Contacts of the strand formed by residues 353 - 358 (chain D) 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 LYS 353 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310D PHE* 3.5 8.7 - - + -
340D PHE* 3.1 36.1 + - + +
341D THR* 5.3 1.1 - - - +
342D GLY* 5.4 3.8 - - - +
348D LEU* 2.8 51.2 + - + -
349D ALA* 4.2 4.9 - - - +
350D GLY 4.2 1.8 - - - +
351D LYS 2.8 15.9 + - - +
352D PRO* 1.3 75.3 - - - +
354D VAL* 1.3 62.6 + - - +
355D PHE* 4.2 8.7 - - + -
395D ASP 5.9 0.2 - - - -
397D ALA 3.7 22.7 + - - -
398D ASP* 2.9 9.6 + - - +
399D PHE* 3.3 27.8 - - + -
400D LEU 2.9 24.8 + - - +
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Residues in contact with VAL 354 (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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309D CYS* 4.4 11.4 - - - -
310D PHE 2.9 14.7 + - - +
311D ILE* 3.2 11.7 - - + +
312D CYS 2.8 26.3 + - - +
352D PRO* 4.5 1.3 - - + -
353D LYS* 1.3 81.4 - - - +
355D PHE* 1.3 65.5 + - - +
356D PHE* 3.5 39.7 - - + -
400D LEU* 3.4 22.9 - - + +
439D ILE* 5.8 0.2 - - + -
474D LEU* 3.8 28.3 - - + -
476D PHE* 4.7 4.0 - - + -
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Residues in contact with PHE 355 (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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296D LEU* 5.2 1.3 - - + -
310D PHE* 4.3 6.3 - + - -
312D CYS* 3.2 37.5 - - + -
314D ILE* 5.1 2.5 - - + -
336D LEU* 4.4 8.7 - - + -
337D THR* 3.8 33.0 - - + -
340D PHE* 3.6 31.9 - + - -
353D LYS* 4.4 12.1 - - + -
354D VAL* 1.3 82.5 - - - +
356D PHE* 1.3 58.7 + - - +
357D ILE* 4.4 11.9 - - + -
399D PHE* 4.0 24.9 - + - -
400D LEU 2.8 9.0 + - - +
401D LEU* 3.5 20.5 - - + +
402D GLY* 2.7 32.9 + - - +
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Residues in contact with PHE 356 (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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274D PHE* 3.8 26.2 - + - -
311D ILE* 4.1 9.0 - - + -
312D CYS 2.9 6.9 + - - -
313D CYS* 3.4 27.4 - - + +
314D ILE 2.9 27.2 + - - +
315D LEU* 5.3 0.7 - - - +
354D VAL* 3.5 27.4 - - + -
355D PHE* 1.3 75.5 - - - +
357D ILE* 1.3 62.7 + - - +
358D GLN 4.0 0.4 + - - -
400D LEU* 4.8 1.1 - - + -
402D GLY* 3.5 7.2 - - - +
421D TYR* 3.7 21.1 - - + -
422D ILE* 4.7 9.9 - - + -
425D LEU* 3.7 40.4 - - + -
439D ILE* 4.5 13.7 - - + -
443D LEU* 4.4 13.7 - - + -
476D PHE* 5.7 1.6 - + - -
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Residues in contact with ILE 357 (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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314D ILE* 3.6 32.1 - - + +
323D ILE* 3.7 26.9 - - + -
333D ILE* 4.3 15.5 - - + -
336D LEU* 5.8 0.7 - - + -
355D PHE* 4.4 15.7 - - + -
356D PHE* 1.3 77.7 - - - +
358D GLN* 1.3 60.6 + - - +
359D ALA* 3.7 10.1 + - + +
401D LEU* 3.8 13.2 - - + -
402D GLY 2.9 9.3 + - - +
403D MET* 3.7 37.5 - - + +
404D ALA* 3.0 27.3 + - - +
421D TYR* 4.7 3.1 - - - -
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Residues in contact with GLN 358 (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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260D ARG* 4.0 6.3 - - - +
266D ASP* 4.2 1.3 - - - +
314D ILE 2.9 15.1 + - - +
315D LEU* 3.9 6.7 - - + -
316D SER 3.0 26.5 + - - +
356D PHE 4.0 0.8 + - - -
357D ILE* 1.3 71.0 - - - +
359D ALA* 1.3 64.4 - - - +
404D ALA* 3.2 20.9 - - - +
411D SER* 3.1 24.8 + - - -
412D TYR 4.2 2.8 + - - -
419D THR* 3.5 34.8 + - + +
421D TYR* 3.4 14.9 + - - +
422D ILE* 3.7 21.8 - - + -
462D GLN* 4.7 0.2 + - - -
405H 1U8 2.7 25.8 + - - +
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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