Contacts of the strand formed by residues 166 - 169 (chain C) in PDB entry 1SZU
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 VAL 166 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ASP* 4.7 7.9 - - - +
1023A EDO 3.7 16.8 - - - -
131C THR* 3.3 7.0 - - - +
133C ALA* 4.6 2.7 - - + -
144C TYR* 3.7 32.5 - - + +
147C ALA* 3.6 45.1 - - + +
148C LEU* 3.6 24.5 - - + -
163C PRO 4.1 1.8 - - - +
164C GLY 3.3 4.9 - - - +
165C HIS* 1.3 80.9 - - - +
167C TYR* 1.3 66.0 + - - +
168C ARG* 4.3 6.9 + - - +
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Residues in contact with TYR 167 (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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161A LEU* 3.2 24.8 - - + +
162A MET 4.8 1.9 + - - -
166A VAL 5.8 0.9 - - - -
194A ASP* 5.7 0.2 - - - -
1023A EDO 3.6 21.9 + - - -
130C GLY* 4.8 0.2 - - - -
131C THR 2.8 21.9 + - - +
132C ILE* 3.3 6.8 - - + +
133C ALA* 3.0 25.8 + - - +
165C HIS* 3.4 41.2 - - - -
166C VAL* 1.3 75.5 - - - +
168C ARG* 1.3 61.6 + - - +
190C ILE* 3.6 26.9 - - + -
194C ASP* 3.8 34.9 + - + -
195C ALA* 3.6 22.4 - - + -
200C ILE* 4.0 10.5 - - + -
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Residues in contact with ARG 168 (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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189A ARG* 5.4 8.1 - - + -
193A ASN* 3.9 11.2 + - + +
194A ASP* 3.1 37.9 + - - +
133C ALA* 3.3 15.7 - - - +
134C PHE 3.0 19.2 + - - -
135C SER* 3.4 27.8 - - - +
147C ALA 2.7 29.9 + - - -
148C LEU* 2.7 22.0 + - - +
149C THR 3.3 7.7 + - - -
150C GLY* 3.6 9.1 - - - -
166C VAL* 4.3 4.8 + - - +
167C TYR* 1.3 75.1 - - - +
169C ALA* 1.3 63.9 + - - +
170C LEU* 5.6 2.5 - - + +
186C SER* 4.5 2.4 - - - +
190C ILE* 3.4 15.5 - - - +
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Residues in contact with ALA 169 (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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132C ILE* 3.9 11.2 - - + -
133C ALA 2.9 11.4 + - - +
134C PHE* 3.4 22.8 - - + -
135C SER* 2.9 24.4 + - - -
167C TYR 4.0 0.2 + - - -
168C ARG* 1.3 79.2 - - - +
170C LEU* 1.3 66.1 + - - +
186C SER* 3.6 15.0 - - - +
187C ILE* 3.9 16.2 - - + -
190C ILE* 4.2 4.3 - - + -
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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