Contacts of the helix formed by residues 361 - 382 (chain A) in PDB entry 1YOJ
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 ARG 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A TYR* 2.6 29.1 + - - +
360A LEU* 1.3 77.9 - - - +
362A LEU* 1.3 67.8 + - - +
363A PRO* 3.3 10.0 - - + +
364A GLN* 3.0 57.5 + - - +
365A LEU* 3.1 17.0 + - - +
529A TYR* 4.0 2.9 - - - +
531A PRO* 5.3 9.6 - - + -
532A GLY 5.9 1.6 - - - +
534A ASN 4.7 4.3 - - - +
535A LEU* 3.7 21.5 - - - +
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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
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361A ARG* 1.3 71.7 - - - +
363A PRO* 1.4 73.5 - - + +
364A GLN 3.1 0.2 + - - -
365A LEU* 3.1 7.7 + - + -
366A VAL* 2.8 32.5 + - + +
458A THR* 4.2 14.8 - - + -
490A PRO* 3.6 33.7 - - + -
493A LEU* 3.9 22.4 - - + -
521A TYR* 4.0 18.2 - - + -
522A PHE* 3.8 9.2 - - + -
529A TYR* 4.0 12.1 - - + -
535A LEU* 3.1 36.6 + - + +
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Residues in contact with PRO 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 3.4 10.5 - - + +
362A LEU* 1.4 89.2 - - + +
364A GLN* 1.3 69.2 + - - +
366A VAL* 4.1 1.4 - - - +
367A ASP* 3.1 27.4 + - - +
522A PHE* 3.4 26.4 - - + -
529A TYR* 3.4 34.1 - - + +
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Residues in contact with GLN 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 3.9 22.2 - - + -
361A ARG* 3.0 67.1 + - - +
363A PRO* 1.3 87.2 - - - +
365A LEU* 1.3 58.6 + - - +
367A ASP* 3.4 6.0 + - - +
368A MET* 2.9 35.9 + - - +
400A LEU* 3.7 26.3 - - + +
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Residues in contact with LEU 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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352A LEU* 3.7 26.0 - - + -
360A LEU* 4.0 10.3 - - + -
361A ARG 3.1 16.2 + - - +
362A LEU* 3.1 10.0 + - + +
364A GLN* 1.3 75.4 - - - +
366A VAL* 1.3 63.0 + - + +
368A MET* 3.5 18.9 + - + +
369A SER* 3.1 22.2 + - - -
457A LEU* 3.5 41.7 - - + +
458A THR* 4.5 2.5 - - + +
460A LYS* 4.2 11.0 - - + -
535A LEU* 3.3 34.3 - - + -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 2.8 42.0 + - + +
365A LEU* 1.3 69.4 - - - +
367A ASP* 1.3 62.5 + - - +
369A SER* 2.8 9.3 + - - -
370A ALA* 2.8 28.2 + - - +
454A LEU* 6.3 0.4 - - + -
493A LEU* 4.1 16.4 - - + -
518A LEU* 3.2 41.7 - - + +
521A TYR* 3.9 20.4 - - + -
522A PHE* 3.9 16.8 - - + -
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO 3.1 18.6 + - - +
364A GLN* 3.7 7.3 - - - +
365A LEU 3.3 0.2 - - - -
366A VAL* 1.3 77.9 - - - +
368A MET* 1.3 62.4 + - - +
370A ALA* 3.2 9.8 + - - +
371A GLN* 3.0 49.1 + - - +
400A LEU* 4.8 4.0 - - - +
518A LEU 5.7 0.2 - - - -
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Residues in contact with MET 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 4.3 16.2 - - - -
351A PHE* 4.3 7.2 - - - -
360A LEU* 3.7 28.7 - - + -
364A GLN* 2.9 38.1 + - + +
365A LEU* 3.7 21.8 - - + +
367A ASP* 1.3 72.6 + - - +
369A SER* 1.3 61.8 + - - +
371A GLN* 3.2 11.4 + - - +
372A ILE* 3.1 28.6 + - + +
396A VAL* 5.5 0.4 - - - -
400A LEU* 4.0 28.9 - - + +
402A CYS* 3.5 28.6 - - - +
