Contacts of the helix formed by residues 364 - 372 (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 SER 364 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C LEU* 5.4 5.6 - - - -
362C ASN* 3.2 29.0 + - - -
363C LEU* 1.3 75.2 - - - +
365C ARG* 1.3 64.2 + - - +
366C LEU 3.3 0.7 - - - -
367C LYS* 3.8 7.7 + - - +
368C LEU* 3.5 21.0 + - - +
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Residues in contact with ARG 365 (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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292C ASP* 3.1 27.5 + - - -
294C VAL* 3.8 29.4 - - - +
295C MET* 4.5 21.0 - - - +
298C LEU* 4.0 16.3 - - + +
344C ALA 3.5 16.2 + - - -
345C ILE* 2.9 30.0 + - - +
346C LEU* 3.5 14.6 + - - +
347C ASN* 3.8 6.4 + - - -
348C GLY* 3.9 19.1 - - - +
362C ASN 4.7 1.6 + - - -
364C SER* 1.3 77.7 - - - +
366C LEU* 1.3 59.8 + - - +
368C LEU* 3.1 10.0 + - - +
369C ALA* 2.9 25.8 + - - +
377C PHE* 5.0 7.2 - - + -
855C TYR* 3.5 9.1 + - - -
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Residues in contact with LEU 366 (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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346C LEU* 4.3 15.4 + - + +
347C ASN* 5.2 1.3 - - - +
363C LEU* 4.1 23.8 - - + +
364C SER 3.3 0.4 - - - -
365C ARG* 1.3 77.5 - - - +
367C LYS* 1.3 60.4 + - - +
369C ALA* 4.0 2.8 + - + +
370C ILE* 3.6 24.3 + - - +
377C PHE* 3.8 28.5 - - + -
378C VAL* 4.6 8.1 - - + -
383C CYS* 3.7 34.5 - - - -
386C GLN* 4.3 12.6 - - - +
387C LEU* 3.8 21.8 - - + -
751C PHE* 4.0 13.8 - - + -
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Residues in contact with LYS 367 (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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363C LEU* 3.3 30.0 + - - +
364C SER* 3.8 7.8 + - - +
365C ARG 3.3 0.4 - - - -
366C LEU* 1.3 77.3 - - - +
368C LEU* 1.3 58.6 + - - +
369C ALA 3.3 0.4 - - - -
370C ILE* 3.2 8.6 + - - +
371C LYS* 2.9 27.7 + - - +
751C PHE* 3.6 30.3 - - + -
754C PHE* 6.3 2.2 - - - -
755C GLU* 6.0 6.4 - - - +
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Residues in contact with LEU 368 (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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295C MET* 3.7 33.0 - - + -
298C LEU* 4.8 8.3 - - + -
299C GLU* 4.0 2.9 - - - +
364C SER 3.5 12.0 + - - +
365C ARG* 3.1 13.3 + - - +
367C LYS* 1.3 81.1 - - - +
369C ALA* 1.3 55.4 + - - +
371C LYS* 3.9 21.0 - - + +
372C TYR* 2.9 71.1 + - + +
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Residues in contact with ALA 369 (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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298C LEU* 4.8 10.2 - - + +
365C ARG 2.9 14.5 + - - +
366C LEU* 4.2 4.9 - - - +
367C LYS 3.3 0.2 - - - -
368C LEU* 1.3 75.4 - - - +
370C ILE* 1.3 58.9 + - - +
372C TYR* 4.2 0.9 - - - -
374C VAL* 3.0 48.6 + - + +
377C PHE* 3.7 32.3 - - + -
378C VAL* 3.9 9.2 - - + +
744C PHE* 4.2 0.7 - - - -
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Residues in contact with ILE 370 (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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366C LEU 3.6 11.0 - - - +
367C LYS* 3.2 9.9 + - - +
368C LEU 3.2 0.6 - - - -
369C ALA* 1.3 78.5 - - - +
371C LYS* 1.3 63.7 - - - +
372C TYR 3.4 0.2 - - - -
373C GLU* 3.3 9.7 + - - +
378C VAL* 4.1 15.9 - - + -
744C PHE* 3.7 26.4 - - + -
747C ALA 4.4 7.9 - - - +
748C LYS* 3.8 28.8 - - + +
751C PHE* 3.6 44.0 - - + -
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Residues in contact with LYS 371 (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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367C LYS 2.9 16.3 + - - +
368C LEU* 3.5 18.6 + - + +
370C ILE* 1.3 79.8 - - - +
372C TYR* 1.3 84.9 + - + +
373C GLU* 3.2 4.2 + - - +
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Residues in contact with TYR 372 (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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298C LEU* 3.5 36.3 - - + -
299C GLU* 3.0 24.8 + - - -
301C SER* 4.9 4.2 + - - +
302C ASN* 3.4 46.1 + - + -
305C ALA* 6.0 2.3 - - - +
326C LYS* 4.1 9.4 + - - -
368C LEU* 2.9 49.0 + - + +
371C LYS* 1.3 105.3 + - + +
373C GLU* 1.3 69.5 + - - +
374C VAL* 3.5 14.7 - - + +
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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