Contacts of the helix formed by residues 230 - 237 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ALA* 4.7 1.1 - - - +
186E PRO 3.7 23.0 + - - +
187E LEU* 4.6 8.7 - - + -
228E HIS* 3.8 20.6 - - + -
229E ASP* 1.3 80.6 + - - +
231E MET* 1.3 66.6 + - - +
232E LEU* 3.4 17.1 + - - +
233E THR* 2.8 31.2 + - - +
234E ARG* 3.1 16.0 + - - +
261E VAL* 5.7 3.8 - - + -
119F TYR* 4.1 7.2 - - - -
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Residues in contact with MET 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E THR* 1.3 74.0 - - - +
232E LEU* 1.3 69.8 + - + +
234E ARG* 3.5 0.8 + - - -
235E GLU* 3.1 19.8 + - - +
119F TYR* 3.8 26.1 + - + -
122F LEU* 3.9 27.1 - - - -
124F ARG* 4.0 23.8 - - + -
132F ASN* 4.3 28.9 - - - +
133F VAL* 4.9 3.4 - - - -
134F PRO* 3.5 36.8 - - + +
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Residues in contact with LEU 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E ALA* 4.8 0.4 - - + -
186E PRO* 4.0 44.2 - - + +
203E LEU* 4.9 13.5 - - + -
230E THR* 3.1 6.2 + - - +
231E MET* 1.3 82.1 - - + +
233E THR* 1.3 66.4 + - - +
235E GLU* 2.9 9.7 + - + +
236E TRP* 2.9 55.2 + - + +
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Residues in contact with THR 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E ALA* 3.7 18.2 - - + -
227E ASN* 3.5 31.4 - - + +
228E HIS* 2.8 29.8 + - + +
230E THR* 2.8 25.3 + - - +
232E LEU* 1.3 78.9 - - - +
234E ARG* 1.3 55.2 + - - +
236E TRP* 3.6 9.6 - - + -
237E TYR* 2.9 41.9 + - + +
264E LEU* 3.7 12.3 - - - +
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Residues in contact with ARG 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E ASP* 2.8 40.1 + - - +
230E THR 3.1 16.8 + - - +
231E MET 3.7 4.7 - - - +
233E THR* 1.3 73.6 + - - +
235E GLU* 1.3 67.7 + - - +
237E TYR 3.7 1.4 - - - +
238E GLN* 3.4 20.4 + - - +
242E LEU* 4.5 15.5 - - + +
244E VAL* 3.8 15.3 - - - +
264E LEU* 4.3 10.4 - - + +
92F TYR* 3.8 5.5 + - - +
119F TYR* 3.6 36.2 - - - -
134F PRO* 4.0 12.8 - - + -
135F PHE 3.4 22.5 + - - +
136F GLY 3.7 16.8 + - - -
137F ARG* 3.9 17.1 - - - +
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Residues in contact with GLU 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E MET 3.1 13.4 + - - +
232E LEU* 2.9 11.8 + - - +
234E ARG* 1.3 76.9 - - - +
236E TRP* 1.3 72.8 + - + +
238E GLN* 2.6 58.0 + - - +
92F TYR* 4.9 0.4 - - - -
95F ARG* 3.0 34.0 + - - -
132F ASN* 3.4 14.7 - - + +
134F PRO* 3.9 13.1 - - + +
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Residues in contact with TRP 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ALA* 3.2 35.9 - - + -
186E PRO* 4.8 2.9 - - + -
203E LEU* 4.1 17.8 + - + +
206E GLN* 3.2 44.9 - - + -
207E ALA* 3.7 26.8 - - + +
210E ALA* 3.6 21.0 - - + +
214E GLU* 4.3 7.4 - - - +
232E LEU* 2.9 39.7 + - + +
233E THR* 3.6 22.4 - - + +
235E GLU* 1.3 85.0 - - + +
237E TYR* 1.3 75.2 + - + +
238E GLN* 3.1 9.0 + - - +
268E TYR* 4.0 2.4 + - - -
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Residues in contact with TYR 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E PRO* 4.2 3.5 - - - +
206E GLN* 3.8 14.6 + - - -
209E LEU* 4.4 2.0 - - + +
210E ALA* 3.8 15.0 - - + -
225E ILE* 3.5 38.6 - - + +
227E ASN* 2.9 44.2 + - + -
233E THR* 2.9 32.4 + - + +
234E ARG 3.7 4.5 - - - -
236E TRP* 1.3 81.2 - + + +
238E GLN* 1.3 59.9 + - - +
239E ARG 3.4 3.3 + - - -
240E ALA* 3.7 6.0 + - - +
242E LEU* 3.2 25.5 - - + +
264E LEU* 4.4 7.9 - - + -
266E ALA* 3.6 26.9 - - + -
268E TYR* 3.6 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