Contacts of the helix formed by residues 229 - 236 (chain B) in PDB entry 4XDO
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 PHE 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 3.7 36.1 - - + -
84B PHE* 3.7 23.1 - - - -
85B THR* 3.5 25.8 - - + -
225B ALA* 2.8 21.2 + - + +
226B GLN 3.7 3.6 - - - -
228B PHE* 1.3 86.3 - - + +
230B PRO* 1.4 59.1 - - - +
231B SER 3.3 2.7 - - - -
232B SER* 3.3 18.6 + - - +
233B SER* 2.9 26.5 + - - -
239B PHE* 4.0 9.9 - - + -
245B THR* 3.5 31.0 - - + -
246B LEU 4.0 1.8 - - - -
247B ILE* 4.1 7.4 - - + -
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Residues in contact with PRO 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 GLN 3.4 13.4 - - - +
227B GLY* 3.6 11.4 - - - +
228B PHE 3.2 10.8 - - - +
229B PHE* 1.4 90.0 - - - +
231B SER* 1.3 53.6 + - - +
233B SER* 3.7 3.7 - - - -
234B GLN* 2.7 37.2 + - - +
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE 3.3 0.8 - - - -
230B PRO* 1.3 79.3 - - - +
232B SER* 1.3 66.0 + - - +
234B GLN* 3.2 17.5 + - - +
235B GLY* 3.1 18.7 + - - -
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR* 5.3 6.6 + - - +
229B PHE* 3.3 22.8 + - - +
231B SER* 1.3 77.2 - - - +
233B SER* 1.3 62.9 + - - +
235B GLY* 3.1 10.2 + - - -
236B CYS* 3.1 11.3 + - - +
239B PHE* 3.6 34.1 - - - +
242B HIS* 5.6 1.2 - - - -
245B THR* 5.5 0.7 + - - -
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Residues in contact with SER 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLN* 3.7 26.6 - - - +
229B PHE 2.9 17.3 + - - -
230B PRO* 3.7 8.3 - - - -
232B SER* 1.3 72.0 - - - +
234B GLN* 1.3 67.8 + - - +
235B GLY 2.9 2.5 + - - -
236B CYS 3.1 18.9 + - - +
237B ASP* 4.2 4.9 + - - -
239B PHE* 3.6 22.8 - - - -
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Residues in contact with GLN 234 (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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230B PRO 2.7 21.1 + - - +
231B SER* 3.5 16.9 + - - +
233B SER* 1.3 72.9 - - - +
235B GLY* 1.3 59.7 + - - +
236B CYS* 4.7 0.3 - - - -
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Residues in contact with GLY 235 (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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231B SER 3.1 12.7 + - - -
232B SER* 3.1 4.7 + - - -
233B SER 2.9 1.0 - - - -
234B GLN* 1.3 79.5 - - - +
236B CYS* 1.3 61.8 + - - +
310B CYS* 3.8 14.4 - - - +
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Residues in contact with CYS 236 (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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232B SER 3.1 3.4 + - - +
233B SER* 3.1 13.7 + - - +
234B GLN 3.5 0.4 - - - -
235B GLY* 1.3 81.1 - - - +
237B ASP* 1.3 69.8 + - - +
238B ALA* 3.3 18.7 + - - -
239B PHE* 3.3 25.1 + - + +
242B HIS* 3.6 9.9 - - + -
308B CYS* 3.9 5.4 - - - -
309B THR* 4.1 9.4 - - - -
310B CYS* 3.6 7.0 - - + -
401B ZN 2.3 36.8 - - - -
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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