Contacts of the helix formed by residues 402 - 417 (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 CYS 402 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G GLU* 6.1 0.4 - - - -
324G ARG* 6.2 0.4 - - - -
325G LYS* 3.4 47.0 - - + +
328G TYR* 3.6 25.1 - - - -
329G ALA* 4.0 9.2 - - + -
398G ALA 3.2 7.0 - - - +
399G VAL 3.0 8.7 + - - +
401G ASN* 1.3 104.5 - - - +
403G GLN* 1.3 61.4 + - - +
404G ASP 3.5 2.2 - - - -
405G SER 3.8 2.2 + - - +
406G TRP* 3.1 25.2 + - - +
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Residues in contact with GLN 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399G VAL* 3.0 9.9 + - + +
400G GLU* 3.3 25.4 + - + +
401G ASN 3.5 0.4 - - - -
402G CYS* 1.3 76.0 - - - +
404G ASP* 1.3 75.1 + - - +
406G TRP* 3.4 19.2 + - + +
407G ARG* 2.5 55.3 + - - +
427G LEU* 6.1 0.2 - - + -
430G TYR* 4.3 22.9 - - + +
305H LYS 4.7 4.5 - - - +
306H GLY* 3.7 15.2 + - - -
307H PRO* 3.6 13.1 - - - +
308H GLN* 5.5 1.8 + - - -
309H LYS* 6.3 0.6 - - - +
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Residues in contact with ASP 404 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400G GLU 4.8 1.0 + - - -
401G ASN 5.2 1.7 + - - +
402G CYS 3.5 0.2 - - - -
403G GLN* 1.3 89.7 - - - +
405G SER* 1.3 61.9 + - - +
406G TRP 3.3 0.7 + - - -
407G ARG* 3.3 5.4 + - - +
408G ARG* 3.3 46.7 + - - +
309H LYS* 3.5 28.4 + - - -
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Residues in contact with SER 405 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321G GLU* 5.4 1.0 - - - +
322G ASP* 2.8 53.5 + - - +
325G LYS* 3.6 26.3 - - - +
401G ASN 5.6 0.6 + - - -
402G CYS 3.8 2.0 + - - -
403G GLN 3.4 0.2 - - - -
404G ASP* 1.3 74.7 - - - +
406G TRP* 1.3 65.8 + - - +
408G ARG* 3.3 13.7 + - - +
409G ALA* 3.1 19.1 + - - +
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Residues in contact with TRP 406 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G ALA* 3.5 29.1 - - + +
329G ALA* 3.5 23.6 - - + -
330G SER* 3.2 26.6 + - - -
333G ILE* 3.6 25.8 - - + -
399G VAL* 4.7 6.1 - - + -
402G CYS 3.1 22.2 + - - +
403G GLN* 3.5 13.7 - - + +
404G ASP 3.2 0.4 - - - -
405G SER* 1.3 78.1 - - - +
407G ARG* 1.3 61.6 + - + +
409G ALA* 3.6 1.7 + - - +
410G VAL* 3.2 26.0 + - + +
423G PHE* 3.8 12.3 + - - +
426G ALA* 3.3 22.4 - - + -
427G LEU* 3.3 43.4 - - + +
430G TYR* 4.1 15.5 - + + -
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Residues in contact with ARG 407 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403G GLN* 2.5 42.9 + - - +
404G ASP* 3.3 7.2 + - - +
405G SER 3.3 0.4 - - - -
406G TRP* 1.3 75.1 - - - +
408G ARG* 1.3 63.2 + - - +
410G VAL 3.5 0.2 + - - -
411G SER* 3.0 31.0 + - - -
427G LEU* 3.7 27.0 - - + +
430G TYR* 4.4 7.1 - - - -
431G ASP* 2.6 43.6 + - - -
434G ARG* 4.4 1.2 - - - +
306H GLY* 4.5 0.4 - - - -
307H PRO* 3.3 28.7 - - - +
414H VAL* 2.7 50.0 + - + +
415H GLN* 4.5 10.3 - - + +
417H GLY* 3.3 2.6 - - - -
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Residues in contact with ARG 408 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G SER* 5.7 5.7 - - - -
319G PHE* 4.4 3.6 - - + -
322G ASP* 3.3 27.7 + - - +
404G ASP* 3.3 44.0 + - - +
405G SER* 3.3 24.5 + - - +
406G TRP 3.4 0.2 - - - -
407G ARG* 1.3 79.6 - - - +
409G ALA* 1.3 53.6 + - - +
411G SER* 3.4 5.0 + - - -
412G THR* 2.4 37.4 + - - +
415H GLN* 5.8 6.1 - - - +
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Residues in contact with ALA 409 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G LEU* 4.3 9.9 - - + +
319G PHE* 3.7 15.6 - - + -
322G ASP* 3.9 21.1 - - - +
323G ILE* 4.3 8.1 - - + +
326G ALA* 4.2 10.5 - - + -
405G SER 3.1 16.6 + - - +
406G TRP 4.1 3.4 - - - +
408G ARG* 1.3 77.3 - - - +
410G VAL* 1.3 63.0 + - + +
412G THR* 3.2 5.5 + - - -
413G GLY* 3.1 19.9 + - - -
420G MET* 4.0 6.9 - - - +
423G PHE* 5.9 0.7 - - + -
