Contacts of the helix formed by residues 230 - 237 (chain D) in PDB entry 2ORE
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 THR 230 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D ALA* 4.5 5.4 - - + +
186D PRO 4.1 15.3 + - - +
187D LEU* 3.7 29.4 - - + +
228D HIS* 4.0 10.8 - - + -
229D ASP* 1.3 80.1 - - - +
231D MET* 1.3 65.3 + - - +
232D LEU* 3.3 10.9 + - - +
233D THR* 2.7 39.2 + - - +
234D ARG* 3.1 15.1 + - - +
119E TYR* 4.0 11.4 - - - -
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Residues in contact with MET 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D THR* 1.3 74.6 - - - +
232D LEU* 1.3 69.0 + - + +
235D GLU* 3.2 23.8 + - + +
119E TYR* 3.8 24.6 + - + -
122E LEU* 3.2 25.8 - - + -
124E ARG* 3.1 43.7 - - + +
132E ASN* 5.0 9.4 - - - +
133E VAL* 4.7 7.6 - - - -
134E PRO* 3.2 37.0 - - + +
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Residues in contact with LEU 232 (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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185D ALA* 5.4 1.1 - - + -
186D PRO* 4.7 17.9 - - + +
203D LEU* 4.0 33.2 - - + -
230D THR* 3.1 8.3 + - - +
231D MET* 1.3 85.1 - - + +
233D THR* 1.3 59.4 + - - +
235D GLU* 3.3 10.2 + - + +
236D TRP* 3.0 55.6 + - + +
132E ASN* 6.0 4.0 - - - +
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Residues in contact with THR 233 (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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185D ALA* 3.7 28.0 - - + -
227D ASN* 3.9 17.0 - - + +
228D HIS 3.1 20.8 + - - +
229D ASP* 3.6 1.4 - - - -
230D THR* 2.7 36.2 + - - +
232D LEU* 1.3 73.2 - - - +
234D ARG* 1.3 59.2 + - - +
236D TRP* 3.7 12.6 - - + -
237D TYR* 2.9 44.2 + - + +
264D LEU* 4.1 6.8 - - - +
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Residues in contact with ARG 234 (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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229D ASP* 2.7 41.3 + - - +
230D THR 3.1 15.8 + - - +
233D THR* 1.3 76.2 + - - +
235D GLU* 1.3 61.7 + - - +
237D TYR 3.8 0.5 - - - -
238D GLN* 3.2 21.8 + - - -
242D LEU* 4.4 22.8 - - + +
244D VAL* 3.7 18.6 - - - +
264D LEU* 4.3 8.0 - - + +
92E TYR* 3.5 7.7 + - - +
119E TYR* 3.8 28.0 - - - -
134E PRO* 4.0 16.8 - - + -
135E PHE 3.8 15.6 + - - +
136E GLY 3.5 23.8 + - - -
137E ARG* 3.8 19.2 - - - +
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Residues in contact with GLU 235 (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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231D MET* 3.2 18.8 + - + +
232D LEU* 3.3 13.7 - - + +
233D THR 3.1 0.2 - - - -
234D ARG* 1.3 76.5 - - - +
236D TRP* 1.3 69.4 + - + +
238D GLN* 2.9 54.2 + - - +
92E TYR* 4.8 0.2 - - - -
95E ARG* 2.9 21.1 + - - -
132E ASN* 2.7 34.4 - - + +
134E PRO* 3.7 12.8 - - + +
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Residues in contact with TRP 236 (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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185D ALA* 4.0 17.5 - - + -
203D LEU* 3.5 35.8 + - + -
206D GLN* 3.3 47.8 - - + -
207D ALA* 3.5 29.0 - - + +
210D ALA* 3.5 21.9 - - + +
214D GLU* 4.3 10.2 - - - +
232D LEU* 3.0 46.5 + - + +
233D THR* 3.7 14.4 - - + +
235D GLU* 1.3 82.5 - - + +
237D TYR* 1.3 75.5 + - + +
238D GLN* 3.2 4.9 + - - +
268D TYR* 4.0 1.9 + - - -
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Residues in contact with TYR 237 (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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182D PRO* 4.4 3.1 - - - +
206D GLN* 4.0 14.7 + - - -
209D LEU* 4.6 2.6 - - + +
210D ALA* 3.7 14.6 - - + -
225D ILE* 3.4 43.5 - - + +
227D ASN* 3.4 33.6 + - + -
233D THR* 2.9 29.0 + - - +
234D ARG 3.8 2.9 - - - -
236D TRP* 1.3 89.1 - + + +
238D GLN* 1.3 62.9 + - - +
239D ARG 3.2 3.6 - - - -
240D ALA* 3.1 13.8 + - - +
242D LEU* 3.5 25.4 - - + +
264D LEU* 4.4 9.2 - - + -
266D ALA* 3.9 19.1 - - + -
268D TYR* 3.5 18.2 - - - +
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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