457A LEU* 4.1 9.6 - - + -
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Residues in contact with SER 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU 3.1 13.2 + - - -
366A VAL* 2.8 21.5 + - - -
368A MET* 1.3 75.4 - - - +
370A ALA* 1.3 56.1 + - - +
372A ILE* 3.4 6.2 + - - -
373A ALA* 2.9 30.5 + - - +
450A PHE* 3.4 9.0 - - - -
454A LEU* 3.7 17.9 - - - +
457A LEU* 3.7 21.5 - - - +
518A LEU* 3.2 20.7 - - - +
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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 VAL 2.8 13.2 + - - +
367A ASP* 3.2 15.7 + - - +
369A SER* 1.3 76.9 + - - +
371A GLN* 1.3 61.3 + - + +
373A ALA* 3.5 4.8 + - - +
374A SER* 3.0 23.2 + - - -
515A GLN* 3.9 6.5 - - - +
518A LEU* 3.9 23.3 - - + +
519A GLU* 4.0 28.0 - - + +
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Residues in contact with GLN 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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323A LYS* 2.9 46.1 + - + +
367A ASP* 3.0 38.5 + - - +
368A MET* 3.2 11.7 + - - +
370A ALA* 1.3 72.7 - - + +
372A ILE* 1.3 66.9 + - - +
374A SER* 3.3 8.9 + - - -
375A GLY 3.1 17.5 + - - -
399A ASN 5.3 0.6 + - - -
400A LEU 3.0 24.0 + - - -
401A VAL* 3.4 4.7 - - - -
402A CYS* 2.9 34.9 + - + +
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Residues in contact with ILE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.7 31.0 - - + -
368A MET 3.1 18.6 + - - +
369A SER* 3.6 14.4 - - - +
371A GLN* 1.3 76.2 - - - +
373A ALA* 1.3 57.5 + - - +
375A GLY* 3.2 3.5 + - - -
376A MET* 2.9 30.9 + - + +
389A LEU* 4.4 8.1 - - + -
394A ILE* 3.9 32.5 - - + -
402A CYS* 4.3 7.9 - - + -
403A LYS* 6.3 0.2 - - - +
404A VAL* 4.0 8.8 - - + +
450A PHE* 3.8 16.4 - - + -
453A LEU* 3.8 22.4 - - + -
457A LEU* 4.3 5.4 - - + -
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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 SER 2.9 17.5 + - - +
370A ALA* 3.6 5.8 - - - +
372A ILE* 1.3 75.9 - - - +
374A SER* 1.3 52.8 + - - +
376A MET* 3.3 1.7 + - - +
377A ALA* 2.7 34.3 + - - +
450A PHE* 3.8 20.3 - - + -
511A PHE* 3.8 15.2 - - + +
514A LEU* 4.3 5.2 - - + -
515A GLN* 3.7 29.4 - - - +
518A LEU* 4.6 0.2 - - + -
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Residues in contact with SER 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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321A HIS* 3.6 24.4 + - - -
323A LYS* 4.0 6.7 - - - +
370A ALA 3.0 12.0 + - - -
371A GLN* 3.5 12.3 - - - -
372A ILE 3.2 0.4 - - - -
373A ALA* 1.3 72.2 - - - +
375A GLY* 1.3 63.7 + - - +
377A ALA* 3.2 3.8 + - - +
378A TYR 3.2 16.1 + - - -
381A ARG* 4.7 1.2 + - - -
515A GLN* 3.5 34.8 + - - +
519A GLU* 5.0 1.3 - - - -
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Residues in contact with GLY 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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321A HIS* 4.1 3.4 - - - -
323A LYS* 3.7 17.6 - - - +
324A LEU* 3.4 23.3 - - - +
371A GLN 3.1 11.1 + - - -
372A ILE 3.6 3.4 - - - -
374A SER* 1.3 75.2 - - - +
376A MET* 1.3 61.8 + - - +
378A TYR* 3.2 6.1 + - - +
379A VAL* 3.1 25.3 + - - +
404A VAL* 4.4 3.4 - - - -
