Contacts of the strand formed by residues 563 - 569 (chain B) in PDB entry 3QFR
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 THR 563 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B VAL* 3.5 10.9 - - + +
533B MET* 4.2 20.9 - - + -
547B ILE* 5.0 4.3 - - + -
550B ARG* 2.7 46.5 + - + +
560B VAL* 4.4 1.0 - - - +
561B GLY 3.6 3.3 + - - -
562B GLU* 1.3 72.2 - - - +
564B LEU* 1.3 59.3 + - - +
590B ALA 3.7 23.5 + - - +
591B LEU* 3.5 10.1 - - + +
592B THR* 2.8 36.6 + - - -
593B GLN 3.5 1.6 + - - -
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Residues in contact with LEU 564 (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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531B VAL 2.8 13.3 + - - +
532B ILE* 4.6 7.2 - - + -
533B MET* 3.1 32.6 + - - +
562B GLU* 3.4 34.5 - - + +
563B THR* 1.3 78.8 - - - +
565B LEU* 1.3 60.9 + - - +
566B TYR* 4.4 16.2 - - + +
592B THR* 4.2 6.5 - - - -
593B GLN* 3.2 37.7 - - + +
615B ASP* 6.4 0.2 - - + -
618B HIS* 4.2 7.0 - - + -
619B LEU* 4.2 19.7 - - + -
622B LEU* 4.1 20.4 - - + -
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Residues in contact with LEU 565 (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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533B MET* 3.3 28.9 - - + +
535B GLY 4.9 0.2 - - - +
540B VAL* 4.4 13.2 - - + -
543B PHE* 3.7 28.9 - - + -
547B ILE* 3.7 23.1 - - + -
564B LEU* 1.3 77.5 - - - +
566B TYR* 1.3 74.7 + - - +
567B TYR* 4.4 2.5 - - + +
582B LEU* 4.1 13.9 - - + -
591B LEU* 3.9 11.9 - - + -
593B GLN* 3.4 8.2 + - - +
594B LEU* 3.8 23.5 - - + +
595B ASN* 3.4 25.8 + - - +
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Residues in contact with TYR 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ILE* 4.5 5.4 - - + -
533B MET 2.7 17.6 + - - +
534B VAL* 3.6 12.1 - - + -
535B GLY 3.0 25.5 + - - +
564B LEU* 4.4 21.4 - - + +
565B LEU* 1.3 78.1 - - - +
567B TYR* 1.3 61.6 + - - +
593B GLN* 4.4 1.2 + - - -
595B ASN* 3.6 26.2 - - + -
608B VAL* 3.7 18.4 - - + +
611B LEU* 2.8 39.9 + - + -
612B LEU* 3.5 28.3 - - + -
615B ASP* 2.5 32.1 + - - +
619B LEU* 4.0 14.9 - - + +
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Residues in contact with TYR 567 (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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535B GLY 3.3 15.5 - - - -
537B GLY* 3.4 23.3 + - - -
540B VAL* 3.6 21.5 - - + -
565B LEU* 3.9 14.8 - - + -
566B TYR* 1.3 76.0 - - - +
568B GLY* 1.3 81.5 + - - +
569B CYS* 3.8 17.9 - - + +
575B ASP 3.4 6.8 + - - -
576B TYR* 3.9 24.0 - + - -
577B LEU* 3.1 41.9 + - + +
582B LEU* 5.1 2.7 - - + -
594B LEU* 4.9 2.0 - - + -
595B ASN 3.1 6.3 + - - +
596B VAL* 3.3 27.6 - - + -
597B ALA 3.0 21.2 + - - -
608B VAL* 3.6 9.8 - - - +
611B LEU* 5.1 0.5 - - - +
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Residues in contact with GLY 568 (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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536B PRO* 3.6 15.0 - - - +
537B GLY 2.8 25.9 + - - -
567B TYR* 1.3 87.3 - - - +
569B CYS* 1.3 65.4 + - - +
596B VAL* 4.5 0.2 - - - -
597B ALA* 3.3 13.7 - - - -
608B VAL* 4.6 4.0 - - - -
753B NAP 3.7 7.0 - - - -
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Residues in contact with CYS 569 (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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537B GLY* 5.3 1.3 - - - +
567B TYR* 3.8 12.1 - - + +
568B GLY* 1.3 75.0 - - - +
570B ARG* 1.3 61.3 + - - +
571B ARG 3.6 18.4 - - - -
575B ASP* 2.9 34.3 - - - +
576B TYR* 3.7 12.6 - - - -
596B VAL* 4.6 0.2 - - - -
597B ALA 3.1 5.3 + - - -
598B PHE* 2.9 47.6 - - - -
599B SER 3.2 0.7 + - - -
753B NAP 3.1 17.2 + - - -
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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