Contacts of the helix formed by residues 248 - 254 (chain B) in PDB entry 6E8Z
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLU* 2.8 27.6 + - - -
240B LYS* 4.8 1.8 - - - +
246B PRO* 5.9 0.3 - - - +
247B VAL* 1.3 74.8 + - - +
249B SER* 1.3 66.5 + - - +
250B ALA* 4.0 10.1 - - - -
251B THR* 3.1 19.5 + - - -
252B PHE* 3.4 15.2 - - - -
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Residues in contact with SER 249 (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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250A ALA* 4.7 15.1 - - - +
253A LEU* 4.1 27.1 - - - +
236B ILE* 3.6 11.8 - - - +
240B LYS* 2.9 29.5 + - - +
248B SER* 1.3 73.4 - - - +
250B ALA* 1.3 61.5 + - - +
252B PHE* 3.2 25.5 + - - +
253B LEU* 4.2 2.4 + - - +
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Residues in contact with ALA 250 (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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249A SER* 4.9 11.2 - - - +
248B SER* 3.1 8.7 - - - -
249B SER* 1.3 76.4 - - - +
251B THR* 1.3 63.5 + - - +
252B PHE 3.2 0.2 - - - -
253B LEU* 3.3 36.6 + - + +
254B GLU* 4.3 6.9 + - - +
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Residues in contact with THR 251 (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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191B VAL* 4.3 26.4 - - + +
193B GLU* 2.8 30.6 + - + +
196B THR* 3.7 24.2 - - + -
197B VAL* 4.4 10.1 - - + +
200B CYS* 6.2 0.2 - - - -
248B SER* 3.1 14.8 + - - -
250B ALA* 1.3 78.1 - - - +
252B PHE* 1.3 56.7 + - - +
253B LEU 3.1 0.9 - - - -
254B GLU* 3.1 27.7 + - + +
256B CYS* 4.0 8.2 - - - -
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Residues in contact with PHE 252 (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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253A LEU* 5.5 2.2 - - + -
196B THR* 3.3 28.3 - - + -
199B ILE* 5.2 1.8 - - + -
200B CYS* 3.6 28.0 - - - -
203B LEU* 6.1 0.2 - - + -
232B LEU* 4.1 20.1 - - + +
235B MET* 4.1 10.8 - - + -
236B ILE* 3.5 55.4 - - + -
239B ALA* 3.9 15.9 - - + -
247B VAL* 4.2 7.6 - - + -
248B SER 3.4 18.2 - - - -
249B SER 3.2 9.4 + - - +
250B ALA 3.2 0.8 - - - -
251B THR* 1.3 75.9 - - - +
253B LEU* 1.3 57.7 + - - +
254B GLU 3.2 4.0 - - - -
257B GLY* 4.1 6.1 - - - -
258B VAL* 2.8 31.4 + - - +
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Residues in contact with LEU 253 (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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229A ARG* 2.9 30.0 + - - +
232A LEU* 4.0 23.3 - - + +
233A MET* 4.1 19.7 - - + +
236A ILE* 3.8 25.1 - - + -
249A SER* 4.3 18.2 - - - +
252A PHE* 5.4 2.2 - - + -
253A LEU* 3.4 33.7 - - + -
249B SER 4.6 0.7 - - - +
250B ALA* 3.5 28.7 - - + +
251B THR 3.1 1.0 - - - -
252B PHE* 1.3 75.8 - - - +
254B GLU* 1.3 64.1 + - + +
258B VAL* 3.7 7.7 - - + +
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Residues in contact with GLU 254 (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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229A ARG* 3.6 19.8 + - - +
233A MET* 5.2 6.0 - - - +
347A GLU* 4.9 6.3 - - - +
165B THR* 3.5 16.7 + - + +
189B THR* 3.4 38.1 + - - +
191B VAL* 4.0 21.6 - - + +
250B ALA 4.6 4.5 - - - +
251B THR* 3.1 24.8 + - + +
253B LEU* 1.3 83.5 - - - +
255B SER* 1.3 67.2 + - - +
256B CYS* 3.1 7.9 - - - -
257B GLY 2.9 11.7 + - - -
258B VAL 3.3 7.3 + - - -
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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