Contacts of the helix formed by residues 184 - 193 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A MET* 3.6 2.5 - - - +
182A TYR* 4.0 2.3 - - - +
183A SER* 1.3 82.0 + - - +
185A ILE* 1.4 57.4 + - - +
186A THR* 2.6 31.8 + - - +
187A ILE* 3.1 28.9 + - + +
188A MET* 3.1 26.2 + - - +
225A PHE* 4.8 0.4 - - - -
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Residues in contact with ILE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TRP* 5.8 3.1 - - + -
178A MET* 3.6 21.0 - - + +
183A SER 4.2 0.2 - - - -
184A ASP* 1.4 70.1 + - - +
186A THR* 1.3 63.7 + - + +
188A MET* 3.5 5.2 + - + +
189A PHE* 3.1 26.9 + - - +
211A VAL* 3.8 27.4 - - + -
223A TYR* 3.4 14.1 - - - +
225A PHE* 3.9 16.5 - - + -
227A GLN* 3.4 45.9 + - - +
228A MET 3.9 0.9 - - - -
229A ILE* 3.7 34.6 - - + +
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Residues in contact with THR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASP* 2.6 21.0 + - - -
185A ILE* 1.3 75.2 - - + +
187A ILE* 1.4 63.0 + - - +
189A PHE* 3.4 3.0 + - - +
190A GLU* 2.9 29.8 + - - +
209A THR* 4.3 9.9 - - - +
211A VAL* 3.8 27.1 - - + -
229A ILE* 4.0 11.2 - - + -
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 3.9 15.0 - - + -
184A ASP* 3.1 32.8 + - + +
186A THR* 1.4 75.0 - - - +
188A MET* 1.3 66.6 + - - +
190A GLU* 3.2 8.6 + - + +
191A GLU* 2.9 46.4 + - + +
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Residues in contact with MET 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TRP* 3.1 46.4 - - + +
177A LEU* 3.3 25.8 - - + -
178A MET* 3.6 28.0 - - + +
182A TYR* 3.6 34.2 - - + -
184A ASP 3.1 6.0 + - - +
185A ILE* 3.6 13.0 - - - +
187A ILE* 1.3 76.0 - - - +
189A PHE* 1.3 60.9 + - - +
192A THR* 2.8 61.1 + - - +
193A GLN* 3.7 1.3 - - - +
229A ILE* 5.8 1.1 - - - -
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TYR* 3.6 24.2 - + - -
174A TRP* 4.3 6.7 - + - -
185A ILE 3.1 15.1 + - - +
186A THR 3.6 7.9 - - - +
187A ILE 3.3 0.2 - - - -
188A MET* 1.3 83.6 - - - +
190A GLU* 1.3 60.7 + - - +
193A GLN* 2.9 41.9 + - + +
194A VAL* 3.2 28.1 + - + -
197A LEU* 3.9 10.3 - - + -
204A ARG* 6.1 0.7 - - - -
207A ILE* 4.1 13.5 - - + -
209A THR* 3.6 23.6 - - + -
229A ILE* 3.9 24.5 - - + -
231A PRO* 3.6 36.3 - - + -
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A THR 2.9 18.1 + - - +
187A ILE* 3.6 11.2 - - + +
189A PHE* 1.3 77.9 - - - +
191A GLU* 1.3 62.7 + - + +
194A VAL* 3.4 33.6 - - - +
195A PRO* 3.6 6.9 - - - +
204A ARG* 2.8 44.1 + - - -
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 2.9 38.3 + - + +
187A ILE* 2.9 30.0 + - + +
190A GLU* 1.3 81.8 - - + +
192A THR* 1.3 58.9 + - - +
193A GLN 3.7 0.2 - - - -
195A PRO* 3.8 14.1 - - - +
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 3.3 21.1 - - - -
177A LEU* 4.5 12.8 - - + -
182A TYR* 3.6 31.2 - - + +
188A MET* 2.8 47.5 + - + +
191A GLU* 1.3 77.4 - - - +
193A GLN* 1.3 68.3 + - - +
195A PRO* 4.4 2.7 - - - +
196A ALA* 5.2 1.6 - - - +
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A HIS 4.9 2.8 + - - -
148A GLN* 3.1 22.9 + - - +
149A PHE* 3.3 14.6 - - - -
168A TYR* 2.8 30.5 + - - +
173A SER* 5.0 2.0 + - - -
174A TRP* 3.2 25.5 - - + +
177A LEU* 5.2 0.2 - - - +
188A MET* 3.7 2.8 - - + +
189A PHE* 2.9 43.9 + - + +
192A THR* 1.3 108.8 + - - +
194A VAL* 1.3 64.7 + - - +
195A PRO* 3.4 2.7 - - - -
196A ALA* 3.3 8.1 + - - +
197A LEU* 3.2 23.2 + - - +
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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