Contacts of the helix formed by residues 334 - 339 (chain B) in PDB entry 2RIO
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 334 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B LYS 3.8 1.8 + - - -
331B PHE 2.9 10.1 + - - -
333B ALA* 1.3 75.6 - - - +
335B SER* 1.3 61.1 + - - +
336B ASP 3.2 2.2 - - - -
337B PHE* 2.8 30.2 + - - +
338B VAL* 2.9 14.8 + - - +
367B LEU* 4.1 7.0 - - - -
413B GLY 6.5 0.2 - - - -
417B ILE* 3.8 17.9 - - - -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B PHE 3.3 3.2 + - - -
332B ASP* 3.4 21.6 + - - -
334B GLY* 1.3 77.2 - - - +
336B ASP* 1.3 64.5 + - - +
338B VAL* 4.5 0.9 - - - +
339B ILE* 2.8 31.5 + - - +
365B SER 3.2 16.3 + - - -
366B LYS* 4.4 1.5 - - - -
367B LEU* 3.4 37.7 - - - +
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Residues in contact with ASP 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ASP 4.5 1.9 + - - +
333B ALA 4.4 9.7 + - - +
334B GLY 3.2 0.8 - - - -
335B SER* 1.3 84.0 + - - +
337B PHE* 1.3 60.0 + - - +
339B ILE 4.2 6.3 - - - +
340B PRO* 3.7 25.8 - - - +
342B GLY* 5.6 3.6 - - - -
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Residues in contact with PHE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ALA* 5.7 0.9 - - + -
333B ALA 5.6 0.4 - - - +
334B GLY* 2.8 20.7 + - - +
336B ASP* 1.3 77.3 - - - +
338B VAL* 1.3 61.5 + - + +
340B PRO* 4.5 5.5 - - - +
409B ASN* 2.7 61.9 + - + -
412B ILE* 4.1 7.9 - - + -
413B GLY* 3.7 16.6 - - - -
416B MET* 3.3 35.4 - - + -
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLY 2.9 16.3 + - - +
335B SER* 4.3 0.4 - - - +
337B PHE* 1.3 79.4 - - + +
339B ILE* 1.3 73.1 + - + +
340B PRO* 3.5 7.3 - - - +
367B LEU* 4.1 25.1 - - + -
370B LEU* 4.0 16.4 - - + -
407B PHE* 3.5 19.8 - - + +
409B ASN* 3.4 28.2 + - - +
410B LEU* 3.9 24.9 - - + +
413B GLY* 4.3 11.0 - - - -
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B SER 2.8 18.1 + - - +
336B ASP* 3.7 6.3 - - - +
338B VAL* 1.3 93.8 - - + +
340B PRO* 1.4 60.0 - - - +
341B SER* 3.4 4.0 - - - +
342B GLY* 3.1 19.0 + - - +
343B ASP 3.8 13.2 - - - +
344B TRP* 3.5 37.0 - - + +
365B SER 4.0 10.1 - - - +
366B LYS 3.8 8.3 - - - +
367B LEU* 3.6 35.4 - - - +
370B LEU* 4.1 19.7 - - + -
407B PHE* 4.4 7.6 - - + -
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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