Contacts of the helix formed by residues 361 - 373 (chain C) in PDB entry 5TF6
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 ASP 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312C THR* 3.8 6.1 - - - -
342C ASP* 5.4 3.6 - - - +
359C PHE* 4.0 4.1 - - - +
360C ARG* 1.3 86.7 + - - +
362C SER* 1.3 61.4 + - - +
363C LYS* 3.2 14.4 - - + +
364C PHE* 3.3 34.5 + - - +
365C ALA* 3.1 24.3 + - - +
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Residues in contact with SER 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C GLU* 3.3 62.1 + - - +
312C THR* 3.6 7.5 - - - +
361C ASP* 1.3 72.2 - - - +
363C LYS* 1.3 66.6 + - - +
365C ALA* 3.9 0.9 - - - -
366C ALA* 3.1 23.0 + - - +
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Residues in contact with LYS 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C ASP* 3.2 13.7 + - + +
362C SER* 1.3 82.1 + - - +
364C PHE* 1.3 62.2 + - - +
366C ALA* 3.4 7.2 + - - +
367C LYS* 3.2 20.8 + - - +
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Residues in contact with PHE 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C ILE* 4.2 12.3 - - + -
342C ASP* 3.7 38.1 - - + -
359C PHE* 3.6 35.9 - + + -
361C ASP* 3.3 30.2 + - - +
363C LYS* 1.3 75.7 - - - +
365C ALA* 1.3 65.2 + - - +
367C LYS* 2.9 41.7 + - - +
368C MET* 3.0 39.6 + - + +
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Residues in contact with ALA 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C GLU 3.3 25.8 - - - +
312C THR 3.7 21.8 - - - +
313C LEU 4.2 0.9 - - - +
314C ILE* 3.6 21.2 - - + +
359C PHE* 4.0 15.2 - - + +
361C ASP 3.1 10.7 + - - +
362C SER 3.7 2.5 - - - +
364C PHE* 1.3 74.2 - - - +
366C ALA* 1.3 58.8 + - - +
368C MET* 3.2 2.1 + - - +
369C LEU* 2.9 24.8 + - - +
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Residues in contact with ALA 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C SER 3.1 15.7 + - - +
363C LYS* 3.6 7.4 - - + +
364C PHE 3.2 0.2 - - - -
365C ALA* 1.3 78.2 - - - +
367C LYS* 1.3 62.2 + - - +
369C LEU* 3.5 20.4 - - - +
370C MET* 4.1 10.9 + - - +
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Residues in contact with LYS 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C LYS 3.2 11.4 + - - +
364C PHE* 2.9 31.8 + - - +
366C ALA* 1.3 76.2 - - - +
368C MET* 1.3 83.8 + - + +
370C MET* 3.2 18.5 + - - +
371C ILE* 3.3 19.6 + - + +
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Residues in contact with MET 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ILE* 4.5 1.3 - - + -
336C ILE* 4.9 2.9 - - - -
338C ILE* 3.5 33.0 - - + -
359C PHE* 3.8 19.5 - - + -
364C PHE* 3.0 36.4 + - + +
365C ALA 3.7 5.8 - - - +
367C LYS* 1.3 102.9 - - + +
369C LEU* 1.3 67.0 + - - +
370C MET 3.1 2.2 - - - -
371C ILE* 3.7 25.6 - - + +
372C LEU* 2.9 41.4 + - + +
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Residues in contact with LEU 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ILE* 4.5 15.7 - - + +
365C ALA 2.9 13.2 + - - +
366C ALA* 3.5 17.3 - - - +
367C LYS 3.2 0.2 - - - -
368C MET* 1.3 77.0 - - - +
370C MET* 1.3 67.4 + - + +
373C ASN* 3.4 6.8 + - - +
384C SER* 2.5 42.1 + - - +
385C GLY* 3.8 29.6 - - - +
386C THR* 6.1 4.5 - - + -
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Residues in contact with MET 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C ALA 4.3 12.1 - - - +
367C LYS* 3.2 8.4 + - - +
368C MET 3.1 0.6 - - - -
369C LEU* 1.3 85.1 - - + +
371C ILE* 1.3 61.4 + - + +
372C LEU 3.5 0.2 + - - -
373C ASN* 3.6 12.8 + - - +
501C K 3.0 16.5 - - - -
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Residues in contact with ILE 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C ILE* 3.7 31.8 - - + +
367C LYS* 3.3 18.8 + - + +
368C MET* 3.2 29.3 + - + +
370C MET* 1.3 79.7 - - + +
372C LEU* 1.3 59.4 + - - +
373C ASN 3.7 0.3 - - - +
375C SER* 4.4 8.0 - - - -
501C K 2.9 18.2 - - - -
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ILE* 3.3 28.0 - - + -
316C LEU* 3.9 22.2 - - + +
331C PHE* 4.3 9.0 - - + -
332C LEU* 3.7 25.1 - - + -
336C ILE* 3.6 39.5 - - + -
338C ILE* 4.9 0.9 - - + -
357C ILE* 5.3 0.9 - - + -
359C PHE* 4.5 5.8 - - + -
368C MET* 2.9 27.5 + - + +
371C ILE* 1.3 74.4 - - + +
373C ASN* 1.3 66.1 + - - +
374C GLY 3.1 1.9 + - - -
375C SER* 2.7 23.9 + - - +
382C ILE* 3.9 6.8 - - - +
383C ARG 4.9 0.2 - - - -
384C SER* 4.1 6.0 + - - -
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Residues in contact with ASN 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C LEU 3.4 11.0 + - - +
370C MET* 3.8 7.9 - - - +
371C ILE 3.3 1.0 - - - -
372C LEU* 1.3 77.0 - - - +
374C GLY* 1.3 61.5 + - - +
383C ARG* 3.4 27.3 + - - +
384C SER* 3.2 38.7 + - - +
501C K 2.7 26.5 - - - -
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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