Contacts of the strand formed by residues 494 - 506 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B ILE* 5.1 3.4 - - + -
421B PHE 3.4 10.8 - - - +
422B ASP* 4.5 6.3 - - + -
443B THR* 2.8 27.0 + - - -
444B ALA 2.7 16.2 + - - +
445B ASP 3.9 14.4 - - - -
446B SER* 3.9 16.8 - - - +
447B LEU* 3.4 52.4 - - + +
450B LEU* 3.9 8.7 - - + +
465B VAL* 4.5 3.3 - - + +
489B LEU* 3.6 28.5 + - + -
490B ASN* 4.5 9.7 + - - +
492B GLY 4.3 10.3 + - - -
493B ASN* 1.3 77.8 - - - +
495B TYR* 1.3 63.7 + - - +
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Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LEU 3.4 0.6 - - - +
420B ILE* 3.2 7.4 - - - +
421B PHE* 2.7 71.7 + + + +
422B ASP 3.9 7.4 - - - -
423B ASP* 2.6 31.7 + - - -
426B ARG* 3.4 16.3 + - - -
436B ILE* 3.6 26.7 - - + +
441B ALA* 3.7 15.5 - - + +
442B PRO 3.3 5.8 - - - +
443B THR* 3.2 35.3 + - + -
450B LEU* 3.6 7.0 - - - +
493B ASN* 3.7 15.8 - - + +
494B TYR* 1.3 77.8 - - - +
496B ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B TYR* 4.0 17.9 - - + -
419B LEU 3.0 9.9 - - - +
420B ILE* 3.9 15.3 - - + -
441B ALA* 3.4 4.5 - - - -
442B PRO* 3.1 30.1 + - - +
450B LEU* 3.8 19.3 - - + +
454B GLU* 4.1 9.9 - - + -
456B ILE* 4.6 2.2 - - + -
495B TYR* 1.3 74.0 - - - +
497B ILE* 1.3 64.2 + - - +
498B GLU 4.1 0.4 - - - -
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Residues in contact with ILE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B SER* 4.3 2.9 - - - +
376B VAL* 3.8 38.6 - - + -
380B VAL* 5.4 0.7 - - + -
418B TYR* 3.2 2.3 - - - -
419B LEU* 2.9 37.8 + - + -
421B PHE* 3.8 26.9 - - + -
435B TYR* 4.0 21.5 - - + -
440B VAL* 3.5 24.5 - - + +
441B ALA* 3.6 16.8 - - + -
442B PRO* 5.1 0.2 - - - -
496B ALA* 1.3 79.8 - - - +
498B GLU* 1.3 72.1 - - - +
499B VAL* 3.4 6.1 + - + +
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Residues in contact with GLU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B SER* 3.4 7.1 + - - -
370B VAL* 2.7 57.8 + - + +
371B LYS* 4.4 5.1 + - + +
390B ARG* 2.9 18.0 + - - -
416B SER* 2.6 28.2 + - - +
417B ALA 3.3 11.9 - - - +
418B TYR* 3.5 30.9 + - + -
440B VAL 4.7 1.6 + - - -
442B PRO* 5.9 0.2 - - - +
454B GLU* 4.8 7.6 + - - +
496B ALA 4.1 0.6 - - - -
497B ILE* 1.3 73.3 - - - +
499B VAL* 1.3 56.7 + - - +
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B PRO 4.5 0.2 - - - -
367B THR* 3.6 44.0 - - + +
368B LEU 3.1 11.2 - - - +
370B VAL* 3.8 2.9 - - - -
376B VAL* 4.2 1.6 - - + -
387B LEU* 3.7 20.9 - - + -
409B ILE* 3.9 5.6 - - + +
416B SER* 3.0 4.3 - - - -
417B ALA 2.6 49.7 + - - +
419B LEU* 3.8 15.3 - - + -
497B ILE* 3.6 19.1 - - + +
498B GLU* 1.3 80.1 - - - +
500B THR* 1.3 60.0 + - - +
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Residues in contact with THR 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B ILE* 6.1 2.0 - - + -
366B PRO 3.2 5.4 + - - -
368B LEU* 2.9 49.4 + - + +
370B VAL* 3.7 21.8 - - + -
