Contacts of the strand formed by residues 176 - 183 (chain C) in PDB entry 2PI8
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 ASN 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C TYR* 4.1 0.9 - - - -
167C ILE 2.8 37.2 + - - +
169C PHE* 4.3 15.5 - - + -
174C PRO 3.4 4.8 + - - +
175C LEU* 1.3 70.3 - - - +
177C PHE* 1.3 61.0 + - - +
178C PHE* 3.4 23.9 + - + -
238C PRO* 3.3 19.1 - - - +
239C GLN 3.1 11.3 + - - -
240C SER* 2.9 38.8 + - - +
241C PHE 3.7 4.3 - - - +
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Residues in contact with PHE 177 (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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103C THR* 4.2 2.2 - - + -
164C SER* 3.4 37.9 - - - -
165C GLY 4.0 12.8 - - - -
166C TYR* 3.7 20.2 - + + -
175C LEU 3.6 3.6 + - - -
176C ASN* 1.3 71.8 + - - +
178C PHE* 1.3 62.1 + - - +
179C SER* 3.3 25.0 + - - -
237C LYS 3.4 0.3 - - - +
239C GLN* 2.9 42.5 + - + +
240C SER 3.9 0.6 - - - +
241C PHE 3.8 3.8 - - - +
242C ALA* 3.5 25.4 - - + +
243C PRO 4.0 9.6 - - - -
244C VAL* 3.8 26.5 - - + -
245C LYS* 3.8 26.9 - - + -
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Residues in contact with PHE 178 (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 ILE* 3.8 27.6 - - + -
147C LEU* 3.7 38.6 - - + -
148C ALA* 4.8 3.1 - - + -
159C MSE 5.0 3.6 - - - -
164C SER* 3.2 26.6 - - - -
165C GLY 3.0 16.6 + - - +
167C ILE* 3.6 33.0 - - + -
169C PHE* 4.6 9.6 - + - -
176C ASN* 3.5 38.4 - - + -
177C PHE* 1.3 68.9 - - - +
179C SER* 1.3 63.7 + - - +
236C PHE* 3.4 18.4 - + + -
237C LYS 3.7 4.9 - - - -
238C PRO* 3.9 15.0 - - + -
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Residues in contact with SER 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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164C SER* 4.1 2.2 - - - -
177C PHE* 3.3 26.6 + - - -
178C PHE* 1.3 74.0 - - - +
180C TYR* 1.3 60.1 + - - +
181C ALA 3.1 4.3 + - - -
236C PHE* 3.1 8.4 - - - -
237C LYS 2.9 42.9 + - - -
239C GLN* 3.0 21.2 + - - -
245C LYS 5.6 1.3 - - - -
5G NAG 3.8 11.9 - - - -
6G NAG 3.7 11.6 - - - +
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Residues in contact with TYR 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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163C GLY* 3.2 33.3 + - - +
164C SER* 4.3 1.4 - - - -
179C SER* 1.3 70.0 - - - +
181C ALA* 1.3 61.1 + - - +
182C GLY* 3.9 20.9 - - - -
183C LYS* 3.5 27.4 - - + +
234C VAL* 3.7 29.4 - - + -
235C PHE 4.2 2.2 - - - -
236C PHE* 4.6 0.9 - - - -
3G NAG 4.1 14.1 + - - -
4G NAG 3.6 54.5 + - - +
5G NAG 2.8 42.2 + - - +
6G NAG 3.7 2.0 - - - +
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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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123C MSE 3.6 34.5 - - + +
179C SER 3.1 1.8 + - - -
180C TYR* 1.3 76.0 - - - +
182C GLY* 1.3 58.4 + - - +
235C PHE 2.9 14.2 + - - +
236C PHE 3.6 21.1 - - - +
237C LYS* 3.7 14.4 - - + -
5G NAG 5.4 0.6 + - - -
6G NAG 3.6 22.5 - - + +
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Residues in contact with GLY 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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123C MSE 3.9 13.0 - - - +
180C TYR* 3.6 14.4 - - - -
181C ALA* 1.3 79.3 - - - +
183C LYS* 1.3 61.5 + - - +
234C VAL* 3.4 10.0 - - - +
235C PHE* 2.9 30.7 + - - +
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Residues in contact with LYS 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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123C MSE 4.8 0.6 - - - -
129C ARG* 4.1 14.2 - - - +
180C TYR* 3.5 19.3 - - - +
182C GLY* 1.3 74.3 - - - +
184C ASN* 1.3 88.0 + - - +
186C HIS 2.8 30.7 + - - +
187C ALA* 4.9 1.6 - - - +
188C TYR* 5.9 3.1 - - + +
232C SER* 3.1 17.9 + - - +
233C PHE 3.2 19.5 - - - +
234C VAL* 4.1 9.2 - - + -
235C PHE* 3.7 13.2 - - - -
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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