Contacts of the strand formed by residues 161 - 166 (chain C) in PDB entry 4JZJ
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 ARG 161 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C TRP* 2.8 22.4 + - + -
135C GLN* 2.8 31.9 + - - +
136C TYR* 3.1 26.8 + - - +
137C ASP* 3.0 26.5 + - - -
149C GLU* 4.4 3.2 + - - -
153C TYR* 3.2 61.1 + - + +
154C LYS 3.4 6.1 - - - +
155C THR* 4.1 11.2 - - + -
160C THR* 1.3 71.5 - - - +
162C ILE* 1.3 62.0 + - - +
186C ARG* 3.9 12.7 - - - +
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Residues in contact with ILE 162 (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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123C SER* 3.4 5.0 - - - -
124C TRP* 2.8 50.4 + - - +
125C ALA* 5.2 0.4 - - - -
126C VAL* 4.1 21.8 - - + +
154C LYS* 2.9 28.5 + - + +
155C THR 3.9 4.7 - - - +
156C ASP* 3.6 31.0 - - + +
160C THR 3.3 13.7 - - - +
161C ARG* 1.3 75.5 - - - +
163C GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C CYS 3.2 14.8 - - - -
123C SER* 4.1 0.9 - - - -
124C TRP* 3.4 11.6 - - - -
153C TYR* 3.3 6.4 - - - +
154C LYS* 2.8 46.3 + - - +
162C ILE* 1.3 80.5 - - - +
164C CYS* 1.3 59.2 + - - +
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Residues in contact with CYS 164 (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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120C LEU 4.0 0.3 - - - +
121C SER* 3.2 5.7 - - - -
122C CYS 2.9 31.0 + - - +
124C TRP* 3.9 3.6 - - + -
138C LEU* 3.5 15.9 - - + +
150C CYS* 2.0 47.6 - - - -
152C HIS 3.4 29.2 - - - -
153C TYR* 3.4 21.1 - - + -
154C LYS* 5.4 0.2 - - - -
163C GLY* 1.3 72.4 - - - +
165C ARG* 1.3 61.2 + - - +
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Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C HIS* 4.1 13.5 - - - +
119C PHE* 3.9 18.6 - - + -
120C LEU 3.5 3.1 - - - +
121C SER* 3.2 20.6 - - - +
150C CYS* 3.3 14.4 - - - -
151C LEU 4.7 0.7 + - - -
152C HIS* 3.3 51.5 + - - +
164C CYS* 1.3 78.2 - - - +
166C PHE* 1.3 69.2 + - - +
167C ASP* 3.2 29.1 + - - -
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Residues in contact with PHE 166 (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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118C ASP 4.0 0.2 - - - +
119C PHE* 3.5 6.6 - - - -
120C LEU* 2.7 65.4 + - + +
138C LEU* 3.4 27.8 - - + -
139C TYR 4.1 1.1 - - - -
140C LEU* 3.6 34.8 - - + -
148C TYR* 3.7 9.9 - - + -
149C GLU 4.0 2.7 - - - -
150C CYS* 3.5 35.9 - - + -
165C ARG* 1.3 75.7 - - - +
167C ASP* 1.3 64.2 + - - +
169C ILE* 4.5 4.4 + - + -
172C LEU* 3.6 32.3 - - + -
181C ILE* 4.6 3.4 - - + -
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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