Contacts of the strand formed by residues 189 - 194 (chain F) in PDB entry 1I3O
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 LEU 189 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166F ARG* 3.1 14.4 - - - +
184F LEU* 3.2 22.4 + - + +
185F ALA* 3.3 12.8 + - - -
187F ALA* 3.2 19.0 - - + +
188F GLY* 1.3 79.4 - - - +
190F TYR* 1.3 60.1 + - - +
198F VAL* 4.0 19.5 - - + +
199F GLN* 3.1 5.2 - - - +
200F CYS* 3.7 32.1 - - + +
205F GLY 5.1 0.9 - - - +
207F LEU* 4.0 15.3 - - + -
210F TRP* 3.8 29.2 - - + -
216F ALA 4.6 4.0 - - - +
220F HIS* 3.8 18.2 - - + +
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Residues in contact with TYR 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F ASN* 3.4 21.9 + - - +
160F MET* 3.5 45.8 - - + -
166F ARG* 3.6 20.2 - - + +
169F SER* 4.7 3.4 - - - +
188F GLY 4.6 0.7 - - - -
189F LEU* 1.3 74.1 - - - +
191F TYR* 1.3 74.5 + - - +
192F THR* 5.2 4.0 - - + -
198F VAL* 4.0 2.7 - - - -
199F GLN* 2.6 87.2 + - + -
200F CYS 4.0 2.2 + - - -
201F PHE* 3.8 22.4 - - + -
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Residues in contact with TYR 191 (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 ARG 5.6 0.4 + - - -
169F SER* 3.1 43.8 + - - +
179F LEU* 5.7 9.2 - - + -
190F TYR* 1.3 87.4 - - - +
192F THR* 1.3 64.7 + - - +
193F GLY* 3.0 45.1 + - - -
194F ILE 3.2 11.2 + - - -
195F GLY 2.5 32.3 + - - -
196F ASP* 4.1 3.4 - - - -
197F GLN 3.5 11.7 - - - -
198F VAL* 3.9 14.8 - - + +
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Residues in contact with THR 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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190F TYR* 4.1 4.6 + - + -
191F TYR* 1.3 73.5 - - - +
193F GLY* 1.3 58.9 + - - +
194F ILE* 3.3 19.1 + - + +
197F GLN* 2.7 36.8 + - - +
198F VAL 3.7 11.3 - - - -
199F GLN* 3.9 13.2 + - - +
206F LYS* 4.0 19.4 + - - +
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Residues in contact with GLY 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 TYR* 3.0 36.4 + - - -
192F THR* 1.3 78.6 - - - +
194F ILE* 1.3 60.4 + - - +
195F GLY 4.3 0.3 + - - -
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Residues in contact with ILE 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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191F TYR* 3.3 1.3 - - - -
192F THR* 3.3 20.2 - - + +
193F GLY* 1.3 81.9 - - - +
195F GLY* 1.3 75.9 + - - +
197F GLN* 2.8 37.0 + - + +
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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