Contacts of the helix formed by residues 248 - 254 (chain D) in PDB entry 6E90
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 SER 248 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D GLU* 2.7 24.6 + - - -
196D THR* 4.8 0.8 + - - +
240D LYS* 4.8 3.4 - - - +
247D VAL* 1.3 76.7 - - - +
249D SER* 1.3 67.1 + - - +
250D ALA* 3.1 10.8 + - - +
251D THR* 3.0 28.8 + - - -
252D PHE* 3.6 9.0 - - - -
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Residues in contact with SER 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ILE* 3.6 22.5 - - - +
240D LYS* 3.3 28.2 + - - +
248D SER* 1.3 72.7 - - - +
250D ALA* 1.3 63.5 + - - +
252D PHE* 3.0 27.4 + - - +
253D LEU* 3.8 7.0 + - - +
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D SER* 3.1 10.4 - - - +
249D SER* 1.3 79.3 - - - +
251D THR* 1.3 62.4 + - - +
253D LEU* 3.0 25.4 + - - +
254D GLU* 3.8 10.5 + - - +
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Residues in contact with THR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D VAL* 4.4 15.2 - - + +
193D GLU* 2.6 31.2 + - + +
196D THR* 3.6 22.4 - - + +
197D VAL* 3.8 27.4 - - + +
200D CYS* 5.9 0.4 - - - -
248D SER* 3.0 15.2 + - - -
250D ALA* 1.3 78.0 - - - +
252D PHE* 1.3 57.1 + - - +
253D LEU 3.2 0.2 - - - -
254D GLU* 3.1 30.6 + - + +
256D CYS* 3.9 9.3 - - - -
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Residues in contact with PHE 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D THR* 3.2 28.3 - - + -
199D ILE* 4.7 4.0 - - + -
200D CYS* 3.7 25.4 - - - -
203D LEU* 5.6 0.4 - - + -
232D LEU* 4.0 10.4 - - + +
235D MET* 3.9 32.8 - - + -
236D ILE* 3.3 35.7 - - + -
239D ALA* 3.4 31.0 - - + -
240D LYS* 6.1 1.1 - - + -
247D VAL* 5.6 1.1 - - + -
248D SER 3.6 18.4 - - - -
249D SER* 3.0 10.8 + - - +
251D THR* 1.3 76.5 - - - +
253D LEU* 1.3 61.5 + - + +
254D GLU 3.4 0.4 - - - -
257D GLY* 3.5 5.6 - - - -
258D VAL* 2.9 28.6 + - - +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D LEU* 4.1 20.6 - - + -
236D ILE* 6.3 0.9 - - + -
249D SER 4.5 7.0 - - - +
250D ALA* 3.0 16.9 + - - +
252D PHE* 1.3 82.5 - - + +
254D GLU* 1.3 65.9 + - - +
258D VAL* 3.7 24.1 - - + +
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Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D THR* 3.6 13.5 - - + +
189D THR* 3.2 38.7 + - - +
191D VAL* 4.0 22.3 - - + +
250D ALA* 4.1 7.8 - - - +
251D THR* 3.1 22.6 + - + +
253D LEU* 1.3 84.0 - - - +
255D SER* 1.3 68.0 + - - +
256D CYS* 3.2 5.6 - - - -
257D GLY 3.0 10.5 + - - -
258D VAL* 3.3 11.9 + - - +
259D ALA* 5.2 0.2 - - - -
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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