Contacts of the helix formed by residues 191 - 196 (chain F) in PDB entry 6O81
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 SER 191 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170F ARG* 4.7 9.4 - - - +
188F ARG 5.2 2.4 + - - -
190F ASN* 1.3 79.4 + - - +
192F LEU* 1.3 64.2 + - - +
193F THR* 3.4 18.2 - - - -
194F GLN* 3.4 28.1 - - - +
195F PHE* 5.4 1.9 - - - -
212F LEU* 5.3 9.2 - - - +
215F SER* 4.6 10.6 + - - -
216F GLN* 5.3 9.7 + - - +
119J ASP* 4.5 7.6 + - - -
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F VAL* 3.8 5.6 - - + -
168F PRO* 3.4 50.0 - - + +
169F THR 4.1 2.5 - - - +
170F ARG* 3.8 35.6 - - + +
191F SER* 1.3 70.8 - - - +
193F THR* 1.3 58.4 + - - +
194F GLN 3.1 5.4 - - - -
195F PHE* 3.0 31.2 + - + +
196F MET* 3.8 4.7 - - - +
212F LEU* 6.2 0.2 - - - +
262F PHE* 3.7 33.4 - - + -
265F GLN* 3.4 18.4 - - + +
266F CYS* 5.3 5.5 - - - -
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Residues in contact with THR 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F SER* 3.4 8.9 - - - -
192F LEU* 1.3 70.3 - - - +
194F GLN* 1.3 62.0 + - - +
195F PHE 3.1 1.1 + - - -
196F MET* 3.6 41.1 + - + +
198F ILE* 5.3 1.2 - - - +
208F VAL* 3.8 11.9 - - + -
212F LEU* 3.7 25.2 - - + +
262F PHE* 4.9 2.0 - - + -
115J HIS* 3.6 19.1 - - - +
119J ASP* 2.8 36.5 + - - +
122J ARG* 4.5 9.2 - - - +
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Residues in contact with GLN 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F GLN 4.8 2.0 + - - -
190F ASN* 3.7 16.3 - - - +
191F SER* 3.4 38.5 - - - +
192F LEU 3.1 0.6 + - - -
193F THR* 1.3 78.7 + - - +
195F PHE* 1.3 82.9 + - + +
196F MET 3.5 1.8 + - - +
115J HIS* 3.4 37.9 + - + +
119J ASP* 5.6 0.2 - - - +
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Residues in contact with PHE 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F GLN 4.5 4.9 - - - +
168F PRO* 4.0 29.9 - - + +
191F SER 5.4 2.2 - - - -
192F LEU* 3.0 13.2 + - + +
194F GLN* 1.3 102.3 - - + +
196F MET* 1.3 65.0 + - - +
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Residues in contact with MET 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F GLN 5.6 2.0 - - - +
167F VAL* 5.3 6.5 - - + -
168F PRO* 5.2 4.3 - - + -
192F LEU* 3.8 14.6 - - + +
193F THR* 3.6 36.3 + - + +
194F GLN 3.5 2.8 - - - +
195F PHE* 1.3 83.9 - - - +
197F SER* 1.3 65.5 + - - +
198F ILE* 4.4 3.6 - - - +
200F SER* 4.0 15.7 - - - +
202F VAL* 5.0 8.3 - - + -
203F ILE* 3.8 26.2 - - + -
208F VAL* 3.9 19.3 - - + -
262F PHE* 3.8 24.2 - - - -
46J VAL* 3.5 14.5 - - - +
115J HIS* 5.4 0.7 - - - +
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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