Contacts of the strand formed by residues 355 - 359 (chain A) in PDB entry 1SZU
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 ILE 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A PHE* 3.3 4.6 - - - -
328A GLY* 3.9 8.1 - - - +
331A LEU* 3.9 24.9 - - + -
332A LYS* 3.8 26.2 - - + -
335A LEU* 3.6 30.7 - - + -
349A ARG 3.4 13.5 - - - +
350A GLY* 4.0 8.7 - - - +
352A GLY 3.4 20.9 - - - +
353A ALA* 3.0 17.0 + - - +
354A MET* 1.3 77.2 - - - +
356A ALA* 1.3 65.2 + - - +
398A ARG* 3.3 3.3 - - - -
399A ILE* 2.7 37.1 + - + -
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLY 4.5 1.1 - - - +
214A PHE* 3.6 29.8 - - + -
335A LEU* 5.7 0.2 - - - -
349A ARG* 3.0 40.2 + - - +
355A ILE* 1.3 80.3 - - - +
357A ILE* 1.3 68.8 + - - +
396A VAL* 3.8 13.7 - - + -
397A LEU 3.0 14.6 - - - +
398A ARG* 4.0 1.6 - - - +
399A ILE* 6.0 1.1 - - - -
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A LEU* 3.7 46.0 - - + -
345A ILE* 4.1 14.6 - - + -
347A ASP 3.0 13.0 - - - +
348A VAL* 4.2 8.7 - - + -
349A ARG* 5.2 1.1 - - - +
356A ALA* 1.3 81.4 - - - +
358A GLU* 1.3 59.7 + - - +
359A LEU* 4.2 9.3 + - + +
395A ASN 4.1 0.2 - - - +
396A VAL* 3.5 4.4 - - - +
397A LEU* 2.9 52.0 + - + +
417A ILE* 5.5 1.3 - - + -
421A PHE* 3.9 33.2 - - + -
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 3.4 4.0 - - - +
176A HIS* 2.7 28.9 + - - -
215A TYR* 2.6 22.6 + - - -
344A GLU 3.6 0.2 - - - +
345A ILE* 3.6 2.4 - - - -
346A GLY* 2.9 27.4 + - - -
347A ASP* 3.0 15.1 + - + -
349A ARG* 2.9 26.9 + - - +
357A ILE* 1.3 75.0 - - - +
359A LEU* 1.3 61.5 + - - +
360A PHE* 3.5 14.5 - - + -
393A TYR* 5.8 0.9 - - - -
395A ASN* 3.0 37.6 + - - +
396A VAL* 3.6 12.3 - - + -
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A GLU* 3.0 7.9 - - + +
345A ILE* 3.6 33.4 - - + +
357A ILE* 4.2 10.3 - - + +
358A GLU* 1.3 78.3 - - - +
360A PHE* 1.3 61.6 + - - +
369A ASP* 3.0 29.6 + - + -
372A LEU* 3.9 18.8 - - + -
373A THR* 3.5 43.1 - - - +
376A ILE* 4.6 0.9 - - + -
395A ASN* 2.9 23.7 + - - +
397A LEU* 4.3 10.5 - - + -
421A PHE* 3.7 21.1 - - + -
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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