Contacts of the helix formed by residues 274 - 281 (chain B) in PDB entry 2C6T
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 GLU 274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 3.1 24.5 - - - +
272B PRO 3.8 1.3 + - - +
273B PRO* 1.3 76.4 - - - +
275B VAL* 1.3 60.3 + - - +
276B ALA* 4.0 16.6 - - - +
277B GLU* 3.0 40.1 + - - +
278B PHE* 3.3 12.9 + - - -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR 4.5 6.3 - - - +
42A GLU* 3.3 38.5 + - + +
262B LEU* 4.2 15.7 - - + -
266B LYS* 5.4 0.4 - - - -
273B PRO 4.1 0.2 + - - -
274B GLU* 1.3 73.4 - - - +
276B ALA* 1.3 57.6 + - - +
278B PHE* 3.2 9.3 + - - +
279B VAL* 2.9 28.0 + - + +
288B LYS* 4.2 20.6 - - + +
291B VAL* 4.2 21.8 - - + -
292B LEU* 3.8 27.4 - - + -
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Residues in contact with ALA 276 (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 GLU* 5.0 0.4 + - - -
274B GLU* 3.2 14.4 - - + +
275B VAL* 1.3 79.4 - - - +
277B GLU* 1.3 58.4 + - + +
279B VAL* 3.6 9.9 - - - +
280B TYR* 2.9 29.3 + - - +
288B LYS* 4.8 15.3 - - + +
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Residues in contact with GLU 277 (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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225B TYR* 3.5 43.6 + - + +
273B PRO* 3.8 8.8 - - + +
274B GLU* 3.0 41.3 + - + +
276B ALA* 1.3 76.1 - - + +
278B PHE* 1.3 60.4 + - - +
280B TYR* 3.4 6.6 + - + +
281B ILE* 3.1 30.0 + - - +
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Residues in contact with PHE 278 (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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221B VAL* 4.6 8.3 - - + -
225B TYR* 6.3 1.6 - + - -
227B LEU* 5.0 1.1 - - + -
258B THR* 3.7 30.3 - - + +
261B MET* 3.7 28.5 - - + -
262B LEU* 3.7 32.3 - - + -
265B SER* 3.7 22.2 - - - -
273B PRO* 3.6 40.4 - - + -
274B GLU 3.3 20.1 + - - -
275B VAL* 3.2 7.9 + - - +
277B GLU* 1.3 73.9 - - - +
279B VAL* 1.3 64.7 + - - +
281B ILE* 3.7 17.1 + - + +
282B THR* 3.3 25.3 + - - +
291B VAL* 4.9 6.1 - - + -
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Residues in contact with VAL 279 (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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275B VAL* 2.9 18.5 + - + +
276B ALA* 3.6 11.0 - - - +
278B PHE* 1.3 75.4 - - - +
280B TYR* 1.3 64.9 + - - +
282B THR* 2.8 24.7 + - - -
284B ASP* 3.5 23.0 + - - +
286B TYR 3.7 16.2 - - - +
287B THR* 4.0 5.8 - - - +
288B LYS* 3.6 38.4 - - + +
291B VAL* 4.0 13.0 - - + -
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Residues in contact with TYR 280 (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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224B GLU* 6.1 0.9 - - - -
225B TYR* 4.2 14.4 - - - -
276B ALA 2.9 18.0 + - - +
277B GLU* 3.7 8.1 - - + +
278B PHE 3.3 0.2 - - - -
279B VAL* 1.3 78.1 - - - +
281B ILE* 1.3 65.4 + - + +
283B ASP* 3.1 24.5 + - - +
284B ASP* 4.3 10.9 - - - +
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Residues in contact with ILE 281 (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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217B TRP* 3.5 48.3 + - + +
221B VAL* 3.8 25.4 - - + -
224B GLU* 5.0 10.3 - - + +
225B TYR* 3.7 33.2 - - + +
254B GLN* 4.6 0.2 - - - +
258B THR* 5.2 0.2 - - + -
277B GLU 3.1 16.5 + - - +
278B PHE* 3.8 23.3 - - + +
280B TYR* 1.3 80.7 - - + +
282B THR* 1.3 57.1 + - - +
283B ASP* 3.1 16.2 + - - +
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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