Contacts of the strand formed by residues 416 - 421 (chain F) in PDB entry 3QS7
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 416 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369F PHE* 3.5 35.9 - + + -
383F TRP* 4.1 10.4 - + + -
384F THR 3.8 4.3 - - - -
385F PHE* 3.7 36.5 - + + -
406F PHE* 3.8 37.0 - + - -
408F ASN 4.9 0.8 + - - -
409F HIS* 2.6 31.1 + - + -
412F GLN* 3.0 29.9 + - - +
414F GLY 3.6 16.8 - - - -
415F GLU* 1.3 70.5 - - - +
417F ILE* 1.3 62.4 + - - +
431F PHE* 2.9 40.6 + - + +
433F LEU* 4.4 7.6 - - + -
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Residues in contact with ILE 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F THR 3.7 1.9 - - - +
383F TRP* 3.7 2.3 - - - -
384F THR* 2.9 45.8 + - - +
385F PHE* 5.6 1.1 - - - -
415F GLU* 3.4 47.3 - - + +
416F TYR* 1.3 72.7 - - - +
418F PHE* 1.3 67.2 + - - +
419F HIS* 3.9 5.1 + - + +
428F THR* 4.6 11.2 - - - -
429F LYS 3.4 15.5 - - - +
430F MET* 4.1 8.7 - - + +
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Residues in contact with PHE 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371F VAL* 3.7 27.6 - - + -
373F PHE* 4.4 13.5 - + + -
381F CYS* 3.8 20.0 - - + -
382F THR 3.6 5.8 - - - -
383F TRP* 3.4 45.1 - + + -
392F CYS* 4.2 0.4 - - - -
404F SER* 3.6 25.8 - - - -
416F TYR 4.0 1.0 + - - -
417F ILE* 1.3 70.3 - - - +
419F HIS* 1.4 59.7 + - - +
420F ALA* 3.7 27.5 + - + -
427F PHE* 3.9 22.7 - + - -
428F THR* 3.3 3.4 - - - -
429F LYS* 2.9 40.9 + - + +
431F PHE* 4.8 0.9 - - + -
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Residues in contact with HIS 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380F ARG 4.0 1.4 - - - +
381F CYS* 3.6 1.4 - - - -
382F THR* 2.9 44.6 + - - +
384F THR* 6.6 0.2 - - - -
417F ILE* 3.9 6.4 + - + +
418F PHE* 1.4 73.2 - - - +
420F ALA* 1.3 59.3 + - - +
427F PHE 3.3 10.8 - - - +
428F THR* 4.2 8.1 - - - +
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Residues in contact with ALA 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F ILE* 3.4 7.9 - - + +
373F PHE* 6.4 0.2 - - + -
379F ILE* 3.6 29.2 - - + -
380F ARG 3.4 5.4 - - - +
381F CYS* 4.2 1.1 - - + -
418F PHE* 3.7 25.4 + - + -
419F HIS* 1.3 74.4 - - - +
421F GLU* 1.3 60.4 + - - +
427F PHE* 2.9 43.7 + - + +
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Residues in contact with GLU 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350F ILE* 3.8 2.9 - - - -
379F ILE* 3.9 5.5 - - - +
380F ARG* 2.9 36.7 + - + +
420F ALA* 1.3 75.3 - - - +
422F ASN* 1.3 61.9 + - - +
425F ALA 3.4 13.9 - - - +
426F GLN* 3.8 12.8 - - + -
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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