Contacts of the helix formed by residues 348 - 358 (chain G) in PDB entry 6IY6
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 TYR 348 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347G GLU* 1.3 71.9 - - - +
349G CYS* 1.3 61.4 + - - +
351G ALA* 3.2 7.2 + - + +
352G LEU* 3.1 45.5 + - + +
362G MET* 3.5 4.8 - - + +
364G ASP 4.1 8.3 - - - -
366G ASP 2.6 23.0 + - - -
367G ASP* 3.3 2.6 - - - -
368G LEU* 3.0 29.8 + - + -
391G LEU* 3.8 28.3 - - + -
392G ASP 2.9 8.9 + - - +
393G LYS* 3.3 22.2 + - + +
394G TYR* 3.7 29.8 - + - -
395G PRO* 3.3 34.1 - - + -
412G GLN* 5.3 2.9 - - - +
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Residues in contact with CYS 349 (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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347G GLU* 4.3 17.3 - - - -
348G TYR* 1.3 77.6 - - - +
350G GLU* 1.3 83.2 + - - +
352G LEU* 3.3 14.6 + - - +
353G ALA* 3.1 21.7 + - - +
412G GLN* 5.0 15.8 - - - +
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Residues in contact with GLU 350 (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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345G ARG 4.4 3.7 - - - +
346G LEU* 3.5 20.4 - - + +
347G GLU* 2.7 43.7 + - - +
349G CYS* 1.3 91.7 - - - +
351G ALA* 1.3 61.7 + - - +
353G ALA* 3.4 9.9 + - - +
354G MET* 3.2 27.6 + - - +
149I LEU* 5.9 2.6 - - - +
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Residues in contact with ALA 351 (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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346G LEU* 5.1 4.0 - - + +
347G GLU 3.2 1.8 + - - +
348G TYR* 3.2 11.5 + - + +
350G GLU* 1.3 76.0 - - - +
352G LEU* 1.3 58.9 + - + +
354G MET* 3.2 9.0 + - - +
355G LEU* 3.0 35.7 + - + +
368G LEU* 5.3 2.0 - - + -
376G LEU* 3.8 26.8 - - + +
391G LEU* 3.5 30.5 - - + -
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Residues in contact with LEU 352 (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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348G TYR* 3.1 30.9 + - + +
349G CYS* 3.5 14.4 - - - +
351G ALA* 1.3 73.7 - - + +
353G ALA* 1.3 53.1 + - - +
355G LEU* 3.3 7.7 + - + +
356G ARG* 2.8 57.2 + - - +
362G MET* 3.4 41.7 - - + -
363G GLY 3.9 9.6 - - - +
364G ASP* 3.7 42.4 - - - +
368G LEU* 5.3 0.4 - - + -
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Residues in contact with ALA 353 (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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349G CYS 3.1 12.7 + - - +
350G GLU* 3.4 12.8 - - - +
351G ALA 3.3 0.2 - - - -
352G LEU* 1.3 74.6 - - - +
354G MET* 1.3 56.0 + - - +
356G ARG* 4.0 6.4 - - - +
357G GLU* 2.9 31.6 + - - +
118I ALA* 4.1 22.2 - - + +
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Residues in contact with MET 354 (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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346G LEU* 3.7 25.6 - - + -
350G GLU* 3.2 17.9 + - - +
351G ALA* 3.2 7.6 + - - +
353G ALA* 1.3 75.7 - - - +
355G LEU* 1.3 56.5 + - - +
357G GLU* 3.7 11.5 + - - +
358G ALA* 3.0 28.4 + - - +
376G LEU* 4.2 12.6 - - + -
379G LEU* 3.7 40.3 - - + +
380G VAL* 4.2 9.6 - - + +
383G LYS* 3.9 23.7 + - + +
384G TYR* 5.4 5.8 - - + -
118I ALA 5.7 0.7 - - - +
119I LEU* 4.3 18.8 - - + -
202I GLN* 5.4 0.2 - - - +
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Residues in contact with LEU 355 (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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351G ALA 3.0 23.8 + - - +
352G LEU* 3.7 6.7 - - + +
354G MET* 1.3 72.8 - - - +
356G ARG* 1.3 60.2 + - + +
358G ALA* 3.2 4.7 + - - +
359G GLY 3.0 21.1 + - - -
360G VAL* 3.0 28.4 + - + +
362G MET* 4.2 14.6 - - + -
368G LEU* 3.4 33.0 - - + -
372G ASN* 4.1 17.9 - - + +
375G LEU* 3.6 33.4 - - + -
376G LEU* 4.2 13.2 - - + -
379G LEU* 4.2 7.2 - - + -
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Residues in contact with ARG 356 (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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352G LEU* 2.8 40.8 + - + +
353G ALA* 4.0 5.4 - - - +
355G LEU* 1.3 68.4 - - + +
357G GLU* 1.3 60.4 + - - +
359G GLY* 3.0 18.9 + - - -
360G VAL 3.6 21.3 - - - +
362G MET* 2.7 31.5 + - + +
363G GLY* 3.6 15.2 + - - -
364G ASP* 3.6 31.3 + - - +
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Residues in contact with GLU 357 (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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353G ALA 2.9 18.7 + - - +
354G MET* 3.7 6.6 - - - +
356G ARG* 1.3 75.9 - - - +
358G ALA* 1.3 57.0 + - - +
359G GLY 3.2 1.1 + - - -
383G LYS* 4.4 0.7 + - - -
118I ALA* 3.4 35.7 + - + +
119I LEU* 2.9 33.2 - - - +
200I SER* 4.6 5.5 - - - -
202I GLN* 3.2 42.4 + - + +
203I THR* 5.2 2.6 - - - +
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Residues in contact with ALA 358 (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 MET 3.0 19.2 + - - +
355G LEU* 3.4 7.0 - - - +
356G ARG 3.2 0.4 - - - -
357G GLU* 1.3 74.7 + - - +
359G GLY* 1.3 63.0 - - - +
360G VAL* 4.7 1.6 - - - +
375G LEU* 4.8 9.7 - - + +
379G LEU* 3.9 26.7 - - + -
202I GLN* 4.3 15.3 - - - +
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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