Contacts of the helix formed by residues 329 - 339 (chain L) in PDB entry 6NR8
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 GLU 329 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209L LYS* 3.8 11.8 + - - -
230L THR* 4.4 7.7 - - - +
302L LYS* 3.8 13.6 - - - +
327L ASP 3.9 0.6 + - - -
328L ILE* 1.3 85.9 - - + +
330L ARG* 1.3 64.9 + - - +
331L GLU* 3.9 10.2 - - - +
332L ASP* 3.3 41.9 + - - +
333L ILE* 3.5 14.3 - - - +
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Residues in contact with ARG 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L GLN* 4.8 5.3 + - - +
301L GLN* 4.4 17.0 + - - +
302L LYS* 5.0 16.5 - - + +
328L ILE 5.2 2.0 - - - -
329L GLU* 1.3 77.0 - - - +
331L GLU* 1.3 61.4 + - - +
333L ILE* 3.2 41.1 + - - +
334L GLU* 3.1 39.2 + - - +
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Residues in contact with GLU 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L ARG* 4.2 14.5 - - - +
209L LYS* 3.7 17.0 - - - +
329L GLU* 3.2 15.7 - - - +
330L ARG* 1.3 78.0 - - - +
332L ASP* 1.3 64.6 + - - +
334L GLU* 3.0 33.3 + - - +
335L PHE* 3.2 48.2 + - + -
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Residues in contact with ASP 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L LYS* 3.2 26.9 + - - +
229L LEU* 4.2 24.8 - - + +
230L THR* 3.9 17.4 - - - +
231L GLN* 5.0 3.3 + - - -
299L LEU* 4.4 5.3 - - + +
328L ILE* 3.3 30.0 - - + +
329L GLU* 3.3 32.0 + - - +
330L ARG 3.3 0.4 - - - -
331L GLU* 1.3 76.4 - - - +
333L ILE* 1.3 64.4 + - - +
335L PHE 3.7 0.3 + - - -
336L ILE* 3.4 24.1 + - - +
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Residues in contact with ILE 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248L LEU* 3.8 20.6 - - + -
250L GLN* 3.7 22.2 - - - +
299L LEU* 5.6 0.2 - - + -
301L GLN* 3.8 28.9 - - + +
328L ILE* 3.8 16.4 - - + +
329L GLU 3.5 15.9 - - - +
330L ARG* 3.2 41.0 + - - +
332L ASP* 1.3 76.5 - - - +
334L GLU* 1.3 64.7 + - + +
336L ILE* 3.3 7.6 - - - +
337L CYS* 3.3 27.2 + - - -
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Residues in contact with GLU 334 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L ARG* 5.6 2.3 - - - +
330L ARG* 3.1 29.1 + - + +
331L GLU* 3.0 33.8 + - - +
333L ILE* 1.3 81.3 - - + +
335L PHE* 1.3 63.5 + - + +
337L CYS* 3.7 5.1 + - - +
338L LYS* 3.1 27.6 + - - +
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Residues in contact with PHE 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L LEU 4.5 3.8 - - - -
206L ARG* 3.1 40.2 - - + -
207L ASP 3.8 13.0 - - - -
209L LYS* 3.6 52.9 - - + -
227L LEU* 3.8 24.0 - - + -
229L LEU* 4.3 6.1 - - + -
331L GLU* 3.2 33.8 + - + +
332L ASP 3.7 0.4 + - - +
334L GLU* 1.3 80.3 - - + +
336L ILE* 1.3 57.6 + - - +
338L LYS* 3.6 17.5 - - - -
339L THR* 2.6 41.5 + - - +
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Residues in contact with ILE 336 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227L LEU* 3.7 16.1 - - + +
229L LEU* 4.1 8.3 - - + -
246L ILE* 3.7 28.7 - - + -
248L LEU* 3.7 24.2 - - + -
299L LEU* 3.8 15.9 - - + -
332L ASP 3.4 14.0 + - - +
333L ILE 3.3 13.2 - - - +
335L PHE* 1.3 79.3 - - - +
337L CYS* 1.3 61.1 + - - +
339L THR 4.6 0.2 - - - +
340L ILE* 3.7 30.2 + - + -
341L GLY 3.7 5.2 + - - -
342L THR* 3.3 27.9 + - - +
376L ILE* 5.0 0.4 - - + -
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Residues in contact with CYS 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248L LEU* 3.7 24.2 - - - -
250L GLN* 5.4 0.7 - - - -
333L ILE* 3.3 22.7 + - - +
334L GLU* 4.0 5.2 - - - +
335L PHE 3.2 0.2 - - - -
336L ILE* 1.3 78.8 - - - +
338L LYS* 1.3 61.2 + - - +
341L GLY* 3.3 17.9 - - - -
342L THR 3.3 24.0 - - - +
343L LYS* 4.7 20.0 + - - +
344L PRO* 5.7 1.6 - - - -
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Residues in contact with LYS 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L ARG 3.3 22.4 - - - +
207L ASP* 3.1 17.8 + - - +
334L GLU 3.1 15.5 + - - +
335L PHE* 3.0 21.6 + - - +
337L CYS* 1.3 79.9 - - - +
339L THR* 1.3 66.5 + - - +
341L GLY* 4.3 1.9 + - - -
382L PRO* 3.6 21.5 - - + +
384L LYS* 5.7 2.7 - - - +
385L THR* 2.4 42.8 + - - +
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Residues in contact with THR 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227L LEU* 3.6 34.1 - - + +
335L PHE 2.6 22.4 + - - -
338L LYS* 1.3 79.5 + - - +
340L ILE* 1.3 63.1 + - - +
379L CYS* 4.0 6.5 - - - -
380L ALA 2.9 23.3 - - - +
381L SER* 3.3 25.6 - - - +
382L PRO* 3.3 7.4 - - - +
385L THR* 3.3 34.1 - - + +
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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