Contacts of the strand formed by residues 366 - 373 (chain F) in PDB entry 1TYE
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 LEU 366 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90F LEU* 5.2 2.7 - - + -
92F LEU* 5.6 0.4 - - + -
362F LEU* 3.5 32.3 - - + +
363F PRO* 3.3 34.5 - - + +
364F GLU* 3.8 0.6 - - - -
365F GLU* 1.3 81.1 - - + +
367F SER* 1.3 71.6 + - - +
368F LEU* 4.6 1.8 - - + -
401F ALA* 3.8 21.5 - - + -
402F LYS 3.3 7.9 - - - +
403F VAL* 3.7 24.2 - - + -
414F PHE* 4.7 3.6 - - + -
429F VAL* 4.0 34.1 - - + -
431F PHE* 4.5 4.9 - - + -
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Residues in contact with SER 367 (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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362F LEU* 5.1 2.2 - - - -
366F LEU* 1.3 75.3 - - - +
368F LEU* 1.3 72.4 + - - +
400F GLU 3.7 0.4 - - - +
401F ALA* 3.5 0.2 - - - -
402F LYS* 3.0 46.9 + - - +
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Residues in contact with LEU 368 (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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100F PHE* 4.9 2.7 - - + -
359F VAL* 4.0 26.2 - - + -
362F LEU* 4.3 18.7 - - + +
366F LEU* 4.6 3.8 - - + -
367F SER* 1.3 86.7 - - - +
369F SER* 1.3 62.8 + - - +
370F PHE* 4.0 19.3 - - + -
399F ILE* 3.6 16.8 - - + -
400F GLU 3.3 12.3 - - - +
401F ALA* 3.6 18.4 - - + +
414F PHE* 4.2 16.6 - - + -
416F ILE* 4.1 18.6 - - + -
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Residues in contact with SER 369 (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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368F LEU* 1.3 75.2 + - - +
370F PHE* 1.3 63.7 + - - +
398F SER 4.3 0.2 - - - -
399F ILE* 3.2 12.5 - - - +
400F GLU* 3.0 51.9 + - - +
1020F NAG 4.3 10.8 - - - -
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Residues in contact with PHE 370 (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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357F LEU* 3.9 23.3 - - + -
359F VAL* 4.0 26.7 - - + -
368F LEU* 4.0 24.9 - - + -
369F SER* 1.3 76.2 - - - +
371F ASN* 1.3 72.3 + - - +
382F GLY* 2.9 31.7 + - - +
383F LEU 3.9 14.4 - - - +
384F LYS* 3.9 36.8 - - + -
397F PHE* 5.1 3.6 - + + -
398F SER 3.5 2.9 - - - -
399F ILE* 3.5 35.9 - - + -
416F ILE* 4.8 7.0 - - + -
1020F NAG 4.9 0.7 - - - -
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Residues in contact with ASN 371 (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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370F PHE* 1.3 89.0 - - - +
372F ALA* 1.3 60.8 + - - +
373F THR* 5.0 1.5 + - - -
379F VAL* 3.7 19.4 - - + +
380F ILE 3.7 3.6 - - - -
381F PRO* 3.4 17.8 - - - +
382F GLY 3.9 0.3 + - - -
383F LEU 4.2 0.4 - - - -
397F PHE* 3.4 3.9 - - - -
398F SER* 2.7 44.6 + - - +
1020F NAG 1.5 66.6 + - - +
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Residues in contact with ALA 372 (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 ASN* 1.3 73.9 - - - +
373F THR* 1.3 61.9 + - - +
374F CYS* 3.8 2.9 - - - -
378F GLU 3.1 3.1 - - - +
379F VAL* 3.6 2.3 - - - -
380F ILE* 2.8 41.1 + - + +
383F LEU* 3.4 27.9 + - + +
384F LYS* 4.7 0.2 - - - -
386F CYS* 4.2 12.3 - - - -
396F SER 3.8 3.6 - - - -
397F PHE* 3.6 24.0 - - + -
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Residues in contact with THR 373 (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 ASN 5.0 1.9 + - - -
372F ALA* 1.3 74.4 + - - +
374F CYS* 1.3 63.4 + - - +
377F ASN* 3.8 37.8 + - + +
378F GLU 3.6 6.5 - - - +
379F VAL* 4.5 14.2 - - + +
386F CYS* 4.2 1.6 - - - -
395F VAL* 3.5 3.3 - - - +
396F SER* 2.8 48.1 + - - +
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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