Contacts of the helix formed by residues 349 - 360 (chain A) in PDB entry 1OQY
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 ASN 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A ASN* 3.4 6.0 + - + +
348A GLU* 1.3 100.9 + - - +
350A LEU* 1.3 77.6 + - + +
351A ALA 2.6 3.0 + - - -
352A ALA 2.6 1.0 + - - -
353A ASN* 2.3 52.6 + - + +
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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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343A ALA* 3.5 8.9 - - + +
344A CYS* 3.2 44.6 - - + +
345A GLU* 4.5 17.9 - - - +
347A ASN* 4.8 15.2 - - + +
349A ASN* 1.3 82.5 - - + +
351A ALA* 1.3 57.3 + - - +
353A ASN* 4.3 4.7 - - + -
354A PHE* 3.1 29.4 - - + +
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Residues in contact with ALA 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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340A ALA* 2.8 33.4 - - + +
341A TYR* 3.4 15.5 - - + +
343A ALA* 3.0 16.8 - - + +
347A ASN 4.7 7.5 + - - +
348A GLU* 5.5 0.9 - - - -
349A ASN 2.6 5.8 + - - +
350A LEU* 1.3 72.8 - - - +
352A ALA* 1.3 58.8 + - - +
354A PHE* 2.7 28.6 - - - -
355A LEU* 3.3 10.8 - - - +
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Residues in contact with ALA 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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327A LEU* 4.7 19.0 - - + +
332A PHE* 4.4 13.5 - - + -
348A GLU* 3.1 22.8 + - - +
349A ASN 2.6 6.5 + - - -
351A ALA* 1.3 74.0 - - + +
353A ASN* 1.3 57.1 + - - +
354A PHE 3.1 1.3 - - - -
355A LEU* 2.6 29.7 + - - +
356A LEU* 2.8 27.1 + - + +
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Residues in contact with ASN 353 (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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349A ASN* 2.3 53.9 + - + +
350A LEU* 3.9 3.8 - - - +
352A ALA* 1.3 71.4 - - - +
354A PHE* 1.3 63.1 + - - +
356A LEU* 3.4 12.7 + - - +
357A SER* 3.2 23.1 + - - -
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Residues in contact with PHE 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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340A ALA* 4.7 12.1 - - + -
343A ALA* 5.1 3.8 - - + -
350A LEU* 3.1 18.2 + - + +
351A ALA* 2.7 32.5 - - - -
352A ALA 3.1 0.8 - - - -
353A ASN* 1.3 83.0 - - - +
355A LEU* 1.3 77.4 + - + +
357A SER* 3.4 5.9 + - - -
358A GLN* 2.8 56.6 + - + +
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Residues in contact with LEU 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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332A PHE* 3.2 42.6 - - + -
333A PRO* 4.7 11.4 - - + -
336A LEU* 4.3 15.5 - - + +
337A VAL* 5.3 1.1 - - + -
340A ALA* 4.3 19.7 - - + -
351A ALA 3.3 13.5 - - - +
352A ALA 2.6 16.6 + - - +
354A PHE* 1.3 92.0 - - + +
356A LEU* 1.3 60.7 + - - +
358A GLN* 3.1 6.0 + - + +
359A ASN* 3.0 23.5 + - + +
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Residues in contact with LEU 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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330A LEU* 5.0 8.3 - - + -
332A PHE* 3.8 24.9 - - + -
352A ALA* 2.8 47.3 + - + +
353A ASN* 3.4 11.4 - - - +
355A LEU* 1.3 73.3 - - - +
357A SER* 1.3 63.3 + - - +
358A GLN 3.1 1.2 + - - -
359A ASN* 3.1 16.1 + - - +
360A PHE* 3.2 11.1 + - - -
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Residues in contact with SER 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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353A ASN* 3.2 18.8 + - - -
354A PHE* 3.7 7.6 - - - -
355A LEU 3.3 0.2 - - - -
356A LEU* 1.3 79.8 - - - +
358A GLN* 1.3 61.0 + - - +
360A PHE* 2.7 44.5 - - - -
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Residues in contact with GLN 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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354A PHE* 2.8 46.6 + - + +
355A LEU* 3.4 8.5 - - + +
356A LEU 3.0 0.8 - - - -
357A SER* 1.3 80.0 - - - +
359A ASN* 1.3 64.2 + - - +
360A PHE* 4.3 5.0 - - - +
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Residues in contact with ASN 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 LEU* 3.0 15.9 + - + +
356A LEU* 3.1 11.0 + - - +
358A GLN* 1.3 78.4 - - - +
360A PHE* 1.3 84.2 + - - +
361A ASP* 4.5 1.0 - - - +
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Residues in contact with PHE 360 (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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356A LEU 3.2 9.5 + - - -
357A SER* 2.7 37.2 - - - -
358A GLN* 4.3 4.7 - - - +
359A ASN* 1.3 102.7 + - - +
361A ASP* 1.3 67.0 + - - +
362A ASP 5.0 2.2 - - - +
363A GLU* 6.1 1.3 - - - -
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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