Contacts of the helix formed by residues 193 - 200 (chain B) 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 GLN 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B HIS 5.0 2.8 + - - -
148B GLN* 3.0 22.2 + - - +
149B PHE* 3.3 14.6 - - - -
168B TYR* 2.9 30.8 + - - +
173B SER* 5.1 1.0 + - - -
174B TRP* 3.2 25.4 - - + +
177B LEU* 5.0 2.6 - - - +
188B MET* 4.8 0.2 - - - -
189B PHE* 2.9 43.7 + - + +
192B THR* 1.3 108.8 + - - +
194B VAL* 1.4 64.5 + - - +
195B PRO* 3.4 2.5 - - - -
196B ALA* 3.3 8.3 + - - +
197B LEU* 3.2 22.9 + - - +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B PHE* 3.3 21.0 + - + +
190B GLU* 3.4 47.1 - - - +
193B GLN* 1.4 75.0 - - - +
195B PRO* 1.4 66.1 - - + +
197B LEU* 3.0 9.1 + - - +
198B LEU* 3.0 36.5 + - + +
204B ARG* 3.7 33.7 - - - +
207B ILE* 4.6 8.1 - - + -
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Residues in contact with PRO 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B GLU 3.6 13.9 - - - +
191B GLU* 3.8 18.8 - - - +
192B THR 4.4 1.8 - - - +
193B GLN 3.6 5.4 - - - +
194B VAL* 1.4 87.2 - - + +
196B ALA* 1.4 56.5 + - - +
198B LEU* 3.3 12.7 + - + +
199B GLU* 3.0 31.9 + - - +
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PHE* 3.4 50.9 - - + -
152B ILE* 5.3 1.1 - - - +
153B LYS* 4.1 11.9 - - + +
192B THR 5.2 1.3 + - - +
193B GLN 3.3 3.3 + - - +
195B PRO* 1.4 76.8 - - - +
197B LEU* 1.4 57.2 + - - +
199B GLU* 3.4 13.9 + - - +
200B ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PHE* 5.5 2.2 - - + -
152B ILE* 3.8 39.0 - - + -
166B LEU* 4.9 2.2 - - + -
168B TYR* 4.0 11.9 - - + +
189B PHE* 4.1 19.3 - - + -
193B GLN 3.2 14.3 + - - +
194B VAL* 3.0 9.2 + - - +
196B ALA* 1.4 74.8 - - - +
198B LEU* 1.3 62.4 + - - +
200B ALA* 3.5 11.6 + - - +
202B PHE* 3.3 28.1 + - + +
207B ILE* 3.8 27.8 - - + -
233B VAL* 3.7 31.2 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B VAL* 3.0 31.9 + - + +
195B PRO* 3.6 10.8 - - + +
197B LEU* 1.3 72.6 - - - +
199B GLU* 1.3 65.1 + - - +
201B GLY* 3.1 15.2 + - - -
202B PHE 3.4 19.8 - - - +
203B ARG* 4.4 0.4 - - - -
204B ARG* 3.5 36.6 - - + +
207B ILE* 4.0 7.9 - - + -
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Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LYS* 4.2 29.9 + - + +
195B PRO* 3.0 16.3 + - - +
196B ALA* 3.4 15.7 - - - +
198B LEU* 1.3 74.4 - - - +
200B ALA* 1.4 61.8 + - - +
201B GLY* 3.3 1.9 + - - -
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ILE* 3.8 28.5 - - + +
153B LYS* 3.9 28.1 - - + +
157B PHE* 3.4 24.8 - - - +
196B ALA 3.0 16.5 + - - +
197B LEU 3.5 9.6 - - - +
198B LEU 3.2 0.2 - - - -
199B GLU* 1.4 74.9 - - - +
201B GLY* 1.3 56.4 + - - +
202B PHE* 3.7 4.9 - - + -
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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