Contacts of the strand formed by residues 234 - 238 (chain D) 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 VAL 234 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D TYR 4.5 1.0 + - - +
160D ASP* 2.9 46.8 + - - +
163D GLY 4.5 0.4 - - - +
180D TYR* 3.7 33.4 - - + -
182D GLY 3.5 10.5 - - - +
183D LYS* 4.2 13.2 - - + -
232D SER* 5.2 1.1 - - - +
233D PHE* 1.3 91.9 - - - +
235D PHE* 1.3 72.5 + - - +
236D PHE* 3.8 33.2 - - + -
3H NAG 6.0 0.4 - - - +
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Residues in contact with PHE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D TYR* 3.7 11.2 - - + -
122D ARG 3.2 27.1 - - - -
123D MSE 3.9 15.3 - - + +
124D PRO* 3.8 18.2 - - + -
128D GLY 5.0 0.7 - - - -
129D ARG* 4.0 16.6 - - + -
136D ILE* 4.3 7.6 - - + -
141D LEU* 3.7 25.6 - - + -
181D ALA* 2.9 22.2 + - - -
182D GLY 2.9 14.9 + - - +
183D LYS* 3.7 35.7 - - - -
184D ASN* 3.7 10.3 - - + -
233D PHE* 3.6 25.4 - + - -
234D VAL* 1.3 80.6 - - - +
236D PHE* 1.3 62.0 + - - +
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Residues in contact with PHE 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ILE* 3.8 20.6 - - + -
121D TYR 3.2 11.2 + - - +
122D ARG* 3.4 25.3 - - - +
123D MSE 4.0 0.5 + - - -
147D LEU* 3.8 3.7 - - + +
159D MSE 3.6 42.4 - - + -
160D ASP* 4.0 10.8 - - + -
163D GLY 3.4 28.3 - - - -
164D SER* 3.8 6.3 - - - -
178D PHE* 3.3 39.9 - + + -
179D SER 3.1 10.5 - - - +
181D ALA* 3.6 5.9 - - - +
234D VAL* 3.8 28.7 - - + -
235D PHE* 1.3 76.2 - - - +
237D LYS* 1.3 62.9 + - - +
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Residues in contact with LYS 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A PO4 3.0 28.8 + - - -
177D PHE 3.4 0.9 - - - +
178D PHE* 4.2 1.3 - - - -
179D SER* 2.9 44.8 + - - +
181D ALA* 3.7 14.6 - - + -
236D PHE* 1.3 74.6 - - - +
238D PRO* 1.3 74.4 - - + +
239D GLN* 3.4 10.7 + - - +
698D PO4 2.8 35.8 + - - -
6H NAG 3.7 18.2 - - + -
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Residues in contact with PRO 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LYS* 5.9 2.2 + - - +
122D ARG* 5.5 1.3 - - + -
147D LEU* 3.9 33.2 - - + -
176D ASN* 3.2 27.6 - - - +
177D PHE 3.6 2.9 - - - +
178D PHE* 3.8 19.3 - - + -
236D PHE 4.2 0.2 - - - +
237D LYS* 1.3 94.4 - - + +
239D GLN* 1.3 65.4 + - - +
240D SER* 5.4 0.2 - - - -
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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