Contacts of the strand formed by residues 494 - 506 (chain A) in PDB entry 1JRX
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 TYR 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A ILE* 5.3 2.2 - - + -
421A PHE 3.2 13.2 - - - +
422A ASP* 4.6 5.6 - - + -
443A THR* 2.8 26.3 + - - -
444A ALA 3.0 8.6 + - - +
445A ASP 3.7 24.0 - - - -
446A SER* 4.0 3.1 - - - -
447A LEU* 3.5 62.5 - - + +
450A LEU* 4.0 9.4 - - + +
465A VAL* 4.4 3.3 - - + +
489A LEU* 3.4 29.9 + - + -
490A ASN* 4.2 11.2 - - - +
492A GLY 4.3 9.9 - - - -
493A ASN* 1.3 77.1 - - - +
495A TYR* 1.3 62.9 + - - +
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Residues in contact with TYR 495 (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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419A LEU 4.2 0.2 - - - -
420A ILE* 3.4 6.2 - - - +
421A PHE* 2.6 70.6 + + + -
422A ASP 3.8 7.4 - - - -
423A ASP* 2.3 42.6 + - - -
426A ARG* 3.2 16.5 + - - -
436A ILE* 3.7 25.7 - - + +
441A ALA* 3.6 13.5 - - + +
442A PRO 3.3 6.5 - - - +
443A THR* 3.4 33.0 - - + -
450A LEU* 3.7 7.2 - - - +
493A ASN* 3.7 12.7 + - + +
494A TYR* 1.3 75.0 - - - +
496A ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 496 (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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418A TYR* 4.1 16.8 - - + -
419A LEU 3.0 7.9 - - - +
420A ILE* 3.9 10.1 - - + -
441A ALA* 3.5 2.4 - - - -
442A PRO* 3.0 33.8 + - - +
450A LEU* 3.7 25.4 - - + -
454A GLU* 4.3 8.7 - - + -
456A ILE* 4.6 2.0 - - + -
495A TYR* 1.3 76.0 - - - +
497A ILE* 1.3 63.4 - - - +
498A GLU 4.1 0.2 - - - -
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Residues in contact with ILE 497 (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* 4.3 3.1 - - - +
376A VAL* 3.8 38.4 - - + -
380A VAL* 5.3 0.7 - - + -
418A TYR* 3.3 2.8 - - - -
419A LEU* 2.7 43.1 + - + -
421A PHE* 3.7 29.8 - - + -
435A TYR* 4.0 22.4 - - + -
440A VAL* 3.6 22.4 - - + +
441A ALA* 3.8 14.8 - - + -
496A ALA* 1.3 79.9 - - - +
498A GLU* 1.3 69.1 - - - +
499A VAL* 3.4 10.4 + - + +
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Residues in contact with GLU 498 (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* 3.4 7.4 + - - -
370A VAL* 2.7 58.3 + - + +
371A LYS* 4.4 5.1 + - + +
390A ARG* 2.8 21.1 + - - -
416A SER* 2.5 27.9 + - - +
417A ALA 3.5 10.8 - - - +
418A TYR* 3.6 27.3 + - + -
440A VAL 4.6 2.2 + - - -
442A PRO* 5.8 0.6 - - - +
454A GLU* 4.9 6.2 + - - +
496A ALA 4.1 0.6 + - - -
497A ILE* 1.3 74.0 - - - +
499A VAL* 1.3 55.7 + - - +
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Residues in contact with VAL 499 (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 THR* 3.6 44.0 - - + +
368A LEU 3.2 9.2 - - - +
370A VAL* 3.9 2.7 - - - -
376A VAL* 4.2 2.9 - - + -
387A LEU* 3.8 20.4 - - + -
409A ILE* 3.8 6.0 - - + +
416A SER* 3.1 4.7 - - - -
417A ALA 2.6 49.3 + - - +
419A LEU* 4.0 9.9 - - + +
497A ILE* 3.6 24.2 - - + +
498A GLU* 1.3 80.9 - - - +
500A THR* 1.3 61.9 + - - +
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Residues in contact with THR 500 (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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334A ILE* 6.2 0.9 - - + -
366A PRO 3.2 5.6 - - - -
368A LEU* 2.8 51.1 + - + +
370A VAL* 3.9 20.0 - - + -
409A ILE* 4.2 1.1 - - - -
