Contacts of the helix formed by residues 339 - 347 (chain D) in PDB entry 6UZA
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 THR 339 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A HIS 5.5 1.8 - - - +
265A ASP* 3.3 29.7 + - - +
267A PHE* 4.5 8.1 - - - -
338D ASN* 1.3 74.7 - - - +
340D GLU* 1.3 65.0 + - + +
341D GLU 3.3 0.9 - - - -
342D VAL* 3.8 9.3 - - - +
343D GLU* 2.9 40.9 + - - +
385D GLN* 5.4 4.7 + - - -
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Residues in contact with GLU 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ASN* 3.5 29.3 + - + +
339D THR* 1.3 82.0 - - + +
341D GLU* 1.3 62.6 + - + +
343D GLU* 3.5 9.8 + - - +
344D ALA* 2.9 28.9 + - - +
854D GLN* 3.7 11.4 - - - +
858D ILE* 3.6 29.1 - - + +
861D ARG* 3.9 14.6 + - - -
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Residues in contact with GLU 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D CYS* 3.6 14.3 - - + -
337D ARG 3.3 15.1 + - - +
338D ASN* 3.2 29.8 + - + +
339D THR* 3.3 0.6 - - - +
340D GLU* 1.3 79.0 - - + +
342D VAL* 1.3 60.1 + - - +
344D ALA* 3.2 1.0 + - - +
345D ILE* 3.0 35.0 + - - +
858D ILE* 4.0 21.1 - - + -
861D ARG* 3.6 14.3 + - - +
862D LEU* 3.6 12.0 - - + +
865D ARG* 2.4 49.7 + - - -
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Residues in contact with VAL 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE* 4.1 21.5 - - + -
333D LEU* 4.9 1.8 - - + -
336D CYS* 3.7 21.3 - - + -
338D ASN 3.3 19.1 - - - +
339D THR* 3.5 11.4 + - - +
340D GLU 3.4 0.4 - - - -
341D GLU* 1.3 77.2 - - - +
343D GLU* 1.3 56.5 - - + +
345D ILE* 3.3 1.4 + - - +
346D LEU* 2.9 41.9 + - + +
382D ASN* 3.6 32.3 - - + +
385D GLN* 3.7 14.8 - - - +
386D GLN* 4.7 2.7 - - - +
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Residues in contact with GLU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D THR* 2.9 31.4 + - - +
340D GLU* 3.6 8.5 - - - +
341D GLU 3.3 0.2 - - - -
342D VAL* 1.3 78.1 - - + +
344D ALA* 1.3 57.2 + - - +
347D ASN* 2.9 38.6 - - - +
348D GLY 4.1 2.6 - - - +
350D VAL* 4.4 15.5 - - + +
361D PRO* 4.5 18.4 - - - +
386D GLN* 4.3 13.4 - - - +
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Residues in contact with ALA 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D GLU 2.9 17.1 + - - +
341D GLU 3.2 2.6 + - - +
343D GLU* 1.3 74.1 - - - +
345D ILE* 1.3 63.7 + - + +
347D ASN 2.9 18.6 - - - +
348D GLY 4.5 2.2 - - - -
350D VAL* 5.8 1.1 - - - -
365D ARG* 3.5 8.5 + - - -
855D TYR* 3.6 31.4 + - + -
858D ILE* 3.7 27.6 - - + -
859D MET* 4.4 4.4 - - - +
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Residues in contact with ILE 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D VAL* 4.2 21.1 - - + +
329D VAL* 5.0 1.8 - - + +
332D LEU* 4.3 16.6 - - + +
333D LEU* 3.8 32.5 - - + +
336D CYS* 3.7 16.4 - - - -
341D GLU 3.0 17.8 + - - +
342D VAL 4.1 2.0 - - - +
344D ALA* 1.3 77.3 - - - +
346D LEU* 1.3 61.5 + - - +
365D ARG* 2.9 26.7 + - - +
377D PHE* 3.9 18.4 - - + -
859D MET* 4.0 16.8 - - - -
862D LEU* 3.8 20.6 - - + -
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Residues in contact with LEU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D LEU* 3.9 19.3 - - + -
342D VAL* 2.9 21.5 + - + +
345D ILE* 1.3 76.1 - - - +
347D ASN* 1.3 62.7 + - - +
365D ARG* 3.5 23.4 - - - +
366D LEU* 4.3 13.6 + - + +
377D PHE* 3.7 29.4 - - + -
382D ASN 3.4 24.0 - - - +
383D CYS* 4.0 30.1 - - + -
386D GLN* 3.4 37.2 - - + +
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Residues in contact with ASN 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D GLU* 2.9 28.1 + - - +
344D ALA 2.9 20.6 - - - +
346D LEU* 1.3 82.5 - - - +
348D GLY* 1.3 68.5 + - - +
350D VAL* 5.0 7.7 - - + +
353D LEU* 5.8 0.4 - - + -
361D PRO* 3.4 20.5 - - - +
362D ASN* 2.9 31.2 - - + +
363D LEU* 4.5 4.7 - - - +
365D ARG* 3.8 6.4 + - - -
366D LEU* 5.2 1.9 + - - +
386D GLN* 3.3 32.7 + - - +
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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