Contacts of the helix formed by residues 353 - 359 (chain A) in PDB entry 4Y05
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 GLY 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A ARG* 6.4 0.7 - - - -
351A GLY 3.5 0.8 - - - -
352A SER* 1.3 79.1 - - - +
354A LYS* 1.3 58.1 + - - +
355A THR 3.5 2.0 - - - -
356A HIS* 3.7 0.9 + - - +
357A THR* 2.7 39.6 + - - -
564A THR* 3.9 5.2 - - - -
702A ADP 3.1 38.1 + - - -
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Residues in contact with LYS 354 (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 ALA* 3.6 34.8 - - + +
347A TYR* 4.0 0.7 - - - -
348A GLY 3.0 23.6 + - - +
349A GLN 2.9 23.4 + - - -
350A THR* 3.7 3.6 + - - +
353A GLY* 1.3 76.9 - - - +
355A THR* 1.3 58.1 + - - +
357A THR* 3.3 2.6 + - - -
358A MET* 3.0 33.1 + - - +
468A SER* 6.3 2.2 - - - +
492A ASP* 3.4 12.8 - - - +
493A LEU 3.2 27.8 - - - +
494A ALA 4.8 0.9 - - - +
495A GLY* 4.1 9.9 - - - +
564A THR* 3.3 19.5 - - - +
702A ADP 2.7 34.5 + - - +
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Residues in contact with THR 355 (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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354A LYS* 1.3 71.4 - - - +
356A HIS* 1.3 60.8 + - - +
358A MET 4.5 0.4 - - - +
359A GLY* 2.7 36.3 + - - +
360A GLY 3.1 11.1 + - - +
362A LEU* 6.6 0.2 - - + -
492A ASP* 2.7 23.0 + - - +
701A MG 2.0 32.9 - - - -
702A ADP 3.0 14.0 + - - +
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Residues in contact with HIS 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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264A ARG* 3.8 8.8 + - - -
321A ASN* 3.0 48.9 + - - -
353A GLY 3.7 2.2 - - - +
355A THR* 1.3 72.7 - - - +
357A THR* 1.4 60.3 + - - +
360A GLY* 3.3 20.9 + - - +
361A ASP* 3.6 31.4 + - + +
702A ADP 2.7 96.6 + + + +
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Residues in contact with THR 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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264A ARG* 2.9 36.3 + - - +
321A ASN* 4.0 4.6 + - - +
324A VAL* 4.3 6.3 - - + -
346A ALA* 5.0 2.0 - - + -
353A GLY 2.7 24.3 + - - -
354A LYS* 3.6 6.3 - - - -
355A THR 3.2 0.2 - - - -
356A HIS* 1.4 78.0 - - - +
358A MET* 1.3 61.3 + - - +
372A GLY* 3.7 3.5 + - - -
373A ILE* 3.0 46.7 + - + +
562A ILE* 4.1 21.1 - - + -
564A THR* 4.0 4.7 - - - +
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Residues in contact with MET 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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344A CYS* 4.2 14.6 - - - +
346A ALA* 3.8 25.1 - - + -
354A LYS 3.0 19.2 + - - +
355A THR 4.4 0.2 - - - +
357A THR* 1.3 79.9 - - - +
359A GLY* 1.3 60.4 + - - +
372A GLY* 3.3 1.6 - - - -
373A ILE* 2.9 41.8 + - + +
374A TYR* 3.0 40.4 + - + +
490A LEU* 3.7 39.3 - - + -
491A VAL 4.1 9.6 - - - +
492A ASP* 4.1 16.8 - - + +
562A ILE* 4.9 1.1 - - - -
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Residues in contact with GLY 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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355A THR* 2.7 22.7 + - - +
358A MET* 1.3 74.7 - - - +
360A GLY* 1.3 56.3 + - - -
362A LEU* 4.9 6.5 - - - +
370A SER 4.7 1.0 - - - +
371A LYS* 4.7 3.3 - - - -
372A GLY* 3.6 8.9 - - - -
374A TYR* 4.0 15.9 - - - +
375A ALA* 5.8 2.3 - - - +
449A ILE* 5.3 9.1 - - - +
453A SER* 5.7 2.9 - - - -
492A ASP* 5.6 0.2 + - - -
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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