Contacts of the helix formed by residues 335 - 340 (chain G) in PDB entry 2R9R
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 GLY 335 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305G GLN* 3.7 14.8 + - - -
331G MET 3.5 6.3 + - - -
332G GLU 2.9 12.1 + - - -
334G ILE* 1.3 75.6 - - - +
336G ALA* 1.3 64.3 + - - +
337G ILE 2.9 3.1 - - - -
338G GLN* 2.9 32.5 + - - +
339G VAL* 3.7 6.4 + - - +
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Residues in contact with ALA 336 (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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52G LEU* 5.6 0.7 - - + -
305G GLN* 3.2 35.6 - - - +
308G ILE* 3.5 26.2 - - + -
309G ALA* 3.4 12.2 - - - +
312G LEU* 6.0 1.3 - - + -
332G GLU 3.7 2.6 + - - -
333G ASN 2.9 18.2 + - - +
335G GLY* 1.3 78.4 - - - +
337G ILE* 1.3 62.6 + - + +
339G VAL* 3.0 11.7 + - - +
340G LEU 3.3 8.5 + - - -
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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
----------------------------------------------------------
36G LEU* 5.5 9.3 + - - +
38G PHE* 3.3 41.3 - - + -
51G CYS* 3.6 20.0 - - - -
52G LEU* 3.9 18.6 - - + -
312G LEU* 4.8 6.5 - - + -
334G ILE* 3.8 15.0 - - + +
335G GLY 2.9 0.8 - - - -
336G ALA* 1.3 79.3 - - + +
338G GLN* 1.3 71.2 - - - +
340G LEU* 3.3 22.5 + - + +
341G PRO* 3.3 9.9 - - - +
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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 ILE 5.8 0.2 - - - -
335G GLY* 2.9 21.4 + - - +
337G ILE* 1.3 88.6 - - + +
339G VAL* 1.3 58.4 + - + +
340G LEU 3.3 0.2 - - - -
341G PRO* 3.2 16.8 - - - +
342G LYS* 4.1 16.7 - - - -
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Residues in contact with VAL 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G LEU* 4.7 9.2 - - + -
301G CYS* 3.5 42.6 - - + -
305G GLN* 3.9 17.3 - - + +
306G LEU* 4.4 16.6 - - + -
309G ALA* 4.0 13.7 - - + -
335G GLY 4.0 6.5 - - - +
336G ALA 3.0 10.9 + - - +
338G GLN* 1.3 79.3 - - + +
340G LEU* 1.3 66.0 + - - +
341G PRO* 3.3 1.6 - - - -
342G LYS* 3.1 25.7 + - + +
343G LEU* 3.7 6.7 + - + +
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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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36G LEU* 4.1 22.0 - - + +
40G ARG* 5.0 8.1 - - - +
51G CYS* 6.1 1.1 - - - -
309G ALA* 3.2 35.4 - - + +
312G LEU* 4.1 35.7 - - + +
313G ARG* 4.3 4.3 - - + +
336G ALA 3.3 5.6 + - - +
337G ILE* 3.3 20.6 - - + +
339G VAL* 1.3 78.9 - - - +
341G PRO* 1.3 66.4 - - + +
343G LEU* 3.2 25.4 + - + +
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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