Contacts of the strand formed by residues 235 - 240 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLY* 1.3 74.2 - - - -
236C CYS* 1.3 60.1 + - - +
237C LEU* 3.9 17.5 - - + -
279C PHE* 4.1 2.8 - - - -
280C GLU* 3.4 36.8 + - + +
282C LYS* 3.9 24.7 - - + -
299C TYR* 3.9 9.4 - + + -
302C MET* 3.8 27.9 - - + -
303C ASP 5.4 4.0 + - - -
304C HIS* 3.8 27.1 - + - -
307C MET* 3.6 25.9 - - + +
309C CYS 4.0 2.8 + - - -
310C PHE* 3.7 10.7 - - + -
311C ILE 3.0 24.8 + - - +
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Residues in contact with CYS 236 (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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234C GLY 3.8 0.6 + - - -
235C TYR* 1.3 71.2 - - - +
237C LEU* 1.3 66.0 + - - +
238C ILE* 3.7 6.9 + - - -
270C LEU 5.3 0.2 - - - -
274C PHE* 3.8 31.6 - - - -
279C PHE* 4.0 12.3 - - + -
280C GLU 3.0 8.3 + - - -
281C ILE* 3.5 25.0 - - + +
282C LYS 2.9 23.6 + - - -
311C ILE* 3.3 25.8 - - + -
313C CYS* 4.1 11.7 - - - -
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Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C TYR* 4.2 3.8 - - + -
236C CYS* 1.3 74.6 - - - +
238C ILE* 1.3 64.4 + - - +
239C ILE* 4.1 2.2 - - + -
282C LYS* 3.4 17.7 - - + +
284C HIS* 4.6 5.2 - - + +
295C ILE* 4.0 10.5 - - + -
296C LEU* 3.8 27.1 - - + -
299C TYR* 3.5 54.3 - - + -
310C PHE* 3.9 25.6 - - + -
311C ILE 2.8 10.1 + - - +
312C CYS* 3.6 11.8 - - - -
313C CYS* 2.8 27.8 + - - +
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Residues in contact with ILE 238 (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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236C CYS* 4.3 6.5 - - - +
237C LEU* 1.3 80.0 - - - +
239C ILE* 1.3 63.4 + - - +
240C ASN* 4.2 10.5 - - + -
267C ALA* 3.9 12.8 - - + +
270C LEU* 3.9 26.0 - - + -
271C THR* 3.7 24.5 - - - +
281C ILE* 3.7 20.0 - - + -
282C LYS 3.0 7.3 + - - -
283C PRO* 4.2 11.2 - - + -
284C HIS* 2.8 31.9 + - - +
313C CYS* 3.4 11.2 - - + +
315C LEU* 3.8 28.3 - - + -
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Residues in contact with ILE 239 (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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237C LEU* 5.1 2.7 - - + -
238C ILE* 1.3 72.2 - - - +
240C ASN* 1.3 58.5 + - - +
241C ASN* 4.0 11.9 - - - +
284C HIS* 3.5 30.7 - - + -
287C CYS* 4.0 12.1 - - - -
292C ILE* 3.9 36.3 - - + -
295C ILE* 3.7 28.3 - - + -
296C LEU* 5.7 2.7 - - + -
312C CYS* 4.8 9.4 - - - -
313C CYS 2.7 15.9 + - - +
314C ILE* 4.4 20.9 - - + -
315C LEU* 2.9 31.9 + - - +
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Residues in contact with ASN 240 (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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238C ILE* 4.2 12.8 - - + -
239C ILE* 1.3 74.1 - - - +
241C ASN* 1.3 60.3 + - - +
242C HIS* 3.6 3.2 + - - +
263C THR* 2.5 44.5 + - - +
264C HIS* 4.3 4.6 - - - +
267C ALA* 3.4 22.8 - - + +
283C PRO* 6.2 1.1 - - + -
284C HIS 2.7 11.2 + - - +
285C ASP* 3.3 25.2 + - - +
286C ASP* 2.8 21.5 + - - +
315C LEU* 3.6 10.3 - - - +
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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