Contacts of the strand formed by residues 674 - 679 (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 TYR 674 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629B ILE* 3.2 29.8 - - + -
631B VAL* 4.0 24.3 - - + +
639B ALA 5.3 0.2 + - - -
643B GLN* 3.5 29.2 + - + +
646B PHE* 3.4 34.5 - + + -
665B ILE* 3.9 21.1 - - + -
668B LEU* 3.5 20.3 + - + -
669B MET* 3.5 45.5 - - + +
672B GLY 3.6 0.4 - - - -
673B ARG* 1.3 78.4 - - - +
675B SER* 1.3 63.5 + - - +
676B LEU* 4.2 20.9 + - + +
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Residues in contact with SER 675 (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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520B GLN 4.5 9.3 + - - -
521B PHE* 3.8 28.1 - - - -
522B ARG 5.2 0.5 + - - -
629B ILE 2.9 7.9 + - - +
630B TYR* 3.5 18.3 - - - -
631B VAL* 3.1 24.9 + - - +
672B GLY* 4.1 17.5 + - - -
673B ARG 4.0 0.6 - - - -
674B TYR* 1.3 77.7 + - - +
676B LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 676 (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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145B GLU* 6.4 2.2 - - + -
182B GLU* 3.9 32.5 - - + +
521B PHE* 3.9 8.6 - - - +
631B VAL* 3.4 29.8 - - + +
639B ALA* 4.6 9.4 - - + -
643B GLN* 4.8 9.2 - - - +
669B MET* 4.6 9.9 - - - -
674B TYR* 4.3 17.7 - - + +
675B SER* 1.3 77.3 - - - +
677B ASP* 1.3 61.2 + - - +
678B VAL* 3.9 20.9 - - + -
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Residues in contact with ASP 677 (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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320B GLY 5.7 0.4 - - - -
322B HIS* 2.8 32.7 + - - -
460B SER* 3.0 26.9 + - - -
521B PHE* 3.8 30.0 - - + +
542B PRO* 4.1 4.0 - - - +
631B VAL 3.0 8.0 + - - +
632B CYS* 3.1 21.5 - - - -
633B GLY 3.0 21.1 + - - -
676B LEU* 1.3 73.6 - - - +
678B VAL* 1.3 61.0 + - - +
679B TRP* 3.7 3.9 - - - -
752B FAD 4.3 6.2 - - - +
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Residues in contact with VAL 678 (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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180B THR 5.9 1.6 - - - +
181B TYR* 3.5 28.7 + - + -
631B VAL* 4.3 11.0 - - + +
632B CYS 4.5 1.8 - - - -
633B GLY 3.1 20.0 - - - +
634B ASP 4.1 2.7 - - - +
635B ALA* 3.6 19.3 - - + -
638B MET* 4.7 0.2 - - + -
639B ALA* 3.9 26.0 - - + -
676B LEU* 3.9 19.9 - - + -
677B ASP* 1.3 80.3 - - - +
679B TRP* 1.3 65.8 + - - +
751B FMN 4.8 10.0 - - - +
752B FAD 5.1 3.6 - - - +
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Residues in contact with TRP 679 (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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181B TYR* 3.7 6.5 - - - -
460B SER* 3.4 18.2 - - - -
538B THR* 3.3 33.7 + - - -
632B CYS* 3.5 29.4 - - - -
633B GLY* 3.0 22.7 + - - +
634B ASP* 4.0 5.1 - - - +
635B ALA* 3.4 17.4 + - - -
677B ASP* 3.7 11.9 - - - -
678B VAL* 1.3 78.2 - - - +
680B SER* 1.3 69.4 + - - +
751B FMN 6.0 0.2 - - - -
752B FAD 3.4 90.8 + + + -
753B NAP 5.5 3.4 + - - -
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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