Contacts of the strand formed by residues 173 - 176 (chain G) in PDB entry 1P8J
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 PHE 173 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477F GLU* 3.5 35.2 - - + -
172G SER* 1.3 79.0 - - - +
174G ASP* 1.3 86.9 + - - +
175G VAL* 3.7 14.4 - - + -
178G GLN* 4.2 8.3 - - - -
179G ASP* 3.4 24.9 - - - -
180G PRO* 3.6 31.4 + - + -
182G PRO* 3.9 3.6 - - - +
223G GLY 3.0 6.6 + - - +
224G VAL* 3.1 9.4 - - + +
225G ARG 2.9 23.7 + - - -
238G ARG* 4.2 13.5 - - - -
242G LEU* 3.9 28.5 - - + +
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Residues in contact with ASP 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G PHE* 1.3 74.1 - - - +
175G VAL* 1.3 57.7 + - - +
176G ASN 3.0 5.5 + - - -
177G ASP* 2.8 30.1 + - - +
178G GLN* 2.9 22.0 + - - -
179G ASP* 2.7 27.9 + - + +
180G PRO 4.2 0.4 + - - -
181G ASP 3.0 26.5 - - - +
183G GLN 5.0 0.5 - - - +
225G ARG* 2.9 45.7 + - + +
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Residues in contact with VAL 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453F GLU* 5.1 3.3 - - - +
173G PHE* 3.8 17.7 - - + -
174G ASP* 1.3 72.9 - - - +
176G ASN* 1.3 65.9 + - - +
177G ASP 3.4 0.3 + - - -
178G GLN* 3.5 15.7 + - - +
224G VAL* 3.7 14.8 - - + -
225G ARG 2.9 9.2 + - - +
226G MET* 4.2 3.6 - - + -
235G VAL* 3.8 40.8 - - + +
238G ARG* 4.0 31.4 + - + +
239G SER* 3.6 23.3 - - - +
242G LEU* 5.9 2.0 - - + -
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Residues in contact with ASN 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G ASP* 3.0 8.4 + - - +
175G VAL* 1.3 81.0 - - - +
177G ASP* 1.3 62.6 + - - +
178G GLN* 4.9 3.3 - - - +
225G ARG* 3.2 14.1 + - - +
226G MET* 3.2 33.1 + - - +
227G LEU 3.4 0.5 + - - -
228G ASP* 2.8 49.4 + - - +
229G GLY* 4.4 4.7 - - - +
230G GLU 4.5 9.1 + - - -
235G VAL* 4.3 9.8 - - - +
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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
------------------------------------------------------------
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