Contacts of the strand formed by residues 310 - 315 (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 PHE 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B TYR* 3.7 13.9 - - + -
237B LEU* 3.8 38.4 - - + -
299B TYR* 4.2 7.9 - + + -
304B HIS* 3.8 24.2 - + - -
309B CYS* 1.3 75.9 - - - +
311B ILE* 1.3 71.3 + - - +
312B CYS* 4.1 16.2 - - + -
340B PHE* 3.7 48.5 - + - -
348B LEU* 3.6 23.5 - - + +
352B PRO 3.1 9.9 + - - +
353B LYS* 3.4 6.5 - - + -
354B VAL* 2.8 25.8 + - - +
355B PHE* 4.2 10.5 - + - -
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Residues in contact with ILE 311 (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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235B TYR 3.0 11.4 + - - +
236B CYS* 3.3 19.2 - - - -
237B LEU* 2.9 26.2 + - - +
274B PHE* 3.4 34.8 - - + -
279B PHE* 3.5 33.7 - - + -
309B CYS* 4.1 6.1 - - - -
310B PHE* 1.3 84.4 - - - +
312B CYS* 1.3 64.8 + - - +
313B CYS* 4.1 13.9 - - - -
354B VAL* 3.2 16.2 - - + +
356B PHE* 4.2 16.6 - - + -
476B PHE* 4.3 7.9 - - + -
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Residues in contact with CYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 3.6 17.3 - - + -
239B ILE* 4.6 4.5 - - - -
296B LEU* 4.1 20.6 - - - -
310B PHE* 4.1 12.1 - - + -
311B ILE* 1.3 76.1 - - - +
313B CYS* 1.3 65.0 + - - +
314B ILE* 4.0 21.7 - - - +
354B VAL 2.8 9.5 + - - -
355B PHE* 3.1 37.0 - - + +
356B PHE 3.0 22.7 + - - +
357B ILE* 5.3 0.2 - - - +
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Residues in contact with CYS 313 (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* 4.1 18.8 - - - -
237B LEU 2.9 16.3 + - - +
238B ILE* 3.5 6.0 - - + -
239B ILE* 2.8 33.1 + - - +
270B LEU* 3.9 42.4 - - + -
274B PHE* 4.7 0.4 - - - -
311B ILE* 4.1 2.2 - - - -
312B CYS* 1.3 76.1 - - - +
314B ILE* 1.3 60.2 + - - +
315B LEU* 4.2 3.6 - - + -
356B PHE* 3.3 28.0 - - + +
422B ILE* 5.8 0.2 - - + -
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Residues in contact with ILE 314 (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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239B ILE* 3.7 21.5 - - + -
292B ILE* 5.4 4.3 - - + -
296B LEU* 5.7 1.1 - - + -
312B CYS* 4.0 20.6 - - - +
313B CYS* 1.3 78.3 - - - +
315B LEU* 1.3 64.9 + - - +
316B SER* 4.4 9.2 - - - -
323B ILE* 4.1 35.2 - - + -
336B LEU* 3.6 30.5 - - + -
355B PHE* 4.7 5.6 - - + -
356B PHE 2.8 7.8 + - - +
357B ILE* 3.6 24.4 - - + +
358B GLN 2.9 28.1 + - - +
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Residues in contact with LEU 315 (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* 3.9 24.2 - - + -
239B ILE 2.9 13.0 + - - +
240B ASN* 3.7 19.5 - - - +
241B ASN* 3.0 24.3 + - - +
260B ARG* 3.4 9.3 + - - +
263B THR* 3.7 17.0 - - - +
266B ASP* 4.0 16.6 - - + +
267B ALA 4.1 5.8 - - - +
270B LEU* 4.1 13.2 - - + -
313B CYS* 4.8 0.7 - - + -
314B ILE* 1.3 84.2 - - - +
316B SER* 1.3 63.0 + - - +
358B GLN* 3.6 8.7 - - + -
422B ILE* 3.9 30.3 - - + -
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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