410A LEU* 4.4 2.8 - - - +
415A LYS* 2.6 25.9 + - - +
416A SER* 4.0 1.7 - - - -
499A VAL* 1.3 76.7 - - - +
501A PRO* 1.3 77.2 + - - +
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Residues in contact with PRO 501 (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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333A PHE* 3.5 28.3 - - + +
334A ILE 4.7 1.9 + - - +
364A ALA* 4.1 5.6 - - + -
365A HIS 3.0 13.5 - - - +
366A PRO 3.6 5.2 - - - +
368A LEU* 4.6 2.1 - - - +
406A SER* 3.5 45.3 - - - +
409A ILE* 3.7 14.1 - - + -
410A LEU* 3.7 16.6 - - + -
500A THR* 1.3 104.0 + - - +
502A GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 502 (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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333A PHE* 4.3 2.9 - - - -
334A ILE 3.1 14.4 - - - -
336A THR* 4.9 2.7 - - - -
364A ALA* 3.1 6.5 - - - -
365A HIS* 2.8 32.7 + - - +
368A LEU* 4.1 16.4 - - - +
500A THR 3.6 2.0 + - - -
501A PRO* 1.3 76.0 - - - +
503A VAL* 1.3 65.1 + - - -
504A HIS* 3.9 0.9 - - - +
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Residues in contact with VAL 503 (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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317A ALA* 3.5 26.2 - - + +
320A ASN* 4.1 11.0 - - - +
323A VAL* 4.0 10.1 - - + -
330A LEU* 4.0 20.6 - - + +
333A PHE* 3.6 26.5 - - + +
334A ILE 2.8 10.4 + - - +
335A SER* 3.1 9.9 + - - -
336A THR 3.0 22.9 + - - -
362A ILE* 3.8 28.5 - - + -
363A GLN 4.0 2.7 - - - +
364A ALA* 4.3 2.2 - - - +
502A GLY* 1.3 70.5 - - - -
504A HIS* 1.3 62.2 + - - +
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Residues in contact with HIS 504 (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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164A ASN* 5.2 0.3 + - - -
317A ALA* 3.5 7.9 - - - +
336A THR* 2.7 22.6 + - - +
337A ASN* 2.9 20.7 + - - +
363A GLN* 2.7 29.6 + - - +
365A HIS* 3.6 32.9 - + + +
375A MET* 3.5 17.5 - - - -
503A VAL* 1.3 77.5 - - - +
505A HIS* 1.3 60.2 + - + +
534A GLU* 3.9 4.2 - - - +
544A ARG* 3.6 14.3 + - - -
1805A FAD 3.1 40.1 - + - +
1806A FUM 2.5 28.9 + - - -
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Residues in contact with HIS 505 (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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317A ALA* 3.7 2.0 - - - +
362A ILE* 3.7 2.6 - - - +
363A GLN* 2.8 41.5 + - + +
504A HIS* 1.3 83.5 + - + +
506A THR* 1.3 90.9 + - - +
507A MET* 3.7 12.6 + - - -
534A GLU* 3.2 34.3 + - + +
540A HIS* 4.1 9.7 + + - -
544A ARG* 3.0 53.3 + - - +
549A ALA* 3.7 4.5 - - + -
552A ASP* 5.8 0.2 - - - -
553A ILE* 6.5 0.2 - - + -
1805A FAD 3.2 25.6 + - - -
1810A NA 4.5 1.8 - - - -
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Residues in contact with THR 506 (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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315A GLY* 3.0 11.3 - - - -
316A PHE* 2.9 71.0 + - + -
317A ALA* 3.7 16.6 - - - +
323A VAL* 4.7 0.2 - - + -
359A MET 5.9 0.2 - - - -
361A TYR 4.3 3.4 - - - -
362A ILE* 4.1 12.1 - - + +
505A HIS* 1.3 83.2 - - - +
507A MET* 1.3 54.6 + - - +
508A GLY 3.2 2.1 + - - -
534A GLU* 2.8 9.4 + - - +
1810A NA 2.5 25.8 - - - -
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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