Contacts of the helix formed by residues 223 - 230 (chain B) in PDB entry 6D6U
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 ILE 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B PRO* 4.6 19.1 - - + +
148B MET* 3.6 40.2 - - + -
221B ARG 3.6 3.9 + - - +
222B LYS* 1.3 71.0 - - - +
224B GLY* 1.3 67.6 + - - +
225B TYR 3.0 5.2 + - - -
226B PHE* 3.5 7.1 + - + +
227B VAL* 3.3 32.1 + - + +
231B TYR* 5.6 1.1 - - + -
341B TRP* 4.4 17.9 - - + -
345B LEU* 6.0 2.7 - - + -
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Residues in contact with GLY 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A VAL* 4.8 7.9 - - - +
222B LYS* 3.5 5.9 - - - +
223B ILE* 1.3 81.1 - - - +
225B TYR* 1.3 59.9 + - - +
227B VAL* 4.3 5.3 + - - +
228B ILE* 3.9 22.0 + - - +
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Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ARG* 4.9 9.5 + - - +
274A LYS* 6.2 1.6 - - - +
275A ILE 3.6 21.3 + - - -
276A PRO* 3.1 37.2 - - + +
277A TYR* 3.9 15.7 - - - -
278A VAL* 4.7 2.9 - - - -
279A LYS* 5.1 6.0 + - - -
282A ASP* 5.6 1.3 - - - -
222B LYS* 4.8 5.4 + - + +
223B ILE 3.1 0.8 - - - -
224B GLY* 1.3 75.2 - - - +
226B PHE* 1.3 90.4 + + + +
227B VAL 3.0 5.2 + - - -
228B ILE* 3.2 16.4 + - + +
229B GLN* 2.5 69.9 + - + +
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Residues in contact with PHE 226 (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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276A PRO* 5.8 2.0 - - + -
146B PHE* 3.4 33.9 - + - -
147B PRO* 3.4 32.1 - - + -
190B GLN* 4.8 14.1 - - + -
221B ARG* 3.9 21.8 - - + -
222B LYS 5.0 6.5 - - - -
223B ILE* 3.5 8.6 + - + +
225B TYR* 1.3 103.5 - + + +
227B VAL* 1.3 63.1 + - - +
229B GLN* 3.9 9.2 - - + -
230B THR* 3.5 8.6 + - - +
231B TYR* 3.4 29.5 + - + -
276B SER* 5.4 11.4 - - - -
286B MET* 6.0 5.2 - - - -
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Residues in contact with VAL 227 (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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223B ILE* 3.3 36.6 - - + +
224B GLY* 4.4 6.5 - - - +
225B TYR 3.0 0.6 + - - -
226B PHE* 1.3 79.7 - - - +
228B ILE* 1.3 66.7 + - + +
229B GLN 3.1 3.7 + - - -
231B TYR* 3.5 8.2 + - + -
232B LEU* 2.8 42.5 + - + +
341B TRP* 4.7 16.2 - - + -
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ARG* 4.8 21.3 + - - +
278A VAL* 3.9 34.1 - - + -
282A ASP* 5.6 6.3 - - + +
224B GLY 3.9 10.3 + - - +
225B TYR* 3.2 19.0 + - + +
227B VAL* 1.3 81.6 - - + +
229B GLN* 1.3 60.4 + - + +
232B LEU* 4.2 19.5 - - + +
233B PRO* 4.1 10.3 - - - +
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Residues in contact with GLN 229 (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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269A ARG* 3.1 38.4 - - - +
225B TYR* 2.5 67.0 + - + +
226B PHE* 4.0 9.6 - - + -
227B VAL 3.1 0.2 - - - -
228B ILE* 1.3 80.0 - - - +
230B THR* 1.3 72.8 + - - +
233B PRO* 3.2 16.9 - - - +
269B LEU* 4.4 6.1 - - - +
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Residues in contact with THR 230 (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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226B PHE* 3.5 9.0 + - - -
229B GLN* 1.3 92.6 + - - +
231B TYR* 1.3 78.9 + - + +
232B LEU 3.4 1.1 - - - -
233B PRO* 3.5 2.5 - - - -
234B CYS* 3.1 23.8 + - + +
269B LEU* 3.7 31.7 - - + +
273B ALA* 4.1 23.8 - - + +
286B MET* 4.8 10.9 - - - -
289B PHE* 6.2 0.4 - - + -
290B ILE* 5.2 7.6 - - + -
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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