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Residues in contact with MET 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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372A ILE* 2.9 20.3 + - + +
373A ALA 3.8 0.4 - - - +
375A GLY* 1.3 73.9 - - - +
377A ALA* 1.3 60.3 + - - +
379A VAL* 3.5 22.3 + - + +
380A GLU* 2.9 28.9 + - - +
386A HIS* 4.1 16.2 - - + -
389A LEU* 4.0 25.1 - - + -
404A VAL* 4.3 15.5 - - + -
443A ILE* 3.9 9.4 - - + -
446A ASP* 3.7 25.8 - - + +
511A PHE* 3.4 50.5 - - + -
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Residues in contact with ALA 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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373A ALA 2.7 20.3 + - - +
374A SER 3.2 6.9 + - - +
376A MET* 1.3 74.7 - - - +
378A TYR* 1.3 57.5 + - - +
380A GLU* 3.4 6.7 - - - +
381A ARG* 3.0 50.7 + - - +
511A PHE* 3.7 22.2 - - + -
512A GLU* 4.2 5.2 - - - +
515A GLN* 3.8 14.6 - - - +
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Residues in contact with TYR 378 (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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318A LYS 4.0 4.7 + - - -
319A LEU* 3.5 25.9 - - + -
320A ARG* 2.8 42.1 + - - +
321A HIS* 3.5 40.6 - + + -
324A LEU* 3.7 17.7 - - + -
374A SER 3.2 7.3 + - - +
375A GLY 3.4 7.4 - - - +
376A MET 3.2 0.2 - - - -
377A ALA* 1.3 74.3 - - - +
379A VAL* 1.3 68.5 + - - +
381A ARG* 3.2 21.6 + - + +
382A MET* 2.9 54.9 + - + +
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Residues in contact with VAL 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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319A LEU* 5.1 7.9 - - + -
324A LEU* 4.3 22.0 - - + -
375A GLY 3.1 14.3 + - - +
376A MET* 3.6 35.2 - - + +
378A TYR* 1.3 78.7 - - - +
380A GLU* 1.3 59.9 + - - +
382A MET* 3.2 11.0 + - - +
384A TYR* 2.9 59.1 + - + +
385A VAL 4.1 2.2 - - - +
386A HIS* 4.5 9.0 - - + +
404A VAL* 5.5 3.4 - - + -
443A ILE* 4.3 0.7 - - + -
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Residues in contact with GLU 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 MET 2.9 18.4 + - - +
377A ALA* 3.4 6.7 - - - +
378A TYR 3.2 0.2 - - - -
379A VAL* 1.3 75.0 - - - +
381A ARG* 1.3 65.6 + - + +
383A ASN* 3.2 18.2 + - - +
384A TYR 4.5 1.1 - - - -
443A ILE* 3.8 36.0 - - + +
444A LYS* 5.0 1.7 + - - -
447A VAL* 5.1 0.9 - - - +
510A THR* 3.5 18.7 - - - +
511A PHE* 2.9 31.1 + - + +
512A GLU* 3.5 25.8 + - - +
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A HIS* 4.4 10.3 + - - -
374A SER 4.7 0.8 + - - -
377A ALA* 3.0 45.8 + - - +
378A TYR* 3.2 33.8 + - + +
380A GLU* 1.3 73.7 - - + +
382A MET* 1.3 60.9 + - + +
383A ASN* 3.1 16.1 + - - +
512A GLU* 5.3 12.0 + - - +
515A GLN* 5.2 1.8 + - - -
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Residues in contact with MET 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 4.4 11.9 - - + +
319A LEU* 4.0 10.3 - - + -
378A TYR* 2.9 60.8 + - + +
379A VAL 3.2 2.6 + - - +
381A ARG* 1.3 78.1 - - + +
383A ASN* 1.3 70.8 + - - +
384A TYR* 3.1 35.0 - - + +
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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