Contacts of the helix formed by residues 346 - 352 (chain A) in PDB entry 1Y57
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 LEU 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A GLY 3.7 0.6 + - - -
345A SER* 1.3 72.5 - - - +
347A LEU* 1.3 63.7 + - - +
349A PHE* 3.2 5.6 + - + +
350A LEU* 2.9 43.6 + - + +
366A MET* 4.1 22.9 - - - -
370A ILE* 4.1 23.1 - - + -
389A ALA* 3.4 24.4 + - + +
392A ILE* 2.9 25.1 + - + +
394A VAL* 3.6 23.3 - - + +
400A CYS* 4.3 3.1 - - - -
451A LEU* 4.2 5.4 - - + -
455A LEU* 4.0 19.5 - - + -
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Residues in contact with LEU 347 (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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345A SER* 3.2 6.4 - - - +
346A LEU* 1.3 79.6 - - - +
348A ASP* 1.3 67.7 + - - +
350A LEU* 3.4 3.7 + - - +
351A LYS* 3.2 44.4 + - + +
389A ALA* 3.2 11.1 + - + -
390A ALA* 3.9 32.3 - - + +
454A GLU* 4.0 17.7 - - - +
459A GLY* 3.6 33.4 - - - +
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Residues in contact with ASP 348 (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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343A LYS 5.8 1.3 - - - +
345A SER* 3.2 23.8 + - - +
347A LEU* 1.3 84.1 - - - +
349A PHE* 1.3 65.1 + - - +
351A LYS* 3.4 12.1 + - - +
352A GLY* 3.0 21.0 + - - -
600A MPZ 4.4 15.2 - - - +
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Residues in contact with PHE 349 (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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343A LYS* 4.1 34.2 + - + +
345A SER 3.0 14.8 + - - +
346A LEU* 3.4 20.2 - - + +
348A ASP* 1.3 76.9 - - - +
350A LEU* 1.3 65.2 + - + +
352A GLY* 3.4 10.8 + - - -
354A THR* 3.6 38.5 - - + -
355A GLY 3.8 11.6 + - - -
358A LEU* 4.2 11.2 - - + -
366A MET* 4.7 2.5 - - - -
394A VAL* 4.2 25.6 - - + -
395A GLY 5.4 1.1 - - - -
398A LEU* 3.7 29.6 - - + -
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Residues in contact with LEU 350 (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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346A LEU* 2.9 46.1 + - + +
347A LEU* 3.7 7.2 - - - +
349A PHE* 1.3 77.7 - - + +
351A LYS* 1.3 60.3 + - - +
352A GLY 3.8 0.3 - - - +
355A GLY* 3.4 22.2 - - - -
358A LEU* 4.4 11.2 - - + -
363A LEU* 3.6 30.5 - - + -
366A MET* 4.9 0.7 - - + -
389A ALA* 4.7 4.5 - - + -
454A GLU 3.7 22.7 - - - +
455A LEU* 4.1 19.1 - - + +
458A LYS* 3.6 29.0 - - + +
459A GLY* 4.1 4.9 - - - +
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Residues in contact with LYS 351 (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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347A LEU* 3.2 42.0 + - + +
348A ASP* 3.8 12.4 + - - +
349A PHE 3.3 0.4 - - - -
350A LEU* 1.3 74.3 - - - +
352A GLY* 1.3 61.7 + - - +
458A LYS 3.9 15.5 - - - +
459A GLY* 4.1 14.2 + - - +
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Residues in contact with GLY 352 (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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348A ASP 3.0 15.2 + - - -
349A PHE* 3.4 3.7 + - - -
350A LEU 3.3 1.7 - - - +
351A LYS* 1.3 83.1 - - - +
353A GLU* 1.3 66.6 + - - +
354A THR 3.3 2.7 - - - -
355A GLY* 3.1 15.4 + - - -
356A LYS* 4.0 6.8 + - - +
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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