Contacts of the helix formed by residues 170 - 178 (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 ASN 170 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ASP* 5.6 0.9 - - - -
138C PRO* 4.7 0.5 - - - +
144C TRP 3.1 21.2 + - - +
145C HIS 4.2 0.8 - - - -
147C HIS* 3.3 20.2 + - + +
148C GLN* 2.8 39.6 + - - +
169C CYS* 1.3 76.6 - - - +
171C LEU* 1.3 58.0 + - - +
172C THR* 2.8 27.0 + - - -
173C SER* 3.2 13.4 + - - -
174C TRP* 2.9 42.7 + - + +
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Residues in contact with LEU 171 (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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45C TRP* 4.6 4.0 - - + -
46C GLU* 3.5 38.8 - - + +
49C TYR* 3.7 21.1 - - + -
50C MET* 5.1 0.2 - - + -
135C ASP* 5.8 0.4 + - - -
169C CYS* 4.0 8.4 - - + -
170C ASN* 1.3 72.9 - - - +
172C THR* 1.4 59.7 + - - +
174C TRP* 4.4 13.2 - - + +
175C GLY* 2.8 29.8 + - - -
222C TYR* 3.5 21.4 - - + +
223C TYR* 3.7 17.1 - - + -
228C MET* 3.6 34.3 - - + -
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Residues in contact with THR 172 (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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9C ILE* 4.9 9.6 - - + -
10C PHE* 6.1 0.9 - - + -
137C TYR* 3.6 39.7 - - + +
138C PRO* 3.3 21.0 - - + +
144C TRP* 3.5 23.1 + - - -
170C ASN* 2.8 21.7 + - - -
171C LEU* 1.4 75.3 - - - +
173C SER* 1.4 60.6 + - - +
175C GLY* 4.3 0.5 - - - -
176C GLU* 3.6 13.7 + - - +
222C TYR* 4.4 26.1 - - + +
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Residues in contact with SER 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TRP* 3.7 11.4 - - - -
145C HIS* 2.8 35.8 + - - +
148C GLN* 5.2 0.4 + - - -
170C ASN* 3.2 29.5 + - - -
172C THR* 1.4 82.0 + - - +
174C TRP* 1.4 63.5 + - - +
176C GLU* 3.4 5.5 + - - +
177C LEU* 3.1 38.5 + - - +
193C GLN* 5.0 1.6 + - - -
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Residues in contact with TRP 174 (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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49C TYR* 3.4 25.1 - - - -
148C GLN* 4.3 4.8 - - - +
168C TYR* 3.6 33.7 - + - -
169C CYS* 3.7 17.0 - - - -
170C ASN* 2.9 30.3 + - + +
171C LEU* 4.4 9.2 - - + +
173C SER* 1.4 80.9 - - - +
175C GLY* 1.3 59.0 + - - +
177C LEU* 3.4 6.7 + - + +
178C MET* 3.0 35.8 + - + +
185C ILE* 5.9 0.4 - - + -
188C MET* 3.8 28.0 - - + -
189C PHE* 4.3 5.6 - + - -
193C GLN* 3.2 32.3 + - + +
223C TYR* 4.1 16.6 - - + +
229C ILE* 3.6 22.9 - - + -
231C PRO* 4.3 10.3 - - + -
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Residues in contact with GLY 175 (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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171C LEU 2.8 11.3 + - - -
174C TRP* 1.3 79.3 - - - +
176C GLU* 1.3 59.8 + - - +
178C MET* 3.5 4.5 + - - +
179C LYS* 3.4 29.0 + - - +
222C TYR 3.3 24.5 - - - -
223C TYR* 3.5 17.8 - - - -
224C ALA 5.1 2.2 + - - -
225C PHE 5.8 0.6 + - - -
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Residues in contact with GLU 176 (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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144C TRP* 3.3 28.4 - - + -
145C HIS* 2.9 29.4 + - + -
172C THR 3.6 11.9 + - - +
173C SER 3.4 8.9 + - - +
174C TRP 3.4 0.2 - - - -
175C GLY* 1.3 75.3 - - - +
177C LEU* 1.3 58.9 + - + +
179C LYS* 3.0 34.5 + - + +
180C SER* 3.8 8.5 + - - +
181C LYS* 5.5 0.6 - - - +
222C TYR 4.4 0.8 + - - -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C HIS* 4.0 16.8 - - + +
173C SER* 3.1 38.1 + - - +
174C TRP* 3.4 6.3 + - + +
176C GLU* 1.3 74.7 - - + +
178C MET* 1.3 58.5 + - - +
179C LYS 3.4 0.2 - - - -
181C LYS* 3.5 25.5 + - + -
182C TYR* 2.9 48.6 + - + -
188C MET* 3.9 24.0 - - + -
192C THR* 4.1 28.5 - - + +
193C GLN* 4.9 1.1 - - - +
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Residues in contact with MET 178 (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* 3.0 22.1 + - + +
175C GLY* 4.0 4.5 - - - +
176C GLU 3.2 0.2 - - - -
177C LEU* 1.3 74.4 - - - +
179C LYS* 1.3 61.4 + - - +
182C TYR* 3.1 35.7 - - - +
184C ASP 3.6 9.0 - - - +
185C ILE* 3.6 39.3 - - + +
188C MET* 3.6 33.2 - - + -
223C TYR* 4.8 2.0 - - - +
225C PHE* 3.6 59.4 - - + +
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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