Contacts of the strand formed by residues 188 - 193 (chain C) in PDB entry 4S10
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 CYS 188 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C VAL* 2.7 45.7 + - + +
187C ASP* 1.3 74.5 - - - +
189C PHE* 1.3 68.6 + - - +
200C TRP 3.2 3.1 - - - +
201C CYS* 2.1 44.4 - - - -
205C SER* 2.9 23.5 + - - -
209C GLU* 4.1 1.7 + - - +
210C ARG* 3.8 19.7 - - - -
213C ALA* 3.9 17.5 - - + -
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Residues in contact with PHE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LEU* 3.8 15.9 - - + -
163C PHE 3.3 6.5 - - - +
164C GLN* 3.5 38.6 - - + -
176C VAL* 4.8 3.6 - - + -
182C SER 3.5 27.8 - - - -
183C PHE* 3.5 31.4 - + + -
184C ASN* 3.6 38.8 - - - -
187C ASP* 4.0 16.2 - - + -
188C CYS* 1.3 77.9 - - - +
190C ILE* 1.3 67.2 + - - +
191C LEU 4.0 0.7 - - - -
198C HIS 3.4 1.6 - - - +
200C TRP* 2.6 54.5 + + - +
213C ALA* 5.9 0.2 - - - +
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C LEU* 3.4 6.5 - - - -
163C PHE* 2.9 43.9 + - + +
165C VAL* 4.0 8.1 - - + -
189C PHE* 1.3 80.5 - - - +
191C LEU* 1.3 61.7 + - - +
192C ASP 3.5 1.7 + - - -
197C ILE* 4.0 24.7 - - + -
198C HIS 3.4 2.2 - - - +
199C GLN* 4.3 8.1 - - + -
213C ALA* 3.0 39.3 - - + +
216C VAL* 3.4 25.4 - - + -
217C SER* 3.9 8.5 - - - +
220C ILE* 4.1 20.0 - - + -
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Residues in contact with LEU 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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160C GLN* 5.2 0.2 - - + -
161C ARG 3.4 15.3 - - - +
162C LEU* 3.9 14.5 - - + +
178C VAL* 3.7 27.1 - - + -
183C PHE* 5.3 5.4 - - + -
189C PHE 4.0 0.8 - - - -
190C ILE* 1.3 70.0 - - - +
192C ASP* 1.3 60.2 + - - +
193C LEU* 3.4 40.3 + - + +
197C ILE* 3.7 0.3 - - - -
198C HIS* 2.9 44.5 + - + +
200C TRP* 6.4 0.7 - - + -
243C MET* 4.0 24.5 - - + -
246C VAL* 4.4 9.0 - - + -
247C LEU* 4.2 18.4 - - + -
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Residues in contact with ASP 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C VAL* 3.5 6.5 - - - +
160C GLN* 3.4 5.9 - - - -
161C ARG* 2.8 64.5 + - + +
163C PHE* 4.4 2.5 - - + -
190C ILE 3.5 2.0 + - - -
191C LEU* 1.3 70.4 - - - +
193C LEU* 1.3 67.1 + - - +
194C GLY 3.0 6.9 + - - -
196C ASN 4.6 0.7 - - - -
197C ILE* 4.6 6.0 - - - +
220C ILE* 4.0 20.6 - - + +
225C ARG* 2.5 47.3 + - - -
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Residues in contact with LEU 193 (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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101A HIS* 4.4 13.1 - - + -
159C VAL* 4.0 6.5 - - - -
160C GLN* 3.8 22.2 - - + -
191C LEU* 3.4 35.2 + - + +
192C ASP* 1.3 84.2 - - - +
194C GLY* 1.3 58.2 + - - +
195C ASN* 3.0 14.7 + - - +
196C ASN* 3.0 27.5 + - + +
198C HIS* 3.7 24.5 - - + +
242C ALA* 4.5 8.1 - - + +
246C VAL* 4.2 21.5 - - + -
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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