Contacts of the strand formed by residues 426 - 431 (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 ILE 426 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86F GLN 2.8 16.0 + - - +
87F ARG* 3.4 44.1 - - - +
88F ILE 3.1 24.6 + - - +
413F SER* 4.8 7.4 - - - +
414F PHE 3.5 9.9 - - - +
415F THR* 4.2 13.7 - - + +
424F SER* 4.5 12.1 - - - +
425F LEU* 1.3 75.1 - - - +
427F VAL* 1.3 64.4 + - - +
428F GLN* 3.9 10.7 + - + +
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Residues in contact with VAL 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ILE* 3.7 32.8 - - + -
90F LEU* 3.8 27.8 - - + -
100F PHE* 4.4 11.7 - - + -
413F SER* 3.3 4.5 - - - -
414F PHE* 2.9 69.7 + - + -
416F ILE* 4.6 3.4 - - + -
425F LEU* 4.1 17.9 - - + +
426F ILE* 1.3 76.0 - - - +
428F GLN* 1.3 60.5 + - - +
429F VAL 3.5 2.4 + - - -
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Residues in contact with GLN 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F LEU* 3.1 31.4 - - - +
87F ARG* 3.4 27.5 + - - +
88F ILE 2.9 14.5 + - - +
89F ALA* 3.7 4.3 - - + +
90F LEU* 2.8 29.4 + - - -
411F GLU* 5.1 5.2 - - - +
412F LYS 3.8 7.4 - - - +
413F SER* 3.9 10.7 - - - -
426F ILE* 4.4 5.6 - - + +
427F VAL* 1.3 71.6 - - - +
429F VAL* 1.3 60.7 + - - +
430F THR* 3.5 6.8 + - - +
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Residues in contact with VAL 429 (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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90F LEU* 3.5 24.9 - - + +
92F LEU* 5.0 3.6 - - + -
363F PRO* 5.8 1.1 - - + -
366F LEU* 4.0 14.6 - - + -
410F LYS 3.9 2.8 - - - +
411F GLU* 3.5 7.4 - - - +
412F LYS* 3.0 44.3 + - + +
413F SER* 4.6 0.2 - - - -
414F PHE* 3.6 35.7 - - + -
427F VAL 3.5 1.1 + - - +
428F GLN* 1.3 70.3 - - - +
430F THR* 1.3 62.2 + - - +
431F PHE* 3.4 35.4 - - + -
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Residues in contact with THR 430 (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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89F ALA* 5.0 4.9 - - - +
90F LEU 2.7 12.5 + - - -
91F ARG* 3.4 46.4 - - + +
92F LEU 3.4 5.2 + - - -
410F LYS* 3.9 7.6 - - - +
411F GLU* 4.7 12.0 + - - +
428F GLN* 3.6 10.7 + - - +
429F VAL* 1.3 74.3 + - - +
431F PHE* 1.3 74.2 + - - +
432F ASP* 4.7 0.5 - - - +
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Residues in contact with PHE 431 (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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91F ARG* 5.6 0.3 + - - -
92F LEU* 3.9 11.2 - - + -
363F PRO* 6.4 2.0 - - + -
365F GLU* 5.2 8.1 - - + -
366F LEU* 4.5 5.6 - - + -
403F VAL* 3.6 32.5 - - + -
406F CYS* 4.2 14.6 - - - -
407F PRO* 3.6 35.2 - - + -
409F GLU* 3.1 26.7 - - + -
410F LYS* 3.1 47.4 + - + +
412F LYS* 6.6 0.2 - - + -
429F VAL* 3.4 27.6 - - + -
430F THR* 1.3 83.8 - - - +
432F ASP* 1.3 61.5 - - - +
433F CYS* 4.4 4.5 - - - -
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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