Contacts of the helix formed by residues 338 - 346 (chain Q) in PDB entry 6GYK
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 338 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337Q GLU* 1.3 81.3 + - - +
339Q ALA* 1.3 61.8 + - - +
340Q LYS 3.1 1.3 - - - -
341Q LYS* 2.6 28.5 + - - +
342Q LEU* 2.9 33.5 + - - +
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Residues in contact with ALA 339 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337Q GLU* 3.3 9.3 + - - +
338Q ASN* 1.3 82.6 - - - +
340Q LYS* 1.3 57.1 + - - +
342Q LEU* 3.3 9.1 + - - +
343Q ARG* 2.9 57.1 + - - +
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Residues in contact with LYS 340 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B LYS* 5.4 12.4 - - - +
366B GLN* 5.2 5.9 + - - +
367B LEU* 4.1 30.3 - - + +
368B GLU* 6.3 2.9 - - - -
336Q ASP* 4.2 16.3 + - - +
337Q GLU* 3.0 27.5 + - + +
338Q ASN 3.0 0.2 + - - -
339Q ALA* 1.3 76.4 - - - +
341Q LYS* 1.3 57.4 + - - +
343Q ARG* 3.8 8.6 - - - +
344Q PHE* 2.9 33.2 + - + +
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Residues in contact with LYS 341 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B LYS* 5.3 9.3 - - - +
336Q ASP* 3.7 19.0 + - + +
337Q GLU 3.2 23.0 + - - +
338Q ASN* 2.6 12.3 + - - +
340Q LYS* 1.3 71.0 - - - +
342Q LEU* 1.3 61.9 + - + +
344Q PHE* 3.1 7.6 + - + +
345Q GLU* 2.9 61.3 + - + +
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Residues in contact with LEU 342 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338Q ASN* 2.9 36.3 + - - +
339Q ALA* 3.8 10.3 - - - +
341Q LYS* 1.3 80.5 - - + +
343Q ARG* 1.3 61.9 + - + +
345Q GLU* 3.7 15.8 + - - +
346Q GLU* 3.4 33.2 + - - +
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Residues in contact with ARG 343 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B GLU* 4.6 7.0 - - - +
339Q ALA* 2.9 50.4 + - - +
340Q LYS* 4.0 7.0 - - - +
342Q LEU* 1.3 76.6 - - + +
344Q PHE* 1.3 61.1 + - - +
345Q GLU 3.5 0.2 - - - -
346Q GLU* 3.8 20.1 + - - +
347Q PHE* 5.1 0.9 - - - +
365Q TYR* 3.8 37.7 + - + -
391Q LYS* 4.6 20.5 - - - +
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Residues in contact with PHE 344 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B ASP* 4.6 17.0 - - - -
358B LYS* 5.2 10.8 - - - -
368B GLU* 3.1 33.0 - - - -
336Q ASP* 5.8 2.0 - - - +
340Q LYS* 2.9 24.3 + - + +
341Q LYS* 3.1 11.2 + - + +
343Q ARG* 1.3 76.3 - - - +
345Q GLU* 1.3 68.2 + - + +
346Q GLU 3.3 0.8 + - - -
347Q PHE* 3.2 30.4 - + + +
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Residues in contact with GLU 345 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341Q LYS* 2.9 51.0 + - + +
342Q LEU* 4.2 17.5 - - - +
343Q ARG 3.5 0.2 - - - -
344Q PHE* 1.3 84.1 - - + +
346Q GLU* 1.3 59.2 + - + +
347Q PHE* 3.2 23.0 + - - -
348Q TYR* 4.6 5.9 - - - -
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Residues in contact with GLU 346 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Q ARG* 5.7 2.9 + - - -
141Q ARG* 3.3 30.3 + - - +
342Q LEU* 3.4 22.8 + - - +
343Q ARG* 3.8 13.2 + - - +
344Q PHE 3.3 1.2 - - - -
345Q GLU* 1.3 77.5 - - + +
347Q PHE* 1.3 54.1 + - - +
348Q TYR* 3.2 10.3 + - - +
391Q LYS* 4.0 19.1 + - - -
393Q TYR* 5.6 0.7 + - - -
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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