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Residues in contact with VAL 410 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406G TRP* 3.2 36.2 + - + +
407G ARG 4.0 4.0 - - - +
408G ARG 3.3 0.4 - - - -
409G ALA* 1.3 77.2 - - + +
411G SER* 1.3 65.4 + - - +
414G VAL* 3.0 26.8 + - + +
420G MET* 3.3 9.2 - - + +
423G PHE* 4.2 24.7 - - + +
424G THR* 4.0 25.1 - - + -
427G LEU* 4.3 8.1 - - + -
414H VAL* 4.1 26.9 - - + -
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Residues in contact with SER 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407G ARG 3.0 18.8 + - - -
408G ARG* 3.9 4.5 - - - -
410G VAL* 1.3 77.9 - - - +
412G THR* 1.3 57.7 + - - +
414G VAL* 3.2 7.1 + - - +
415G GLN* 2.9 33.8 + - - +
411H SER* 3.2 31.3 + - - +
414H VAL* 3.6 14.8 - - - +
415H GLN* 3.7 17.2 - - - +
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Residues in contact with THR 412 (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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208G VAL* 5.2 5.4 - - - -
310G PHE* 4.0 10.7 - - + -
312G PHE* 4.8 16.2 - - + -
319G PHE* 2.9 33.1 - - + -
408G ARG 2.4 27.0 + - - +
409G ALA 3.2 3.5 + - - -
411G SER* 1.3 77.1 - - - +
413G GLY* 1.3 56.1 + - - +
415G GLN* 3.2 7.9 + - + +
416G ALA* 2.8 30.1 + - - +
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Residues in contact with GLY 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G LEU* 3.8 27.9 - - - +
208G VAL* 4.8 0.4 - - - -
319G PHE* 5.1 0.2 - - - -
409G ALA 3.1 13.6 + - - -
410G VAL 4.0 1.1 - - - -
412G THR* 1.3 77.3 - - - +
414G VAL* 1.3 56.6 + - - +
416G ALA* 3.6 5.6 - - - -
417G GLY 2.9 7.6 + - - -
418G ILE* 2.8 30.2 + - - +
420G MET* 4.0 9.4 - - - -
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Residues in contact with VAL 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410G VAL* 3.0 29.0 + - + +
411G SER* 3.5 7.4 - - - +
413G GLY* 1.3 73.2 - - - +
415G GLN* 1.3 66.0 + - - +
417G GLY* 3.1 3.2 + - - +
418G ILE 5.1 1.8 - - - +
420G MET* 4.1 10.3 - - + -
424G THR* 4.8 7.2 - - + -
407H ARG* 3.0 54.2 + - + +
410H VAL* 4.0 21.8 - - + -
411H SER* 4.6 4.5 - - - +
414H VAL* 6.0 0.2 - - + -
427H LEU* 3.6 26.2 - - + -
428H SER* 6.0 0.9 - - - +
431H ASP* 5.4 1.3 - - - -
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Residues in contact with GLN 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G PRO* 3.7 18.0 - - - +
310G PHE* 3.6 26.9 - - + +
411G SER 2.9 22.0 + - - +
412G THR* 3.7 7.0 - - - +
414G VAL* 1.3 74.6 - - - +
416G ALA* 1.3 59.6 + - - +
417G GLY 3.6 0.2 + - - -
404H ASP* 5.0 6.9 - - - +
407H ARG* 3.6 36.2 + - - +
408H ARG* 4.2 7.7 - - - +
411H SER* 3.7 15.0 + - - +
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Residues in contact with ALA 416 (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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207G ASP 5.6 1.3 - - - +
208G VAL* 3.9 10.5 - - + -
307G PRO* 3.3 13.8 - - - +
310G PHE* 3.5 32.2 - - + -
412G THR 2.8 17.1 + - - +
413G GLY 3.8 4.5 - - - +
415G GLN* 1.3 76.5 - - - +
417G GLY* 1.3 60.3 + - - +
418G ILE* 3.4 21.7 + - + +
434H ARG* 4.4 1.9 + - - -
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Residues in contact with GLY 417 (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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307G PRO* 4.0 3.1 - - - -
413G GLY 2.9 4.7 + - - -
414G VAL 3.1 5.1 + - - -
415G GLN 3.3 0.6 + - - -
416G ALA* 1.3 79.6 - - - +
418G ILE* 1.3 60.9 + - - +
407H ARG* 3.6 22.2 - - - -
431H ASP* 3.3 17.0 - - - +
434H ARG* 3.1 25.8 + - - -
435H HIS* 3.4 8.4 - - - -
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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
------------------------------------------------------------
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