Contacts of the strand formed by residues 547 - 558 (chain B) in PDB entry 5JJD
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 ILE 547 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B LYS* 3.9 3.8 - - - +
426B GLY* 3.1 49.2 + - - +
427B VAL* 3.4 18.4 - - - +
428B THR* 3.8 12.3 - - + -
531B THR* 4.5 5.6 - - + -
532B LEU 3.3 5.2 - - - +
533B VAL* 4.2 13.2 - - + -
542B ILE* 4.0 16.6 - - + -
543B SER 3.8 10.8 - - - +
544B ARG* 3.5 30.1 - - + +
545B ASP 4.9 1.0 - - - -
546B ASN* 1.3 84.2 - - - +
548B LEU* 1.3 61.4 + - - +
596B ILE* 4.3 5.8 - - + -
598B PHE* 4.3 9.9 - - + -
602B PEG 3.9 4.6 + - - -
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Residues in contact with LEU 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ALA* 3.9 21.8 - - + -
424B VAL 3.5 34.8 - - - +
425B LYS* 3.6 19.3 - - + +
427B VAL 4.0 3.4 - - - -
530B GLN 3.6 0.3 - - - +
531B THR* 3.4 2.7 - - - +
532B LEU* 2.6 53.3 + - + +
547B ILE* 1.3 75.9 - - - +
549B CYS* 1.3 61.4 + - - +
550B LYS* 3.8 5.6 + - - +
602B PEG 3.7 42.2 - - - +
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Residues in contact with CYS 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B HIS 3.5 1.2 - - - +
423B ALA* 3.3 5.6 - - - -
424B VAL* 2.8 43.2 + - + +
427B VAL* 3.3 26.2 + - + +
428B THR 4.2 0.7 - - - -
429B GLY* 3.6 29.4 - - - -
432B VAL* 3.6 18.4 - - + -
529B CYS* 3.7 15.5 - - - -
530B GLN 3.4 4.5 - - - -
531B THR* 4.6 0.9 - - - +
548B LEU* 1.3 70.1 - - - +
550B LYS* 1.3 64.1 + - - +
551B ILE* 3.6 12.2 + - - +
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Residues in contact with LYS 550 (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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92A ASP* 3.2 44.6 - - - +
400B GLU* 5.7 1.2 + - - -
421B THR* 6.4 2.5 - - - -
422B HIS 3.6 7.9 - - - -
423B ALA* 4.3 19.5 - - + +
528B ILE 3.5 2.3 - - - +
529B CYS* 3.3 4.7 - - - -
530B GLN* 2.7 54.1 + - + +
532B LEU* 3.8 25.1 - - + +
548B LEU* 3.8 6.1 + - + +
549B CYS* 1.3 70.5 - - - +
551B ILE* 1.3 60.9 + - - +
552B THR* 5.2 1.2 + - - +
602B PEG 5.7 0.4 - - - -
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Residues in contact with ILE 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ALA 6.3 0.2 - - - -
421B THR* 3.2 7.3 - - - -
422B HIS* 2.7 46.6 + - + +
424B VAL* 3.5 27.4 - - + -
432B VAL* 3.9 20.4 - - + -
527B MET* 3.8 29.8 - - + -
528B ILE 3.6 2.5 - - - -
529B CYS* 3.9 4.0 - - - -
549B CYS* 3.7 21.5 - - - +
550B LYS* 1.3 75.7 - - - +
552B THR* 1.3 70.1 + - - +
553B TYR* 4.4 7.4 - - + +
580B LEU* 5.1 6.3 - - + -
583B PHE* 5.4 0.2 - - + -
584B THR* 3.8 17.0 - - + -
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Residues in contact with THR 552 (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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382B SER 3.5 27.4 - - - +
383B LEU* 3.9 23.4 + - - +
419B LYS* 4.0 14.4 - - - -
420B ALA 3.6 7.2 - - - +
421B THR* 4.4 10.1 - - + +
526B ALA 3.8 1.2 - - - +
527B MET* 3.4 2.8 - - - +
528B ILE* 2.8 49.3 + - + +
550B LYS* 5.2 1.0 + - - +
551B ILE* 1.3 74.4 + - - +
