A LEU* 3.8 22.0 - - + +
543A LEU* 5.8 1.3 - - + -
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Residues in contact with VAL 382 (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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365A LEU* 4.1 20.2 - - + -
374A MET* 3.8 12.1 - - + -
378A GLN 3.1 16.5 + - - +
379A ILE 3.2 3.3 + - - +
381A ALA* 1.3 74.8 - - - +
383A CYS* 1.3 63.4 + - - +
385A GLU* 3.2 3.8 + - - +
386A CYS* 3.0 34.8 + - - -
408A ILE* 5.0 1.3 - - + -
410A LEU* 5.2 0.7 - - + -
416A VAL* 4.3 19.1 - - + -
470A MET* 4.0 24.7 - - + -
543A LEU* 3.8 28.5 - - + -
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Residues in contact with CYS 383 (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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379A ILE* 2.8 30.4 + - - +
380A ALA* 3.7 4.9 - - - +
382A VAL* 1.3 78.1 - - - +
384A ARG* 1.3 57.0 + - - +
386A CYS* 3.3 5.4 + - - +
387A LEU* 2.8 36.8 + - + +
463A LEU* 4.5 9.9 - - + -
467A ALA* 4.4 7.6 - - - -
470A MET* 3.9 20.0 - - - -
510A PHE* 3.9 35.4 - - + -
533A PHE* 4.5 2.0 - - - -
534A LEU* 4.0 5.8 - - + -
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Residues in contact with ARG 384 (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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380A ALA 2.9 16.7 + - - +
381A ALA* 3.6 6.7 - - - +
382A VAL 3.3 0.2 - - - -
383A CYS* 1.3 77.5 - - - +
385A GLU* 1.3 71.7 + - - +
387A LEU* 3.3 3.0 + - - +
388A GLN* 3.0 49.6 + - - +
529A LEU* 3.9 21.0 + - + +
534A LEU* 3.2 48.6 + - + +
535A LYS* 4.4 6.9 - - - +
537A ASP* 2.9 23.8 + - - -
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Residues in contact with GLU 385 (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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339A ASN* 2.8 33.7 + - - +
381A ALA 3.2 15.0 + - - +
382A VAL 3.2 3.8 + - - +
384A ARG* 1.3 90.7 - - - +
386A CYS* 1.3 62.8 + - - +
388A GLN* 3.3 21.5 + - - +
389A ALA* 3.1 18.7 + - - +
416A VAL* 3.6 29.6 + - + +
540A LEU* 3.7 31.0 - - + +
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Residues in contact with CYS 386 (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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382A VAL* 3.0 30.2 + - - +
383A CYS 3.9 3.1 - - - +
385A GLU* 1.3 77.1 - - - +
387A LEU* 1.3 59.6 + - - +
389A ALA* 3.2 8.3 + - - +
390A LEU* 2.9 36.3 + - + +
403A ILE* 6.2 2.7 - - + -
408A ILE* 3.8 20.2 - - + -
416A VAL* 4.1 11.0 - - - -
418A LEU* 6.6 0.2 - - - -
463A LEU* 4.0 17.7 - - + -
466A MET* 3.7 24.7 - - + -
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Residues in contact with LEU 387 (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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383A CYS 2.8 21.8 + - - +
386A CYS* 1.3 74.7 - - - +
388A GLN* 1.3 59.9 + - - +
390A LEU* 3.9 2.8 - - + +
391A ASP* 2.8 31.7 + - - +
460A ILE* 4.0 9.6 - - + -
463A LEU* 3.4 24.7 - - + -
510A PHE* 4.0 16.2 - - + -
525A ALA* 3.9 19.4 - - + +
528A LEU* 3.8 44.6 - - + +
529A LEU* 3.6 18.0 - - + +
534A LEU* 4.0 14.6 - - + -
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Residues in contact with GLN 388 (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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337A ASN* 5.3 1.8 - - - +
339A ASN* 2.9 22.4 - - - +
384A ARG* 3.0 42.3 + - - +
385A GLU* 3.5 22.2 + - - +
386A CYS 3.3 0.2 - - - -
387A LEU* 1.3 75.9 - - - +
389A ALA* 1.3 62.9 + - - +
391A ASP* 3.8 2.6 - - - +
392A PHE* 3.0 24.7 + - - +
529A LEU* 4.1 19.4 - - + +
