Contacts of the strand formed by residues 178 - 184 (chain C) in PDB entry 2PZX
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 ILE 178 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C ILE* 3.4 23.1 - - + -
86C MET* 4.1 14.6 - - - -
90C GLU* 4.2 25.8 - - + +
93C GLU* 4.1 8.4 + - + +
94C LEU* 3.8 20.7 - - + -
95C ASP* 3.4 23.6 + - - +
167C HIS* 4.1 14.1 - - + -
168C LEU 3.5 22.2 - - - +
169C THR* 3.7 18.4 - - + +
176C THR* 5.8 0.9 - - - +
177C SER* 1.3 77.8 - - - +
179C ARG* 1.3 65.1 + - - +
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Residues in contact with ARG 179 (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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95C ASP* 4.5 24.0 - - + -
97C PHE 5.8 2.2 - - - +
132C LEU 4.8 1.0 + - - -
133C ASP* 3.8 5.1 + - - -
134C ASN* 3.2 32.5 + - - +
135C ARG* 3.8 22.1 - - - +
167C HIS* 4.8 0.2 - - - -
168C LEU 3.3 22.7 + - - +
170C PHE* 3.0 57.6 - - + -
177C SER* 4.1 3.5 + - - +
178C ILE* 1.3 78.6 - - - +
180C ILE* 1.3 78.2 + - - +
181C ALA* 3.2 5.9 + - - +
182C PRO* 5.9 0.2 - - - +
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Residues in contact with ILE 180 (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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69C PHE* 4.3 9.6 - - + -
95C ASP 4.1 10.0 + - - +
96C PRO 4.3 5.8 - - - +
97C PHE 5.8 1.5 + - - +
98C LEU* 3.4 38.2 - - + +
112C PHE* 3.4 39.5 - - + -
134C ASN* 5.5 0.9 + - - -
141C TYR* 4.6 3.1 + - - -
165C LEU* 3.5 25.6 - - + -
166C GLN* 3.4 15.3 - - - +
167C HIS* 3.5 25.6 - - + +
179C ARG* 1.3 84.6 + - - +
181C ALA* 1.3 61.8 + - - +
182C PRO* 4.4 2.3 - - - +
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Residues in contact with ALA 181 (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 LEU 3.4 14.4 - - - +
165C LEU* 4.1 3.1 - - - -
166C GLN 3.0 20.8 + - - +
168C LEU* 4.3 12.8 - - + -
170C PHE* 3.4 35.4 - - + -
179C ARG* 3.2 3.7 + - - +
180C ILE* 1.3 74.1 - - - +
182C PRO* 1.3 71.4 - - + +
183C HIS* 3.1 13.0 - - - -
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Residues in contact with PRO 182 (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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131C TYR* 3.7 0.2 - - - +
132C LEU* 3.0 51.4 + - + +
134C ASN* 5.2 2.2 - - - +
141C TYR* 3.3 39.9 - - + +
149C PHE* 3.4 20.6 - - + -
163C TYR* 5.3 1.1 - - + -
165C LEU* 3.2 24.9 - - + -
179C ARG* 5.9 0.4 - - - +
180C ILE 4.4 0.7 - - - +
181C ALA* 1.3 87.0 - - + +
183C HIS* 1.3 69.5 + - - +
184C ASN* 4.3 1.1 - - - +
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Residues in contact with HIS 183 (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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70C CYS* 4.6 2.2 - - - -
77C MET* 3.1 41.7 - - + +
80C GLY* 4.6 4.5 - - - -
125C PRO* 4.7 3.8 - - - +
129C MET* 4.0 32.5 + - + +
130C PHE 3.7 5.2 - - - +
131C TYR* 3.4 15.8 + + + +
162C GLU 4.3 0.2 - - - +
163C TYR* 3.6 5.2 - - - -
164C CYS* 3.1 33.7 + - - +
166C GLN* 4.6 6.8 - - + +
168C LEU* 3.1 30.0 - - + +
181C ALA 3.1 18.5 + - - -
182C PRO* 1.3 91.3 - - - +
184C ASN* 1.3 66.4 + - - +
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Residues in contact with ASN 184 (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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126C CYS* 4.5 0.9 - - - -
129C MET* 3.7 4.5 - - - +
130C PHE* 3.1 55.2 + - + -
132C LEU* 4.1 7.8 - - - +
149C PHE* 3.6 16.5 - - - -
151C ARG* 2.8 44.7 - - - +
158C LEU* 3.1 27.5 - - + +
162C GLU 4.4 3.4 - - - -
163C TYR* 4.0 3.1 - - - +
182C PRO 4.3 0.2 - - - -
183C HIS* 1.3 84.2 + - - +
185C CYS* 1.3 63.4 + - - +
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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