553B TYR* 1.3 61.6 + - - +
554B VAL* 4.5 7.4 - - + -
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Residues in contact with TYR 553 (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 LEU* 4.3 10.3 - - + -
419B LYS* 3.3 2.1 - - - -
420B ALA* 2.7 49.5 + - + +
436B PHE* 4.2 8.7 - + - -
525B VAL* 3.6 33.5 - - + +
526B ALA 3.5 9.6 - - - -
527B MET* 3.8 19.3 - - + -
551B ILE* 4.1 7.1 - - + -
552B THR* 1.3 73.9 - - - +
554B VAL* 1.3 62.6 + - - +
555B ALA* 3.8 23.2 - - + +
576B TYR* 3.9 19.4 - + - -
579B PHE* 3.8 22.2 - + - -
580B LEU* 4.4 17.9 - - + -
601B PEG 5.6 0.3 + - - -
604B PGE 3.8 23.6 + - - -
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Residues in contact with VAL 554 (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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378B HIS* 3.8 10.1 - - + -
382B SER* 3.8 27.8 - - - +
392B TRP* 5.9 0.9 - - + -
418B LEU 3.2 6.7 - - - +
419B LYS* 3.7 34.1 - - + +
524B ASN 4.5 0.7 - - - +
525B VAL* 3.4 5.6 - - - +
526B ALA* 3.0 52.6 + - + +
528B ILE* 5.6 1.1 - - + -
552B THR* 4.5 4.7 - - + +
553B TYR* 1.3 82.8 - - - +
555B ALA* 1.3 61.4 + - - +
556B ASN* 4.8 7.4 - - - +
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Residues in contact with ALA 555 (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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416B ASP 4.3 1.4 - - - +
417B PRO* 3.8 0.3 - - - +
418B LEU* 2.7 43.0 + - + +
524B ASN 3.7 4.5 - - - -
525B VAL* 4.0 11.0 - - + -
553B TYR* 3.8 26.4 - - + +
554B VAL* 1.3 75.8 - - - +
556B ASN* 1.3 60.5 + - - +
557B VAL* 3.9 5.4 + - + +
576B TYR* 3.9 22.2 + - + +
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Residues in contact with ASN 556 (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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378B HIS* 5.7 0.9 - - - -
392B TRP* 6.0 0.5 - - - -
406B ARG* 5.2 2.4 - - - +
417B PRO* 3.4 35.5 - - - +
418B LEU 4.8 1.0 - - - +
522B LYS 3.7 1.6 - - - +
523B ILE* 3.4 3.6 - - - -
524B ASN* 2.9 52.7 + - + +
525B VAL* 4.8 0.2 - - - +
554B VAL* 4.8 8.3 - - - +
555B ALA* 1.3 78.4 + - - +
557B VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 3.9 14.2 - - - +
416B ASP 4.8 9.5 + - - +
521B ALA* 4.6 2.5 - - + -
522B LYS 3.5 2.9 - - - +
523B ILE* 4.1 20.6 - - + -
525B VAL* 5.1 2.0 - - + -
555B ALA* 3.9 12.6 + - + +
556B ASN* 1.3 77.1 - - - +
558B ASN* 1.3 71.7 + - - +
559B PRO* 3.5 13.3 - - + +
576B TYR* 3.7 22.4 - - - +
601B PEG 4.0 40.6 - - - +
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Residues in contact with ASN 558 (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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413B ILE* 3.7 27.8 - - - +
415B LEU* 3.7 18.0 - - + +
521B ALA* 3.3 3.3 - - - -
522B LYS* 2.7 49.8 + - + +
557B VAL* 1.3 73.2 - - - +
559B PRO* 1.3 68.5 - - - +
560B GLY* 3.0 19.6 + - - -
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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
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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