Contacts of the strand formed by residues 235 - 240 (chain B) in PDB entry 4PS1
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 TYR 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU* 4.5 5.2 + - - -
234B GLY* 1.3 73.6 - - - -
236B CYS* 1.3 59.2 + - - +
237B LEU* 4.0 10.5 - - + -
279B PHE* 4.0 3.1 - - - -
280B GLU* 3.4 27.4 - - + +
282B LYS* 3.7 23.1 - - + -
299B TYR* 3.7 19.5 - + + -
302B MET* 3.5 28.6 - - + +
303B ASP 4.9 6.8 + - - -
304B HIS* 3.7 35.2 - + - -
307B MET* 3.6 29.7 - - + +
309B CYS 4.1 2.6 + - - -
310B PHE* 3.7 9.3 - - + +
311B ILE 3.0 25.2 + - - +
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Residues in contact with CYS 236 (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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234B GLY 3.9 0.2 + - - -
235B TYR* 1.3 73.0 - - - +
237B LEU* 1.3 65.3 + - - +
238B ILE* 3.7 8.0 + - - -
274B PHE* 4.0 26.5 - - - -
279B PHE* 3.9 12.3 - - + -
280B GLU 2.9 8.3 + - - -
281B ILE* 3.4 23.6 - - + +
282B LYS 2.9 24.0 + - - -
311B ILE* 3.3 30.1 - - + -
313B CYS* 4.1 13.0 - - - -
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TYR* 4.2 7.0 - - + -
236B CYS* 1.3 73.2 - - - +
238B ILE* 1.3 65.0 + - - +
239B ILE* 5.0 5.4 - - + -
282B LYS* 3.5 26.9 - - + +
284B HIS* 5.6 0.9 - - + -
295B ILE* 3.9 19.3 - - + -
296B LEU* 3.8 29.6 - - + -
299B TYR* 3.7 35.2 - - + -
310B PHE* 3.8 22.9 - - + -
311B ILE 2.9 9.8 + - - +
312B CYS* 3.6 11.4 - - - -
313B CYS* 2.9 26.8 + - - +
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Residues in contact with ILE 238 (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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236B CYS* 4.2 7.0 - - - +
237B LEU* 1.3 79.5 - - - +
239B ILE* 1.3 58.7 + - - +
240B ASN* 3.6 9.9 + - + +
267B ALA* 4.0 11.2 - - + +
270B LEU* 3.9 25.8 - - + -
271B THR* 3.7 16.2 - - - +
281B ILE* 3.7 28.9 - - + -
282B LYS 3.0 8.7 + - - +
283B PRO* 4.2 11.8 - - + +
284B HIS* 2.8 33.6 + - - +
313B CYS* 3.5 12.1 - - + +
315B LEU* 3.9 28.3 - - + -
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Residues in contact with ILE 239 (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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237B LEU* 5.0 5.6 - - + -
238B ILE* 1.3 75.0 - - - +
240B ASN* 1.3 59.0 + - - +
241B ASN* 3.9 19.1 - - - +
284B HIS* 3.5 11.7 - - + -
287B CYS* 4.1 5.2 - - - -
292B ILE* 4.0 35.4 - - + -
295B ILE* 3.9 40.4 - - + -
296B LEU* 5.6 2.0 - - + -
312B CYS* 4.6 10.1 - - - -
313B CYS 2.8 16.9 + - - +
314B ILE* 4.2 21.8 - - + -
315B LEU* 2.9 30.8 + - - +
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Residues in contact with ASN 240 (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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238B ILE* 4.2 13.9 - - + +
239B ILE* 1.3 72.2 - - - +
241B ASN* 1.3 62.0 + - - +
242B HIS* 3.6 2.9 + - - +
263B THR* 2.5 43.8 + - - +
264B HIS* 4.4 4.4 - - - +
267B ALA* 3.3 27.7 - - + +
283B PRO* 6.2 1.1 - - + -
284B HIS 2.9 10.4 + - - +
285B ASP* 3.3 27.3 + - - +
286B ASP* 2.9 19.4 + - - +
315B LEU* 3.7 5.5 - - + +
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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