Contacts of the strand formed by residues 531 - 534 (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 VAL 531 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B LEU* 4.0 14.1 - - + -
524B PRO* 3.5 36.3 - - + -
530B PRO* 1.3 72.3 - - - +
532B ILE* 1.3 64.8 + - - +
533B MET* 3.7 31.6 - - + -
550B ARG* 3.9 15.9 - - - +
562B GLU 2.8 9.7 + - - +
563B THR* 3.5 14.1 - - + +
564B LEU* 2.8 28.8 + - - +
628B HIS* 3.8 1.6 - - + -
630B TYR* 3.8 17.0 - - + -
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Residues in contact with ILE 532 (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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530B PRO 5.4 0.2 - - - -
531B VAL* 1.3 76.3 - - - +
533B MET* 1.3 59.7 + - - +
534B VAL* 4.6 9.2 - - + -
564B LEU* 3.8 7.6 - - + -
566B TYR* 4.5 18.4 - - + -
619B LEU* 3.6 34.3 - - + -
622B LEU* 4.5 21.5 - - + -
623B ILE* 4.4 22.9 - - + -
627B ALA* 4.6 9.4 - - + -
628B HIS 2.9 14.9 + - - +
629B ILE* 4.3 17.3 - - + -
630B TYR* 2.6 35.2 + - - +
646B PHE* 4.8 5.4 - - + -
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Residues in contact with MET 533 (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* 3.7 16.6 - - + -
532B ILE* 1.3 78.0 - - - +
534B VAL* 1.3 56.3 + - - +
543B PHE* 3.3 43.3 - - + -
546B PHE* 3.5 26.0 - - - -
547B ILE* 3.7 27.6 - - + +
550B ARG* 6.3 0.4 - - - -
563B THR* 4.2 12.6 - - + -
564B LEU 3.1 20.7 + - - +
565B LEU* 3.3 18.9 - - + +
566B TYR* 2.7 35.2 + - - +
630B TYR* 3.5 9.4 - - + -
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Residues in contact with VAL 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B ILE* 4.6 8.3 - - + -
533B MET* 1.3 76.2 - - - +
535B GLY* 1.3 60.3 + - - +
536B PRO* 4.2 4.3 - - + -
543B PHE* 3.3 4.5 - - - -
566B TYR* 3.6 15.3 - - + -
608B VAL* 3.9 34.1 - - + -
612B LEU* 4.1 22.9 - - + -
629B ILE* 5.2 0.2 - - + -
630B TYR 2.6 15.9 + - - +
631B VAL* 3.3 13.5 - - + +
632B CYS 2.9 26.5 + - - +
638B MET* 4.9 1.8 - - - -
642B VAL* 4.1 15.7 - - + -
646B PHE* 4.8 6.3 - - + -
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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