Contacts of the helix formed by residues 193 - 200 (chain B) in PDB entry 1OHV
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 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A CYS* 4.5 16.8 - - + -
141A GLU* 3.9 32.1 - - + -
142A ASN* 4.9 4.9 - - - +
145A LYS* 5.3 1.1 - - - +
193A THR* 5.0 1.6 - - - +
800A FES 4.5 6.1 - - - -
137B SER* 3.8 17.0 + - - +
141B GLU* 2.4 35.3 + - + +
191B GLY 3.8 0.2 - - - -
192B ARG* 1.3 79.7 - - - +
194B MET* 1.3 55.0 + - - +
195B GLY 3.1 1.4 + - - -
196B CYS* 3.2 9.5 + - - -
197B LEU* 2.7 30.1 + - - +
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Residues in contact with MET 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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141A GLU* 3.0 15.8 + - - +
144A PHE* 3.4 28.5 - - + -
145A LYS* 4.4 11.2 - - + -
148A PHE* 3.8 25.1 - - - -
195A GLY* 3.3 31.6 - - - +
213A PHE* 4.6 11.3 - - + -
215A TRP* 3.6 20.6 - - + -
192B ARG 4.6 0.2 - - - -
193B THR* 1.3 71.4 - - - +
195B GLY* 1.3 62.6 + - - +
197B LEU* 3.9 8.4 - - - +
198B ALA* 3.5 16.5 + - - +
210B ILE* 4.4 17.0 - - + -
211B PRO* 4.8 13.2 - - - +
212B SER* 5.5 0.9 - - - -
213B PHE* 4.3 8.5 - - - -
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Residues in contact with GLY 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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194A MET* 3.2 31.3 - - - +
195A GLY 4.8 0.2 - - - +
141B GLU* 2.8 14.4 + - - -
144B PHE* 3.7 14.5 - - - -
194B MET* 1.3 74.4 - - - +
196B CYS* 1.3 64.4 + - - +
197B LEU 3.1 0.7 - - - -
198B ALA* 3.1 18.0 + - - +
199B THR 3.7 1.6 + - - -
213B PHE* 4.6 4.7 - - - -
215B TRP* 4.1 3.3 - - - -
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Residues in contact with CYS 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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137B SER* 3.2 33.2 - - - -
140B ASN* 3.7 11.4 - - - -
141B GLU* 3.0 12.0 + - - -
144B PHE* 3.8 4.4 - - - -
190B HIS* 3.3 28.0 - - + +
191B GLY 3.4 14.8 - - - +
193B THR* 3.2 16.4 + - - +
195B GLY* 1.3 75.0 - - - +
197B LEU* 1.3 57.7 + - - +
199B THR* 2.6 32.7 + - - -
200B THR* 3.1 8.8 + - - -
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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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145A LYS* 4.3 2.9 - - + -
191B GLY 3.6 6.3 - - - +
192B ARG* 3.9 31.2 - - + +
193B THR 2.7 21.9 + - - +
194B MET* 4.0 6.1 - - - +
195B GLY 3.1 0.4 - - - -
196B CYS* 1.3 72.9 - - - +
198B ALA* 1.3 54.6 + - - +
200B THR* 3.0 19.0 + - + +
206B HIS* 3.5 26.9 - - + +
207B LYS* 2.7 45.1 + - + +
210B ILE* 3.7 39.5 - - + +
211B PRO 5.4 1.6 - - - +
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Residues in contact with ALA 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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172A ASN* 2.8 25.2 + - - +
184B SER* 4.0 1.6 + - - -
194B MET 3.5 5.7 + - - +
195B GLY 3.1 11.9 + - - +
197B LEU* 1.3 78.3 - - - +
199B THR* 1.3 57.2 + - - +
201B HIS* 3.1 11.4 + - - -
207B LYS* 3.7 1.1 - - - +
212B SER* 3.7 23.8 - - - +
213B PHE* 3.9 30.3 - - + +
215B TRP* 4.0 10.9 - - + +
217B ILE* 5.4 0.2 - - - +
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Residues in contact with THR 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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144B PHE* 3.5 27.8 - - + -
182B ILE* 4.1 13.0 - - + +
184B SER* 3.3 20.9 - - - +
188B ALA* 3.6 2.6 - - - +
190B HIS* 3.2 35.6 - - - +
195B GLY 4.1 0.2 - - - +
196B CYS 2.6 20.9 + - - -
198B ALA* 1.3 75.1 - - - +
200B THR* 1.3 58.7 + - - +
201B HIS* 3.1 16.3 - - - -
215B TRP* 3.8 26.2 - - + -
263B ILE* 3.9 2.2 - - + -
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Residues in contact with THR 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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188B ALA 3.5 10.5 - - - +
189B PHE* 3.6 15.7 - - + +
190B HIS 3.0 16.1 + - - -
191B GLY 2.8 24.4 + - - +
196B CYS 3.1 2.8 + - - -
197B LEU* 3.0 21.7 + - + -
199B THR* 1.3 75.9 - - - +
201B HIS* 1.3 78.5 + - - +
202B SER* 3.3 23.6 - - - +
206B HIS* 5.0 1.6 - - + +
207B LYS* 2.8 24.1 + - + -
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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