Contacts of the helix formed by residues 371 - 383 (chain G) in PDB entry 5UQ9
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 VAL 371 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226G THR 5.8 1.1 - - - +
227G GLU* 5.2 5.2 - - - +
229G ASP* 2.8 47.7 + - + +
363G ARG* 3.0 22.6 - - - +
370G SER* 1.3 65.7 - - - +
372G PHE* 1.3 56.6 + - - +
373G LEU* 2.9 11.2 + - - -
374G GLY 3.3 6.8 + - - -
375G LYS* 3.3 27.7 - - + +
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Residues in contact with PHE 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G GLU 4.7 9.3 + - - +
229G ASP 4.1 2.2 + - - +
328G TYR* 4.2 28.5 - + - -
331G LYS* 3.7 46.7 - - + +
332G ILE* 3.5 27.6 - - + -
335G TYR* 4.2 16.2 - + - -
370G SER* 3.3 18.1 + - - +
371G VAL* 1.3 77.7 - - - +
373G LEU* 1.3 60.2 + - - +
375G LYS* 3.6 14.8 - - + -
376G ILE* 3.0 32.1 + - + +
395G PHE* 3.4 28.9 - + - -
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Residues in contact with LEU 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G THR* 5.5 9.9 - - + +
359G ALA* 3.3 37.0 - - + +
360G LEU* 3.4 16.6 - - + +
363G ARG* 3.5 39.3 - - + +
370G SER* 3.0 20.4 + - - +
371G VAL 2.9 1.2 - - - +
372G PHE* 1.3 75.5 - - - +
374G GLY* 1.3 67.3 + - - +
376G ILE* 2.8 7.9 + - - +
377G LYS* 2.4 59.6 + - + +
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Residues in contact with GLY 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363G ARG* 5.8 0.4 - - - -
371G VAL 3.3 6.5 + - - -
373G LEU* 1.3 85.9 - - - +
375G LYS* 1.3 58.9 + - - +
377G LYS* 3.8 9.6 - - - -
378G ASP* 2.5 49.5 + - - -
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Residues in contact with LYS 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G GLU* 5.7 9.4 - - + +
328G TYR* 5.2 3.8 - - - +
371G VAL* 3.3 33.1 - - + +
372G PHE* 3.6 28.9 - - + +
374G GLY* 1.3 77.3 - - - +
376G ILE* 1.3 59.6 + - - +
378G ASP* 4.5 7.0 + - - +
379G ALA* 3.7 8.3 + - - +
392G ASP* 5.2 0.2 - - - +
394G PHE* 3.4 46.5 - - + -
395G PHE* 3.1 21.0 - - + -
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Residues in contact with ILE 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335G TYR* 3.5 38.6 - - + -
339G PHE* 4.1 13.9 - - + -
359G ALA* 3.6 24.9 - - + -
372G PHE* 3.0 23.0 + - + +
373G LEU* 2.8 7.2 + - - +
375G LYS* 1.3 73.8 - - - +
377G LYS* 1.3 66.8 + - - +
379G ALA* 3.2 16.6 + - - +
380G PHE* 3.6 4.9 + - - +
389G LEU* 3.7 24.6 - - + +
395G PHE* 3.4 23.6 - - + -
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Residues in contact with LYS 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G THR* 5.6 3.1 - - - +
168G GLU* 3.1 27.4 + - - -
356G GLY* 3.7 19.3 + - - +
357G GLY* 4.7 2.4 - - - -
359G ALA* 4.5 4.0 - - + -
360G LEU* 3.2 36.8 - - + +
373G LEU* 2.4 59.9 + - + +
374G GLY* 3.7 6.3 - - - +
376G ILE* 1.3 72.2 - - - +
378G ASP* 1.3 61.7 + - - +
380G PHE* 2.9 26.4 + - + +
381G ASP* 2.8 28.9 + - - +
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Residues in contact with ASP 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374G GLY* 2.5 36.9 + - - +
375G LYS* 4.5 8.2 + - - +
377G LYS* 1.3 77.5 - - - +
379G ALA* 1.3 61.6 + - - +
381G ASP* 3.6 13.6 - - + +
382G ARG* 3.0 38.3 + - + +
394G PHE* 6.1 2.9 - - + -
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Residues in contact with ALA 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375G LYS 3.7 3.8 + - - +
376G ILE 3.2 12.5 + - - +
377G LYS 3.1 1.0 - - - -
378G ASP* 1.3 79.3 - - - +
380G PHE* 1.3 56.7 + - - +
382G ARG* 4.5 3.0 - - - +
383G ASN* 3.2 24.6 + - - +
386G LEU* 5.4 5.5 - - + +
389G LEU* 4.2 11.2 - - + -
392G ASP* 3.8 35.3 - - + +
395G PHE* 3.8 17.9 - - + -
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Residues in contact with PHE 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354G ASN* 3.1 57.4 - - - -
355G TYR* 4.8 2.7 - - + -
356G GLY* 3.3 24.9 - - - +
357G GLY 4.8 0.2 - - - -
376G ILE 3.6 4.1 + - - +
377G LYS* 2.9 12.1 + - + +
379G ALA* 1.3 78.6 - - - +
381G ASP* 1.3 87.7 + - - +
382G ARG 3.2 0.2 - - - -
383G ASN 3.0 5.1 - - - -
384G PRO* 2.9 64.4 - - + +
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Residues in contact with ASP 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G GLU* 5.0 4.2 - - - +
377G LYS* 2.8 45.0 + - - +
378G ASP* 3.3 13.7 + - - +
380G PHE* 1.3 95.1 - - - +
382G ARG* 1.3 62.9 + - + +
384G PRO* 4.6 5.5 - - - +
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Residues in contact with ARG 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378G ASP* 3.0 25.3 + - + +
379G ALA* 4.5 4.7 - - - +
381G ASP* 1.3 81.4 - - + +
383G ASN* 1.3 61.8 + - + +
384G PRO* 4.2 1.9 - - - +
392G ASP* 3.1 35.4 + - - +
393G ASP* 4.7 10.0 - - - +
394G PHE* 3.8 19.4 - - - +
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Residues in contact with ASN 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379G ALA 3.2 18.0 + - - +
380G PHE* 3.0 5.6 + - - -
382G ARG* 1.3 83.0 - - + +
384G PRO* 1.3 67.6 - - - +
385G GLU* 2.8 37.6 + - - +
386G LEU* 4.0 25.5 - - + +
392G ASP* 5.8 2.0 - - - +
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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