Contacts of the helix formed by residues 246 - 252 (chain L) in PDB entry 6E07
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 246 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243L THR* 2.9 12.8 + - - +
244L GLU* 3.5 16.6 - - + +
245L GLY* 1.3 78.3 - - - +
247L GLY* 1.3 63.1 + - - +
248L GLY 3.2 4.2 + - - -
249L TYR* 3.3 57.6 + - + +
250L PHE* 3.7 8.0 + - - +
327L THR* 4.2 1.6 - - - -
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Residues in contact with GLY 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243L THR* 3.6 22.0 - - - -
246L ARG* 1.3 74.1 - - - +
248L GLY* 1.3 58.2 + - - +
250L PHE* 3.2 3.3 + - - +
251L ASP* 2.8 31.7 + - - +
322L TYR* 3.6 2.5 + - - -
325L ASP* 2.9 17.9 + - - -
327L THR* 3.4 0.8 + - - -
328L VAL* 3.6 17.5 - - - -
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Residues in contact with GLY 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246L ARG 3.2 1.0 - - - -
247L GLY* 1.3 74.5 - - - +
249L TYR* 1.3 64.5 + - - +
251L ASP* 3.6 14.4 + - - +
252L GLU* 4.1 10.9 + - - +
327L THR* 2.8 39.2 + - - -
328L VAL 4.7 0.2 - - - -
329L PRO* 5.2 1.1 - - - -
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Residues in contact with TYR 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L ARG* 3.3 57.0 + - + +
247L GLY 3.2 0.4 - - - -
248L GLY* 1.3 78.6 - - - +
250L PHE* 1.3 64.0 + - - +
251L ASP 3.5 0.2 + - - -
252L GLU* 3.6 13.9 + - - +
253L PHE* 3.4 22.8 - - + -
327L THR* 6.1 2.7 - - + -
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Residues in contact with PHE 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243L THR* 4.1 13.7 - - + -
246L ARG 3.7 3.7 + - - +
247L GLY* 3.2 11.6 + - - +
249L TYR* 1.3 78.6 - - - +
251L ASP* 1.3 60.8 + - - +
253L PHE* 2.8 25.8 + - + +
254L GLY* 3.0 27.8 + - - -
255L ILE* 3.4 29.2 - - + -
258L ASP* 3.7 23.1 - - + -
322L TYR* 3.9 17.5 - + - -
334L THR* 4.1 5.4 - - + -
335L ALA 3.6 16.2 - - - -
336L THR* 4.1 17.5 - - + -
360L LYS* 3.6 31.0 - - - -
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Residues in contact with ASP 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247L GLY 2.8 16.8 + - - +
248L GLY 3.9 6.7 - - - +
249L TYR 3.3 0.6 - - - -
250L PHE* 1.3 73.0 - - - +
252L GLU* 1.3 60.5 + - + +
253L PHE 3.3 1.0 + - - -
254L GLY 4.2 0.3 + - - -
322L TYR* 2.6 23.8 + - - +
328L VAL* 5.0 0.2 - - + -
329L PRO* 3.4 35.8 - - + +
332L SER* 2.5 30.8 + - - -
334L THR* 2.7 26.1 + - - +
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Residues in contact with GLU 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175L ARG* 4.6 21.2 - - - +
248L GLY 4.2 9.0 - - - +
249L TYR* 3.7 19.1 - - - +
250L PHE 3.1 0.4 + - - -
251L ASP* 1.3 78.6 - - - +
253L PHE* 1.3 78.6 + - + +
257L ARG* 4.0 11.3 + - - -
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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