Contacts of the strand formed by residues 411 - 419 (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 GLU 411 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409F GLU* 5.0 2.6 - - - +
410F LYS* 1.3 82.2 + - + +
412F LYS* 1.3 94.7 + - - +
413F SER* 5.5 0.3 - - - -
428F GLN* 5.1 5.5 - - - +
429F VAL 3.5 8.3 + - - +
430F THR* 4.7 12.5 + - - +
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Residues in contact with LYS 412 (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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361F ASP* 4.7 6.3 + - - +
363F PRO* 4.1 31.5 - - + +
409F GLU* 4.2 32.5 - - + +
410F LYS 4.2 1.0 - - - -
411F GLU* 1.3 89.4 + - - +
413F SER* 1.3 96.5 + - - +
428F GLN* 3.7 0.7 - - - -
429F VAL* 3.0 39.9 + - + +
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Residues in contact with SER 413 (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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361F ASP* 3.5 4.9 - - - +
363F PRO* 5.1 0.6 - - - +
412F LYS* 1.3 105.6 + - - +
414F PHE* 1.3 70.2 + - - +
426F ILE* 4.8 7.2 - - - +
427F VAL 3.3 15.9 - - - -
428F GLN* 3.9 15.5 - - - -
429F VAL* 4.2 1.8 - - - +
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Residues in contact with PHE 414 (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* 4.8 4.3 - - + -
100F PHE* 5.2 2.0 - + - -
359F VAL* 4.8 1.6 - - + -
360F ARG 3.4 4.9 - - - +
361F ASP* 2.6 33.2 - - - +
362F LEU* 3.8 29.2 - - + -
363F PRO* 4.5 5.4 - - + -
366F LEU* 4.7 5.2 - - + -
368F LEU* 4.2 19.1 - - + -
413F SER* 1.3 75.6 - - - +
415F THR* 1.3 65.3 + - - +
416F ILE* 3.7 34.1 - - + -
426F ILE* 3.5 6.2 - - - +
427F VAL* 2.9 55.4 + - + -
429F VAL* 3.6 26.7 - - + -
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Residues in contact with THR 415 (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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360F ARG* 2.7 64.8 + - - +
361F ASP* 5.1 3.2 + - - -
414F PHE* 1.3 79.6 + - - +
416F ILE* 1.3 67.7 + - - +
417F LYS 4.6 0.2 - - - +
424F SER* 3.6 32.1 - - - +
425F LEU 3.4 7.9 - - - +
426F ILE* 4.2 14.1 - - + +
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Residues in contact with ILE 416 (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 7.9 - - + -
102F ILE* 5.1 5.4 - - + +
357F LEU* 4.5 29.2 - - + -
358F GLU 3.5 11.4 - - - +
359F VAL* 4.4 13.2 - - + -
368F LEU* 4.1 16.2 - - + -
370F PHE* 4.8 7.9 - - + -
399F ILE* 4.9 12.1 - - + -
414F PHE* 3.7 27.8 - - + -
415F THR* 1.3 78.3 - - - +
417F LYS* 1.3 61.4 + - - +
418F PRO* 4.5 1.7 - - - +
424F SER 3.7 0.7 - - - -
425F LEU* 2.9 48.8 + - + +
427F VAL* 4.6 8.7 - - + -
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Residues in contact with LYS 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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357F LEU* 4.5 2.5 - - - -
358F GLU* 3.0 61.1 + - + +
360F ARG* 4.3 18.0 - - - +
415F THR* 4.1 3.5 - - + -
416F ILE* 1.3 75.5 - - - +
418F PRO* 1.3 73.8 + - + +
419F VAL* 4.1 4.4 - - - +
420F GLY 3.7 11.7 - - - +
421F PHE 2.9 21.9 + - - +
422F LYS* 5.0 3.1 - - - +
423F ASP 3.5 27.4 - - - +
424F SER* 3.8 9.6 - - - +
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Residues in contact with PRO 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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83F VAL* 4.3 22.9 - - + -
102F ILE* 6.1 2.0 - - + -
104F VAL* 4.6 4.3 - - + -
355F VAL* 3.8 24.9 - - + -
356F GLU 3.3 9.9 - - - +
357F LEU* 4.1 11.9 - - + -
416F ILE 4.5 1.8 - - - +
417F LYS* 1.3 93.1 + - + +
419F VAL* 1.3 66.7 + - - +
420F GLY 3.1 0.3 + - - -
421F PHE* 3.1 48.8 + - + +
423F ASP 4.8 3.1 - - - +
424F SER* 4.9 1.8 - - - -
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Residues in contact with VAL 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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354F LYS* 4.2 23.0 + - - +
356F GLU* 2.6 39.1 + - + +
357F LEU 5.0 0.2 - - - -
358F GLU* 3.3 34.1 - - + +
417F LYS* 3.5 8.6 + - - +
418F PRO* 1.3 68.7 - - - +
420F GLY* 1.3 62.1 + - - +
421F PHE* 3.9 6.4 + - - -
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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