Contacts of the helix formed by residues 339 - 347 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338C ASN* 1.3 73.9 - - - +
340C GLU* 1.3 63.2 + - + +
341C GLU 3.3 1.8 - - - -
342C VAL* 3.8 9.0 - - - +
343C GLU* 2.9 40.3 + - - +
385C GLN* 5.4 5.3 + - - -
264D HIS 5.5 2.2 - - - +
265D ASP* 3.3 29.1 + - - +
267D PHE* 4.5 7.9 - - - -
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Residues in contact with GLU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C ASN* 3.5 28.9 + - + +
339C THR* 1.3 82.0 - - + +
341C GLU* 1.3 62.5 + - + +
343C GLU* 3.5 9.5 + - - +
344C ALA* 2.9 28.6 + - - +
854C GLN* 3.7 11.2 - - - +
858C ILE* 3.6 29.3 - - + +
861C ARG* 3.9 14.8 + - - -
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Residues in contact with GLU 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C CYS* 3.6 14.8 - - + -
337C ARG* 3.3 15.3 + - - +
338C ASN* 3.2 31.0 + - + +
339C THR* 3.3 0.8 - - - +
340C GLU* 1.3 78.0 - - + +
342C VAL* 1.3 59.3 + - - +
344C ALA* 3.2 1.2 + - - +
345C ILE* 3.0 34.3 + - - +
858C ILE* 4.0 20.6 - - + -
861C ARG* 3.6 13.6 + - - +
862C LEU* 3.6 11.0 - - + +
865C ARG* 2.4 49.4 + - - -
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Residues in contact with VAL 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C LEU* 4.9 1.6 - - + -
336C CYS* 3.7 21.5 - - + -
338C ASN 3.3 19.3 - - - +
339C THR* 3.5 12.2 + - - +
340C GLU 3.4 0.2 - - - -
341C GLU* 1.3 77.0 - - - +
343C GLU* 1.3 57.9 + - + +
345C ILE* 3.3 1.4 + - - +
346C LEU* 2.9 42.5 + - + +
382C ASN* 3.6 32.3 - - + +
385C GLN* 3.7 12.8 - - - +
386C GLN* 4.7 2.7 - - - +
267D PHE* 4.1 21.8 - - + -
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C THR* 2.9 31.3 + - - +
340C GLU* 3.6 8.4 - - - +
342C VAL* 1.3 76.9 - - + +
344C ALA* 1.3 56.8 + - - +
345C ILE 3.5 0.2 - - - -
347C ASN* 2.9 40.3 + - - +
348C GLY 4.1 2.4 - - - +
350C VAL* 4.4 14.6 - - + +
361C PRO* 4.5 18.4 - - - +
386C GLN* 4.3 13.6 - - - +
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Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C GLU 2.9 17.1 + - - +
341C GLU 3.2 3.1 + - - +
343C GLU* 1.3 73.9 - - - +
345C ILE* 1.3 62.8 + - + +
347C ASN 2.9 19.4 - - - +
348C GLY 4.5 1.8 - - - -
350C VAL* 5.8 0.7 - - - -
365C ARG* 3.5 8.7 + - - -
855C TYR* 3.6 32.0 + - + -
858C ILE* 3.7 27.8 - - + -
859C MET* 4.4 4.4 - - - +
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Residues in contact with ILE 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C VAL* 4.2 22.1 - - + +
329C VAL* 5.0 1.6 - - + +
332C LEU* 4.3 17.0 - - + +
333C LEU* 3.8 32.8 - - + +
336C CYS* 3.7 16.4 - - - -
341C GLU 3.0 17.7 + - - +
342C VAL 4.1 2.0 - - - +
344C ALA* 1.3 77.2 - - - +
346C LEU* 1.3 61.7 + - - +
365C ARG* 2.9 27.1 + - - +
377C PHE* 3.9 18.4 - - + -
859C MET* 4.0 17.0 - - - -
862C LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C LEU* 3.9 18.6 - - + -
342C VAL* 2.9 22.0 + - + +
345C ILE* 1.3 75.1 - - - +
347C ASN* 1.3 65.1 + - - +
365C ARG* 3.5 22.9 - - - +
366C LEU* 4.3 13.0 + - + +
377C PHE* 3.7 29.8 - - + -
382C ASN 3.4 23.8 - - - +
383C CYS* 4.0 29.2 - - + -
386C GLN* 3.4 36.3 - - - +
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Residues in contact with ASN 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C GLU* 2.9 29.8 + - - +
344C ALA 2.9 20.6 - - - +
346C LEU* 1.3 82.8 - - - +
348C GLY* 1.3 66.6 + - - +
350C VAL* 5.0 8.2 - - + +
353C LEU* 5.8 0.7 - - + -
361C PRO* 3.4 20.1 - - - +
362C ASN* 2.9 31.6 - - + +
363C LEU* 4.5 4.3 - - - +
365C ARG* 4.2 5.2 - - - +
366C LEU* 5.2 2.4 + - - +
386C GLN* 3.3 33.4 + - - +
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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