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Residues in contact with ALA 389 (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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337A ASN* 4.7 3.4 - - - -
339A ASN* 3.8 29.1 - - + +
340A ILE* 4.2 5.2 - - + -
385A GLU 3.1 12.1 + - - +
386A CYS* 3.5 10.8 - - - +
388A GLN* 1.3 75.7 - - - +
390A LEU* 1.3 57.3 + - - +
392A PHE* 3.2 7.8 + - - +
393A LEU* 2.9 34.2 + - - +
418A LEU* 4.2 20.4 - - + -
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Residues in contact with LEU 390 (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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386A CYS* 2.9 23.0 + - + +
387A LEU* 3.9 4.0 - - + +
388A GLN 3.3 0.2 - - - -
389A ALA* 1.3 74.6 - - + +
391A ASP* 1.3 60.8 + - - +
393A LEU* 4.4 14.4 - - + +
394A HIS* 2.7 47.0 + - + +
400A HIS* 4.6 0.2 - - + -
403A ILE* 3.9 23.8 - - + -
418A LEU* 4.6 2.5 - - + -
459A ASP* 3.8 50.5 - - + +
460A ILE* 4.2 13.7 - - + -
463A LEU* 4.5 17.0 - - + -
525A ALA* 4.1 8.1 - - + -
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Residues in contact with ASP 391 (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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387A LEU 2.8 22.0 + - - +
388A GLN* 3.8 4.0 - - - +
390A LEU* 1.3 72.4 - - - +
392A PHE* 1.3 58.0 + - - +
394A HIS* 4.7 2.7 - - - +
395A SER* 2.9 38.0 + - - -
525A ALA* 3.6 13.0 - - + +
526A LYS* 3.7 32.3 + - - +
529A LEU* 4.1 14.1 - - + +
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Residues in contact with PHE 392 (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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335A ASN* 3.4 41.7 - - + -
336A LYS 3.5 17.7 - - - -
337A ASN* 3.5 36.1 - - + +
340A ILE* 4.6 2.9 - - + -
388A GLN 3.0 13.4 + - - +
389A ALA 3.5 9.4 - - - +
390A LEU 3.2 0.2 - - - -
391A ASP* 1.3 77.2 + - - +
393A LEU* 1.3 72.7 + - + +
395A SER* 2.9 10.8 + - - -
396A ASN* 2.9 48.6 + - - -
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Residues in contact with LEU 393 (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 VAL* 4.3 8.5 - - + -
335A ASN* 4.5 10.5 - - + -
340A ILE* 4.3 8.5 - - + -
389A ALA 2.9 20.9 + - - +
390A LEU* 3.8 7.6 - - + +
392A PHE* 1.3 82.2 - - + +
394A HIS* 1.3 64.5 + - + +
396A ASN* 3.0 13.1 + - - +
397A GLN 3.1 0.2 + - - -
398A VAL* 2.9 50.4 + - + +
400A HIS* 4.5 12.8 - - + +
418A LEU* 3.6 22.2 - - + -
421A PHE* 3.6 34.3 - - + -
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Residues in contact with HIS 394 (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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390A LEU* 2.7 39.3 + - + +
391A ASP* 4.2 4.5 - - - +
393A LEU* 1.3 74.5 - - + +
395A SER* 1.3 57.9 + - - +
397A GLN* 2.9 21.9 + - - +
398A VAL 3.3 19.5 - - - +
427A ILE* 5.8 0.3 - - - +
456A PRO* 3.2 50.3 + - + +
459A ASP* 2.8 34.1 + - + +
460A ILE* 4.6 12.0 - - + +
525A ALA* 4.4 9.9 + - + +
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Residues in contact with SER 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASP* 2.9 22.3 + - - -
392A PHE* 2.9 18.9 + - - -
394A HIS* 1.3 76.4 - - - +
396A ASN* 1.3 65.6 + - - +
397A GLN* 3.3 8.5 + - - +
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Residues in contact with ASN 396 (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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335A ASN* 3.8 25.0 + - - +
392A PHE* 2.9 47.7 + - - +
393A LEU* 3.0 9.3 + - - +
395A SER* 1.3 86.9 + - - +
397A GLN* 1.3 70.4 + - - +
398A VAL* 3.3 7.8 + - + +
426A GLN* 5.3 1.6 - - - +
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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