Contacts of the helix formed by residues 336 - 346 (chain G) in PDB entry 4P0S
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 ARG 336 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334G ARG* 3.9 21.3 - - - +
335G LYS* 1.3 77.1 - - - +
337G LEU* 1.3 60.9 + - - +
338G ASP* 3.5 29.7 + - - +
339G ASP* 3.2 17.5 + - + +
340G LEU* 3.0 25.7 + - - +
369G GLU* 3.2 36.7 + - + +
370G GLU* 3.1 27.6 + - + -
405G ILE* 5.4 2.5 - - - -
55P T 5.2 16.0 + - - +
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Residues in contact with LEU 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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335G LYS 5.4 0.2 - - - +
336G ARG* 1.3 73.6 - - - +
338G ASP* 1.3 61.7 + - - +
340G LEU* 3.2 20.9 + - + +
341G CYS* 3.2 19.2 + - - -
368G VAL* 4.3 15.3 - - + -
369G GLU 3.3 24.2 + - - +
370G GLU* 3.1 36.6 + - + +
371G HIS* 5.5 3.4 - - + +
373G SER* 4.7 10.5 - - - +
375G HIS* 5.3 3.6 - - + +
377G LEU* 3.5 29.4 - - + -
384G LEU* 4.8 10.0 - - + +
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Residues in contact with ASP 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336G ARG* 3.7 35.4 + - - +
337G LEU* 1.3 73.9 - - - +
339G ASP* 1.3 86.0 + - - +
340G LEU 3.4 0.2 + - - -
341G CYS* 3.5 6.0 + - - +
342G SER* 3.4 26.0 + - - -
370G GLU* 4.5 6.8 + - - +
376G ASN 5.8 0.2 - - - +
377G LEU* 3.9 22.0 - - + +
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Residues in contact with ASP 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G ARG* 5.9 0.7 + - - -
335G LYS* 4.1 17.2 - - - +
336G ARG* 3.2 28.0 + - + +
338G ASP* 1.3 89.0 + - - +
340G LEU* 1.3 53.2 + - - +
342G SER* 4.2 3.4 - - - -
343G SER* 2.4 35.1 + - - -
348G ARG* 3.5 14.9 + - - -
55P T 2.7 56.3 + - - +
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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
----------------------------------------------------------
335G LYS* 4.1 17.4 - - + +
336G ARG 3.0 12.4 + - - +
337G LEU* 3.3 18.2 - - + +
338G ASP 3.2 0.2 - - - -
339G ASP* 1.3 74.5 - - - +
341G CYS* 1.3 65.5 + - - +
343G SER* 3.1 7.2 + - - -
344G ILE* 2.9 42.3 + - + +
349G PHE* 3.5 35.9 - - + -
366G TYR* 5.3 1.8 - - + +
384G LEU* 4.3 18.8 - - + -
387G ALA* 5.2 6.5 - - + -
388G VAL* 5.3 9.9 - - + -
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Residues in contact with CYS 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 LEU 3.2 11.6 + - - -
338G ASP* 3.5 8.0 + - - +
340G LEU* 1.3 73.3 - - - +
342G SER* 1.3 68.5 + - - +
344G ILE* 3.2 4.6 + - - +
345G ILE* 3.2 29.8 + - - +
377G LEU* 3.8 21.5 - - - -
378G SER* 3.3 19.3 - - - +
379G LEU* 3.8 25.3 - - + +
384G LEU* 3.5 30.1 - - - -
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Residues in contact with SER 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 ASP 3.4 14.2 + - - -
339G ASP* 4.2 4.9 - - - -
340G LEU 3.4 0.4 - - - -
341G CYS* 1.3 78.3 - - - +
343G SER* 1.3 60.4 + - - +
345G ILE* 3.4 10.7 + - - +
346G ASP* 3.0 35.1 + - - +
348G ARG* 4.4 12.1 - - - -
378G SER* 4.5 2.7 + - - -
55P T 6.2 1.3 - - - -
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Residues in contact with SER 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G LYS* 3.3 11.4 - - - -
339G ASP 2.4 24.2 + - - -
340G LEU* 3.1 11.4 + - - -
341G CYS 3.1 0.8 - - - -
342G SER* 1.3 79.2 - - - +
344G ILE* 1.3 56.6 + - - +
346G ASP* 3.0 6.2 - - - +
347G GLY 3.0 6.8 + - - -
348G ARG* 2.8 55.5 + - - +
349G PHE* 3.1 20.8 + - - -
352G GLN* 5.1 1.3 - - - -
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Residues in contact with ILE 344 (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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340G LEU* 2.9 47.5 + - + +
341G CYS 3.2 3.6 + - - +
343G SER* 1.3 73.4 - - - +
345G ILE* 1.3 66.8 + - - +
347G GLY* 3.2 11.8 + - - -
349G PHE* 3.8 21.1 - - + -
350G ARG* 6.0 1.4 - - - +
379G LEU* 4.6 13.5 - - + -
383G THR* 6.0 1.8 - - + -
384G LEU* 4.1 21.1 - - + -
387G ALA* 4.5 13.9 - - + -
461H LEU* 5.0 1.6 - - - +
1M G 4.9 26.0 - - + +
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Residues in contact with ILE 345 (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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341G CYS 3.2 15.4 + - - +
342G SER* 3.6 7.2 - - - +
344G ILE* 1.3 84.7 - - + +
346G ASP* 1.3 63.9 + - + +
347G GLY 3.1 0.7 + - - -
378G SER* 3.7 26.0 - - - +
379G LEU* 4.1 23.8 - - + -
461H LEU* 4.9 3.8 - - - +
1M G 5.6 4.2 - - - +
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Residues in contact with ASP 346 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G SER* 3.0 24.0 - - - +
343G SER 3.0 9.4 - - - +
345G ILE* 1.3 80.0 - - + +
347G GLY* 1.3 58.5 + - - +
348G ARG* 3.3 33.7 + - - +
461H LEU* 3.7 14.1 - - - +
463H SER 4.9 6.1 - - - +
465H TRP* 5.1 15.4 + - - +
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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
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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