Contacts of the helix formed by residues 332 - 342 (chain G) in PDB entry 4D1Q
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 ASN 332 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307G LEU* 3.7 24.4 - - + +
308G ARG* 3.6 22.3 + - - +
309G SER* 2.7 41.6 + - - +
310G SER 4.1 1.4 + - - -
311G LEU* 3.9 13.6 - - + +
328G SER* 3.1 22.6 + - - +
329G ILE 3.1 5.0 + - - +
330G LEU 2.9 0.4 - - - -
331G ASP* 1.3 80.2 - - - +
333G TRP* 1.3 57.0 + - - +
334G GLU 3.3 3.4 - - - -
335G SER* 3.2 9.9 + - - -
336G VAL* 3.0 28.0 + - + +
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Residues in contact with TRP 333 (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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291G CYS* 5.4 7.4 - - - -
329G ILE* 2.8 44.2 + - + +
330G LEU* 3.1 27.2 + - + +
331G ASP 3.7 0.2 - - - -
332G ASN* 1.3 74.3 - - - +
334G GLU* 1.3 72.7 + - - +
336G VAL* 3.1 22.7 - - + +
337G ILE* 3.2 29.3 + - + +
349G ILE* 3.9 28.7 - - + -
352G ILE* 4.6 20.0 - - + -
354G LYS* 3.3 64.3 - - + +
357G ILE* 5.6 3.8 - - + -
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Residues in contact with GLU 334 (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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330G LEU 5.4 0.5 - - - +
332G ASN 3.3 0.6 - - - -
333G TRP* 1.3 93.3 - - - +
335G SER* 1.3 60.0 + - - +
337G ILE* 3.7 17.2 - - + +
338G GLN* 3.2 26.5 + - - +
354G LYS* 4.0 16.2 + - - -
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Residues in contact with SER 335 (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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306G ARG 5.5 2.0 - - - -
307G LEU* 4.4 28.5 + - - +
308G ARG* 4.7 10.0 + - - -
332G ASN* 3.2 20.2 + - - -
334G GLU* 1.3 80.4 - - - +
336G VAL* 1.3 55.9 + - - +
338G GLN* 3.7 4.8 - - - +
339G ILE* 3.3 33.5 + - - +
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Residues in contact with VAL 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G ILE* 3.8 13.7 - - + -
298G PHE* 3.7 31.9 - - + -
307G LEU* 4.9 4.9 - - + +
311G LEU* 4.9 6.5 - - + -
329G ILE* 4.4 9.0 - - + +
332G ASN* 3.0 18.7 + - + +
333G TRP* 3.1 28.5 - - + +
335G SER* 1.3 75.9 - - - +
337G ILE* 1.3 59.7 + - - +
338G GLN 3.2 1.3 - - - -
339G ILE* 3.7 1.2 + - - +
340G LEU* 3.0 42.1 + - + +
349G ILE* 3.9 14.6 - - + -
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Residues in contact with ILE 337 (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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333G TRP* 3.3 32.3 - - + +
334G GLU* 3.7 28.9 - - + +
336G VAL* 1.3 77.3 - - - +
338G GLN* 1.3 69.5 + - - +
340G LEU* 3.3 4.0 + - - +
341G SER* 3.0 30.3 + - - +
346G THR* 5.6 2.2 - - + +
349G ILE* 3.3 36.1 - - + -
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Residues in contact with GLN 338 (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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334G GLU 3.2 18.2 - - - +
335G SER* 3.7 8.1 - - - +
337G ILE* 1.3 87.1 - - + +
339G ILE* 1.3 70.8 + - + +
341G SER* 3.1 12.6 + - - -
342G GLU* 3.0 36.8 + - - +
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Residues in contact with ILE 339 (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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298G PHE* 4.1 22.4 - - + -
303G LEU* 4.2 32.5 - - + -
306G ARG* 5.3 7.9 - - + +
307G LEU* 6.1 2.0 - - + -
335G SER* 3.3 20.0 + - - +
336G VAL 4.3 2.7 - - - +
338G GLN* 1.3 85.4 - - + +
340G LEU* 1.3 60.9 + - + +
342G GLU* 3.3 31.1 - - - +
343G ALA* 3.3 21.3 - - + +
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Residues in contact with LEU 340 (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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294G ILE* 4.3 12.6 - - + -
297G TYR* 4.5 19.1 - - + +
298G PHE* 4.8 7.4 - - + -
336G VAL* 3.0 38.6 + - + +
337G ILE* 3.9 4.5 - - - +
338G GLN 3.1 0.2 - - - -
339G ILE* 1.3 79.4 - - + +
341G SER* 1.3 61.9 + - - +
342G GLU 3.3 0.2 - - - -
343G ALA* 3.6 3.5 + - + -
344G GLY 3.5 3.8 + - - -
345G GLU* 3.3 54.5 + - + +
346G THR* 3.2 21.1 + - + -
348G ARG* 5.0 5.8 - - + -
349G ILE* 4.1 26.7 - - + +
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Residues in contact with SER 341 (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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337G ILE* 3.0 19.1 + - - +
338G GLN* 3.1 6.0 + - - -
340G LEU* 1.3 76.8 - - - +
342G GLU* 1.3 56.9 + - - +
343G ALA 3.4 1.6 + - - -
344G GLY* 4.2 5.8 + - - -
346G THR* 3.4 23.0 + - - +
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Residues in contact with GLU 342 (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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338G GLN* 3.0 33.0 - - - +
339G ILE* 3.3 34.3 - - + +
341G SER* 1.3 77.6 - - - +
343G ALA* 1.3 58.0 + - + +
344G GLY 3.7 1.6 - - - -
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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