Contacts of the strand formed by residues 340 - 344 (chain B) in PDB entry 4YP9
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 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B PHE* 3.4 27.8 - - + -
179B ASP* 3.3 38.6 - - + -
182B GLU* 3.9 20.2 - - + -
183B GLY* 3.9 5.8 - - - -
186B GLU* 3.7 25.3 - - - +
289B TRP* 3.9 25.4 - + - -
308B VAL* 3.3 24.7 - - + -
309B MET 3.5 4.0 - - - -
310B ARG* 4.1 15.5 - - + -
311B MET* 5.1 0.2 - - - -
337B SER* 5.1 0.4 - - - -
338B GLY 4.2 7.4 - - - -
339B ASP* 1.3 78.5 - - - +
341B GLU* 1.3 75.2 + - - +
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU* 4.7 0.9 - - - -
308B VAL* 4.6 3.4 - - - -
309B MET* 2.8 42.6 + - - +
311B MET* 3.9 21.8 - - + -
339B ASP* 6.2 0.2 - - + -
340B PHE* 1.3 82.4 - - - +
342B ILE* 1.3 65.9 + - - +
343B VAL* 3.7 0.4 - - + +
351B ARG* 3.6 22.1 + - - +
355B LEU* 4.0 14.8 - - + -
358B ARG* 3.2 27.6 + - - +
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Residues in contact with ILE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU* 3.8 45.2 + - + +
187B LEU* 4.1 2.9 - - - +
190B GLU* 4.0 25.8 - - + +
306B ILE* 3.7 25.8 - - + -
307B THR 3.6 11.4 - - - +
308B VAL* 4.1 11.9 - - + -
341B GLU* 1.3 74.9 + - - +
343B VAL* 1.3 69.7 + - - +
344B THR* 4.3 8.7 - - + -
347B ASP* 3.9 0.7 - - - +
351B ARG* 3.6 17.7 + - - -
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU* 4.6 7.4 - - + -
299B ILE* 4.2 9.8 - - + +
306B ILE* 3.2 2.6 - - - +
307B THR* 2.8 50.3 + - + +
309B MET* 3.8 16.8 - - + -
341B GLU 3.7 10.3 - - - +
342B ILE* 1.3 81.5 - - - +
344B THR* 1.3 69.3 + - - +
347B ASP* 3.3 12.1 - - - +
352B ILE* 3.5 27.6 - - + -
355B LEU* 3.6 25.4 - - + -
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Residues in contact with THR 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B GLU* 5.7 2.5 - - - +
299B ILE* 3.7 11.9 - - - +
305B ASP 3.4 10.8 - - - -
306B ILE* 4.0 22.4 - - + -
342B ILE* 4.3 7.9 - - + -
343B VAL* 1.3 78.9 - - - +
345B LYS* 1.3 63.8 + - - +
346B ALA* 3.0 24.0 + - - +
347B ASP* 3.1 32.0 + - - +
352B ILE* 5.0 0.5 - - - +
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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