Contacts of the helix formed by residues 235 - 242 (chain A) in PDB entry 6B0Z
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 TYR 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A HIS* 2.5 40.7 + + - +
197A PHE* 3.5 41.1 - + + -
198A GLN* 3.4 30.9 + - + +
201A LEU* 3.5 24.9 - - + -
230A ILE* 3.7 12.6 - - + -
231A TYR* 3.1 11.3 + - + -
234A GLN* 1.3 90.8 - - + +
236A LYS* 1.3 61.7 + - - +
237A SER 3.3 2.7 - - - -
238A GLN* 3.1 15.1 + - - +
239A PHE* 2.8 45.1 + - + -
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Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A TYR* 2.9 44.3 + - + +
232A ASP* 4.0 26.6 + - - +
233A LYS 5.5 0.2 - - - -
234A GLN 4.0 0.4 - - - -
235A TYR* 1.3 75.9 - - - +
237A SER* 1.3 63.6 + - - +
239A PHE* 3.3 3.3 + - - +
240A GLU* 3.0 57.8 + - - +
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A TYR 3.3 0.4 - - - -
236A LYS* 1.3 80.2 + - - +
238A GLN* 1.3 62.3 + - - +
240A GLU* 3.3 13.7 + - - +
241A ALA* 2.9 29.5 + - - +
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Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.5 37.9 - - + +
234A GLN 2.9 25.4 - - - +
235A TYR* 3.1 15.7 + - - +
237A SER* 1.3 79.1 - - - +
239A PHE* 1.3 61.7 + - - +
241A ALA* 3.5 7.8 + - - +
242A GLN* 3.5 18.9 + - - +
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Residues in contact with PHE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A PHE* 3.7 25.6 - + - -
200A ALA* 3.7 25.4 - - + -
201A LEU* 3.5 25.6 - - + -
207A LEU* 4.4 2.9 - - + -
231A TYR* 3.4 31.4 - + - +
235A TYR* 2.8 37.3 + - + +
236A LYS 3.5 3.4 - - - +
238A GLN* 1.3 74.1 - - - +
240A GLU* 1.3 60.4 + - - +
242A GLN 3.1 3.3 + - - -
243A LYS 2.9 7.8 + - - -
244A ILE* 2.9 55.6 + - + +
245A TRP 3.7 27.1 - - - -
246A TYR* 4.2 4.5 - - + -
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Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A TYR* 5.4 2.7 - - - +
236A LYS* 3.0 57.0 + - + +
237A SER* 3.8 11.6 + - - +
239A PHE* 1.3 76.7 - - - +
241A ALA* 1.3 63.0 + - - +
243A LYS* 3.1 20.0 + - - +
244A ILE 4.4 6.1 - - - +
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A SER 2.9 17.4 + - - +
238A GLN* 3.7 9.0 - - - +
239A PHE 3.2 0.2 - - - -
240A GLU* 1.3 78.5 - - - +
242A GLN* 1.3 60.8 + - + +
243A LYS* 3.7 7.1 + - - +
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 3.1 39.5 + - - +
204A GLY* 3.4 25.4 - - - +
238A GLN 3.5 8.6 + - - +
239A PHE 3.1 6.9 + - - +
241A ALA* 1.3 78.8 - - + +
243A LYS* 1.3 70.5 + - - +
244A ILE* 3.2 18.1 + - + +
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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