Contacts of the helix formed by residues 184 - 193 (chain C) in PDB entry 3ORH
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 ASP 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178C MET* 3.6 2.9 - - - +
182C TYR* 4.0 2.5 - - - +
183C SER* 1.3 83.3 + - - +
185C ILE* 1.4 57.2 + - - +
186C THR* 2.6 29.7 + - - +
187C ILE* 3.1 29.0 + - + +
188C MET* 3.1 26.0 + - - +
225C PHE* 4.8 0.2 - - - -
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Residues in contact with ILE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TRP* 5.8 1.6 - - + -
178C MET* 3.6 16.9 - - + +
183C SER 4.3 0.4 + - - -
184C ASP* 1.4 69.5 + - - +
186C THR* 1.4 63.4 + - + +
188C MET* 3.5 12.9 + - + +
189C PHE* 3.1 27.0 + - - +
211C VAL* 3.8 26.9 - - + -
223C TYR* 3.4 13.5 - - - +
225C PHE* 3.9 16.3 - - + -
227C GLN* 3.4 45.9 + - - +
228C MET 3.9 1.1 - - - -
229C ILE* 3.7 35.3 - - + +
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Residues in contact with THR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ASP* 2.6 21.0 + - - +
185C ILE* 1.4 74.3 - - + +
187C ILE* 1.4 62.3 + - - +
189C PHE* 3.4 3.3 + - - +
190C GLU* 2.9 30.9 + - - +
209C THR* 4.3 9.9 - - - +
211C VAL* 3.8 27.4 - - + -
229C ILE* 4.0 11.9 - - + -
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Residues in contact with ILE 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C TYR* 3.9 15.5 - - + -
184C ASP* 3.1 37.4 + - + +
186C THR* 1.4 75.8 - - - +
188C MET* 1.4 58.5 + - - +
190C GLU* 3.2 9.2 + - + +
191C GLU* 2.9 52.5 + - + +
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Residues in contact with MET 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C TRP* 3.8 46.7 - - + -
177C LEU* 3.9 15.5 - - + -
178C MET* 3.6 25.4 - - + -
182C TYR* 3.6 32.4 - - + -
184C ASP 3.1 6.2 + - - +
185C ILE* 3.6 33.7 - - + +
187C ILE* 1.4 73.8 - - - +
189C PHE* 1.3 60.9 + - + +
192C THR* 2.7 51.6 + - - +
193C GLN* 4.6 0.7 - - - -
229C ILE* 4.2 7.9 - - + -
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Residues in contact with PHE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C TYR* 3.6 24.9 - + - -
174C TRP* 4.3 5.6 - + - -
185C ILE 3.1 14.1 + - - +
186C THR 3.6 8.1 - - - +
187C ILE 3.2 0.2 - - - -
188C MET* 1.3 83.7 - - + +
190C GLU* 1.3 60.8 + - - +
193C GLN* 2.9 41.1 + - + +
194C VAL* 3.2 27.9 + - + -
197C LEU* 3.8 16.2 - - + -
204C ARG* 6.1 1.1 - - - -
207C ILE* 4.1 7.9 - - + -
209C THR* 3.6 24.7 - - + -
229C ILE* 3.9 25.4 - - + -
231C PRO* 3.6 35.2 - - + -
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Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C THR 2.9 17.9 + - - +
187C ILE* 3.2 11.9 + - + +
189C PHE* 1.3 80.4 - - - +
191C GLU* 1.3 62.5 + - + +
194C VAL* 3.4 32.9 - - - +
195C PRO* 3.6 7.1 - - - +
204C ARG* 2.8 44.4 + - - -
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C TYR* 2.9 38.0 + - + +
187C ILE* 2.9 29.2 + - + +
190C GLU* 1.3 81.8 - - + +
192C THR* 1.3 58.5 + - - +
195C PRO* 3.8 14.9 - - - +
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Residues in contact with THR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C PHE* 3.3 20.8 - - - -
177C LEU* 4.1 19.1 - - + +
182C TYR* 3.6 30.7 - - + +
188C MET* 2.7 30.8 + - - +
191C GLU* 1.3 77.6 - - - +
193C GLN* 1.4 79.0 + - - +
195C PRO* 4.4 2.9 - - - +
196C ALA* 5.2 1.6 + - - +
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Residues in contact with GLN 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C HIS 5.1 1.4 + - - -
148C GLN* 3.0 22.9 + - - +
149C PHE* 3.4 15.0 - - - -
168C TYR* 2.8 30.3 + - - +
173C SER* 5.0 2.0 + - - -
174C TRP* 3.2 26.1 - - + +
177C LEU* 4.9 2.4 - - - +
188C MET* 4.6 0.4 - - - -
189C PHE* 2.9 43.9 + - + +
192C THR* 1.4 107.7 + - - +
194C VAL* 1.3 65.2 + - - +
195C PRO* 3.4 2.7 - - - -
196C ALA* 3.3 8.7 + - - +
197C LEU* 3.2 23.1 + - - +
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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