Contacts of the helix formed by residues 358 - 364 (chain B) in PDB entry 5B2R
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 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B GLU 4.8 1.5 + - - -
350B ILE* 3.7 12.3 - - - -
353B ASP 5.1 0.4 + - - -
356B LYS* 3.1 6.7 + - - +
357B ASN* 1.3 81.3 - - - +
359B TYR* 1.3 61.7 + - - -
360B ALA 3.2 2.7 - - - -
361B GLY 3.2 1.4 + - - -
362B TYR* 2.8 26.7 + - - +
372B PHE* 3.6 6.3 - - - -
375B PHE* 3.5 24.4 - - - -
376B ILE* 6.3 0.2 - - - -
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Residues in contact with TYR 359 (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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43A G 2.9 61.8 + + - +
328B HIS* 2.7 34.7 + + - -
332B LEU* 3.4 26.8 - - + +
335B LEU* 5.5 0.9 - - + -
350B ILE* 2.8 17.0 + - + +
351B PHE* 3.7 22.7 - + + -
358B GLY* 1.3 71.6 - - - -
360B ALA* 1.3 57.4 + - - +
362B TYR* 3.2 16.2 + + - +
363B ILE* 2.8 48.7 + - + +
372B PHE* 3.5 21.7 - + + -
399B LEU* 4.5 7.0 - - + -
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Residues in contact with ALA 360 (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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43A G 3.6 16.6 - - - +
350B ILE 3.0 7.1 + - - +
351B PHE* 3.6 14.8 - - - +
352B PHE 3.5 35.0 - - - +
353B ASP 3.7 8.5 - - - +
354B GLN* 4.0 5.6 - - + +
358B GLY 3.2 0.2 - - - -
359B TYR* 1.3 76.7 - - - +
361B GLY* 1.3 55.7 + - - +
363B ILE 3.2 0.2 + - - -
364B ASP* 2.7 34.7 + - - +
365B GLY 3.2 3.2 + - - -
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Residues in contact with GLY 361 (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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353B ASP 3.8 1.2 + - - -
354B GLN 3.4 16.4 - - - -
356B LYS 3.3 24.2 + - - -
358B GLY 3.2 4.0 + - - -
360B ALA* 1.3 79.1 - - - +
362B TYR* 1.3 58.7 + - - +
365B GLY* 3.0 17.8 - - - -
366B GLY 4.6 0.4 - - - -
367B ALA* 2.9 28.2 + - - -
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Residues in contact with TYR 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B HIS* 4.5 0.9 - + - -
358B GLY 2.8 17.3 + - - +
359B TYR* 3.4 19.3 - + - +
360B ALA 3.1 0.2 - - - -
361B GLY* 1.3 78.6 - - - +
363B ILE* 1.3 76.7 + - + +
365B GLY 4.8 2.1 - - - +
367B ALA* 3.7 20.3 - - - +
368B SER 3.9 0.7 - - - -
369B GLN* 3.7 33.8 + - + +
372B PHE* 3.7 43.1 - + + -
398B LEU 4.6 0.6 + - - -
399B LEU 2.7 30.3 + - - -
400B ARG* 3.8 1.9 - - - -
401B LYS* 2.6 62.7 + - + +
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Residues in contact with ILE 363 (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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43A G 3.5 43.3 - - - +
44A U 4.2 19.2 - - - +
328B HIS* 4.5 1.3 - - + -
359B TYR* 2.8 58.7 + - + +
360B ALA 4.1 0.9 - - - +
362B TYR* 1.3 83.8 - - + +
364B ASP* 1.3 73.1 + - - +
365B GLY 4.7 1.4 - - - +
401B LYS* 3.8 27.6 + - - +
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Residues in contact with ASP 364 (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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42A A 5.4 2.4 - - - +
43A G 2.9 29.5 + - - +
354B GLN* 3.5 35.9 + - + +
360B ALA 2.7 12.8 + - - +
363B ILE* 1.3 84.4 - - - +
365B GLY* 1.3 63.2 + - - +
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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