Contacts of the strand formed by residues 189 - 192 (chain C) in PDB entry 1SOZ
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 PHE 189 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C THR* 5.7 3.6 - - - -
126C ASP* 6.4 1.6 - - + -
176C THR* 3.9 1.9 - - - -
177C GLY 3.4 10.7 + - - -
178C ARG* 2.7 33.3 + - - +
179C ILE 3.3 29.6 - - - -
180C GLY* 4.3 3.1 - - - -
181C LEU* 5.2 9.4 - - + -
182C ASN* 5.5 7.6 - - - -
187C GLN* 4.6 13.7 - - + -
188C ASN* 1.3 78.3 - - - +
190C LEU* 1.3 67.9 + - - +
191C GLN 3.9 1.0 + - - -
217C THR* 3.9 22.2 - - + -
218C LEU 5.5 0.2 - - - -
234C PHE* 3.8 26.2 - - + -
235C ALA 3.3 24.7 - - - +
236C ILE* 3.8 22.4 - - + -
237C PRO* 4.5 2.0 - - - -
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Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C PRO* 4.9 9.2 - - + -
173C ILE* 4.1 28.7 - - + -
175C ALA 3.6 3.6 - - - +
176C THR* 3.8 30.3 - - + -
188C ASN* 6.0 0.4 - - - +
189C PHE* 1.3 76.1 - - - +
191C GLN* 1.3 62.6 + - - +
192C THR* 5.2 0.4 - - - +
205C LEU* 4.2 16.4 - - + -
213C MET* 3.5 32.1 - - + +
214C GLY* 4.7 2.2 - - - +
234C PHE* 3.2 5.6 - - - -
235C ALA* 2.8 40.0 + - + +
237C PRO* 4.3 18.0 - - + +
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Residues in contact with GLN 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B LEU* 4.3 4.7 - - - +
167B THR* 3.2 38.4 + - - +
173C ILE* 3.6 4.9 - - - +
174C SER* 2.7 29.7 + - - -
175C ALA* 2.9 25.1 + - + +
178C ARG* 2.7 38.0 + - - -
189C PHE 3.9 0.6 + - - -
190C LEU* 1.3 73.1 - - - +
192C THR* 1.3 66.7 + - - +
231C GLY 5.3 1.0 + - - -
232C ILE* 4.2 28.0 - - + +
233C GLY 3.3 12.6 - - - +
234C PHE* 3.8 15.2 - - + -
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Residues in contact with THR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL* 3.4 13.2 - - - +
172C ILE 3.3 14.3 + - - -
173C ILE* 5.0 0.9 - - - -
174C SER* 3.7 5.4 - - - -
190C LEU* 5.2 1.6 - - - +
191C GLN* 1.3 76.9 - - - +
193C ASP* 1.3 63.6 + - - +
194C ALA* 2.9 29.9 + - + +
196C ILE* 5.3 3.8 - - + -
205C LEU* 4.4 22.7 - - + -
216C ASN* 4.7 7.0 - - - +
231C GLY 3.1 4.1 - - - +
232C ILE* 4.0 0.5 - - - -
233C GLY* 3.0 41.7 + - - +
234C PHE* 4.6 4.0 - - - +
235C ALA 5.3 0.2 - - - +
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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