409B ILE* 4.2 1.6 - - - -
410B LEU* 4.3 2.8 - - - +
415B LYS* 2.6 25.9 + - - +
416B SER* 3.9 2.0 - - - -
499B VAL* 1.3 76.5 - - - +
501B PRO* 1.3 76.9 + - - +
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Residues in contact with PRO 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B PHE* 3.6 23.8 - - + +
334B ILE 4.6 1.9 + - - +
364B ALA* 4.1 8.3 - - + -
365B HIS 2.9 15.0 - - - +
366B PRO 3.5 9.4 - - - +
368B LEU* 4.7 2.1 - - - +
406B SER* 3.5 43.3 - - - +
409B ILE* 3.8 9.9 - - + -
410B LEU* 3.7 19.5 - - + +
500B THR* 1.3 102.4 + - - +
502B GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B PHE* 4.3 3.1 - - - -
334B ILE 3.0 15.5 - - - -
335B SER* 4.6 0.4 - - - -
336B THR* 4.9 1.8 - - - -
364B ALA* 3.2 5.3 - - - -
365B HIS* 2.8 31.6 + - - +
368B LEU* 4.2 16.2 - - - +
500B THR 3.6 1.4 + - - -
501B PRO* 1.3 75.5 - - - +
503B VAL* 1.4 65.6 + - - -
504B HIS* 3.8 0.7 - - - +
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Residues in contact with VAL 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ALA* 3.5 27.1 - - + +
320B ASN* 4.0 17.7 - - - +
323B VAL* 3.9 11.4 - - + -
330B LEU* 4.1 15.5 - - + +
333B PHE* 3.6 25.4 - - + +
334B ILE 2.8 8.7 + - - +
335B SER* 3.2 7.8 + - - -
336B THR 3.0 23.0 + - - -
362B ILE* 3.6 29.2 - - + -
363B GLN 3.9 3.1 - - - +
364B ALA* 4.3 2.9 - - - +
502B GLY* 1.4 71.8 - - - -
504B HIS* 1.3 61.9 + - - +
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Residues in contact with HIS 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ASN* 5.2 0.3 + - - -
317B ALA* 3.5 8.3 - - - +
336B THR* 2.7 24.6 + - - +
337B ASN* 3.0 19.9 + - - +
363B GLN* 2.8 26.8 + - - +
365B HIS* 3.5 33.4 - + + +
375B MET* 3.4 18.8 - - - -
503B VAL* 1.3 78.8 - - - +
505B HIS* 1.3 60.4 + - - +
534B GLU* 3.9 4.2 - - - +
544B ARG* 3.6 18.4 + - - -
2805B FAD 3.2 39.1 - + - +
2806B FUM 2.9 21.9 + - - -
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Residues in contact with HIS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ALA* 3.8 0.6 - - - +
362B ILE* 3.6 3.1 - - - +
363B GLN* 2.7 46.2 + - + +
504B HIS* 1.3 82.5 - - + +
506B THR* 1.3 89.4 + - - +
507B MET* 3.7 14.1 + - - -
534B GLU* 3.2 34.9 + - + +
540B HIS* 4.1 10.8 + + - -
544B ARG* 3.1 53.1 + - - +
549B ALA* 3.7 4.0 - - + -
552B ASP* 5.6 0.7 - - - -
2805B FAD 3.3 23.4 + - - -
2810B NA 4.5 1.6 - - - -
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Residues in contact with THR 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLY* 3.1 10.4 - - - -
316B PHE* 3.0 69.2 + - + -
317B ALA* 3.7 19.5 - - - +
323B VAL* 4.6 0.2 - - + -
361B TYR 4.2 3.8 - - - -
362B ILE* 4.1 12.6 - - + -
505B HIS* 1.3 78.7 - - - +
507B MET* 1.3 54.3 - - - +
508B GLY 3.2 2.8 + - - +
534B GLU* 2.9 11.8 + - - +
2810B NA 2.4 27.2 - - - -
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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