Contacts of the helix formed by residues 190 - 194 (chain B) in PDB entry 2OT7
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 GLU 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B HIS* 3.2 4.3 + - - -
189B THR* 1.3 76.5 - - - +
191B ASP* 1.3 67.7 + - - +
193B ASP* 2.9 13.9 + - - +
194B LEU 3.4 30.4 + - - +
196B SER* 3.4 14.4 - - - +
239B ARG* 3.0 12.7 + - - -
241B LYS* 5.6 2.7 + - - +
270B THR* 3.8 11.0 - - - +
271B PHE 5.9 0.2 - - - +
273B TYR 5.9 0.2 - - - +
276B HIS* 3.0 8.5 + - + -
290B ASN* 2.8 32.4 + - - +
501B NI 2.1 42.3 - - - +
9D MLZ 3.5 15.6 + - - -
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Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 4.1 9.7 - - + +
189B THR 3.8 0.6 + - - -
190B GLU* 1.3 74.5 + - - +
192B MET* 1.3 68.5 + - - +
193B ASP 3.0 1.2 + - - -
194B LEU* 3.0 21.2 + - + +
239B ARG* 4.2 12.2 - - - +
241B LYS* 4.6 13.5 + - - +
290B ASN* 4.9 4.7 + - - +
312B MET* 6.0 0.2 - - - +
313B VAL* 3.8 47.9 + - + +
9D MLZ 4.1 22.7 - - - +
10D SER 5.1 0.7 + - - -
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Residues in contact with MET 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLU 3.3 0.4 + - - -
191B ASP* 1.3 70.7 - - - +
193B ASP* 1.3 60.5 + - - +
194B LEU* 4.1 4.7 - - + -
239B ARG* 4.3 3.8 - - - +
296B TRP* 2.8 34.8 + - + -
300B GLY* 3.3 35.8 - - - +
303B ALA* 4.0 12.1 - - + -
305B LEU* 3.8 35.6 - - + +
313B VAL* 4.2 9.6 + - + +
314B LYS* 4.0 2.5 - - + -
315B ILE* 3.5 55.9 - - + +
317B MET* 4.0 14.6 - - + -
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 2.7 28.4 + - - -
190B GLU 2.9 13.7 + - - +
192B MET* 1.3 78.3 - - - +
194B LEU* 1.3 65.4 + - - +
239B ARG* 2.9 23.4 + - - +
272B PRO* 3.2 20.4 - - - +
273B TYR* 3.6 36.9 - - - +
296B TRP* 3.3 5.4 - - - -
299B TYR* 4.3 17.4 - - + +
303B ALA* 3.8 15.1 - - - -
304B VAL 4.6 0.7 + - - -
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Residues in contact with LEU 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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157B LEU* 3.7 22.0 - - + -
171B VAL* 4.0 26.7 - - + -
190B GLU* 3.4 17.3 + - + +
191B ASP* 3.0 21.1 + - + +
192B MET* 3.1 4.4 - - + -
193B ASP* 1.3 80.9 - - - +
195B TYR* 1.3 68.6 + - - +
271B PHE 4.2 2.6 - - - +
272B PRO* 3.9 9.7 - - - +
273B TYR 4.9 0.5 + - - -
290B ASN* 4.1 11.2 - - + +
291B PHE 3.2 19.7 - - - +
292B ALA* 3.8 3.4 - - + -
296B TRP* 3.5 35.9 - - + +
315B ILE* 4.1 16.6 - - + -
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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
------------------------------------------------------------
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