Contacts of the strand formed by residues 563 - 569 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A VAL* 3.8 7.1 - - + +
533A MET* 3.2 26.7 - - + -
547A ILE* 3.8 14.4 - - + -
550A ARG* 3.1 38.6 + - + +
560A VAL* 4.4 1.4 - - - +
561A GLY 3.6 3.9 + - - -
562A GLU* 1.3 73.7 + - - +
564A LEU* 1.3 59.8 + - - +
590A ALA 3.7 21.9 + - - +
591A LEU* 3.3 6.6 - - + +
592A THR* 2.8 31.7 + - - -
593A GLN 3.4 0.2 + - - -
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Residues in contact with LEU 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A VAL 3.1 16.1 + - - +
532A ILE* 4.5 5.6 - - + -
533A MET* 2.9 33.5 + - - +
562A GLU* 4.1 17.9 - - + +
563A THR* 1.3 78.7 - - - +
565A LEU* 1.3 60.3 + - - +
566A TYR* 4.0 25.7 - - + +
592A THR* 4.9 0.9 - - - -
593A GLN* 3.1 46.4 - - + +
595A ASN* 4.8 0.2 - - - +
618A HIS* 4.2 16.8 - - + +
619A LEU* 4.5 2.7 - - + -
622A LEU* 3.6 26.0 - - + -
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Residues in contact with LEU 565 (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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533A MET* 3.5 15.9 - - + +
535A GLY 4.7 0.7 - - - +
540A VAL* 4.2 16.6 - - + -
543A PHE* 4.1 29.8 - - + -
544A ILE* 5.6 0.2 - - + -
547A ILE* 5.1 4.9 - - + -
564A LEU* 1.3 75.0 - - - +
566A TYR* 1.3 73.8 + - - +
567A TYR* 4.1 10.5 - - + +
582A LEU* 3.7 36.6 - - + -
591A LEU* 4.0 15.6 - - + +
593A GLN 3.1 8.6 + - - +
594A LEU* 3.9 14.8 - - + -
595A ASN* 3.1 31.0 + - - +
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Residues in contact with TYR 566 (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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532A ILE* 4.3 9.2 - - + -
533A MET 2.7 17.6 + - - +
534A VAL* 3.6 13.1 - - + -
535A GLY 3.0 24.6 + - - -
564A LEU* 4.0 23.6 - - + +
565A LEU* 1.3 74.9 - - - +
567A TYR* 1.3 61.7 + - - +
595A ASN* 3.2 36.5 + - + -
608A VAL* 3.8 13.0 - - + +
611A LEU* 4.1 24.7 - - + -
612A LEU* 3.8 31.9 - - + -
615A ASP* 2.6 29.2 + - - +
618A HIS* 6.0 0.3 - - - -
619A LEU* 3.6 23.0 - - + +
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Residues in contact with TYR 567 (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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535A GLY 3.3 16.8 - - - +
537A GLY* 3.5 22.2 - - - -
540A VAL* 3.8 17.5 - - + -
565A LEU* 3.7 20.5 - - + -
566A TYR* 1.3 74.4 - - - +
568A GLY* 1.3 82.8 + - - +
569A CYS* 3.6 7.5 - - + +
575A ASP 3.0 13.5 + - - -
576A TYR* 3.6 31.9 - + - -
577A LEU* 2.9 34.3 + - + +
582A LEU* 5.0 2.9 - - + -
594A LEU* 4.9 1.8 - - + -
595A ASN 2.9 12.5 + - - +
596A VAL* 3.5 29.2 - - + -
597A ALA 3.1 17.2 + - - -
608A VAL* 3.3 13.3 - - - +
611A LEU* 4.8 0.5 - - - +
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Residues in contact with GLY 568 (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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536A PRO* 3.8 7.5 - - - +
537A GLY 2.9 25.4 + - - -
567A TYR* 1.3 89.4 - - - +
569A CYS* 1.3 62.0 + - - +
596A VAL* 4.2 1.3 - - - -
597A ALA* 3.3 15.3 - - - -
608A VAL* 4.1 9.4 - - - -
753A NAP 4.0 5.6 - - - -
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Residues in contact with CYS 569 (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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537A GLY* 5.5 1.6 - - - +
567A TYR* 3.6 11.9 - - - +
568A GLY* 1.3 76.3 - - - +
570A ARG* 1.3 59.1 + - - +
571A ARG 4.2 3.1 - - - -
575A ASP* 3.2 35.2 - - - +
576A TYR* 4.1 13.2 - - - -
596A VAL* 4.4 0.2 - - - -
597A ALA 3.0 6.5 + - - +
598A PHE* 3.3 33.3 - - - -
599A SER 3.0 18.2 + - - -
753A NAP 2.7 25.0 + - - -
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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
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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