Contacts of the helix formed by residues 364 - 372 (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 SER 364 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353D LEU* 5.4 5.2 - - - -
362D ASN* 3.2 29.4 + - - -
363D LEU* 1.3 75.6 - - - +
365D ARG* 1.3 65.0 + - - +
366D LEU 3.3 0.9 - - - -
367D LYS* 3.8 7.6 + - - +
368D LEU* 3.5 19.9 + - - +
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Residues in contact with ARG 365 (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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292D ASP* 3.1 27.7 + - - -
294D VAL* 3.8 29.4 - - - +
295D MET* 4.5 20.2 - - - +
298D LEU* 4.0 16.5 - - + +
344D ALA 3.5 15.6 + - - -
345D ILE* 2.9 30.3 + - - +
346D LEU 3.5 14.8 - - - +
347D ASN* 3.8 7.1 + - - +
348D GLY* 3.9 19.3 - - - +
362D ASN 4.7 1.6 + - - -
364D SER* 1.3 77.6 - - - +
366D LEU* 1.3 58.8 + - - +
368D LEU* 3.1 8.6 + - - +
369D ALA* 2.9 26.7 + - - +
377D PHE* 5.0 7.4 - - + -
855D TYR* 3.5 8.9 + - - -
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Residues in contact with LEU 366 (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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346D LEU* 4.3 15.2 + - + +
347D ASN* 5.2 1.3 - - - +
362D ASN 5.5 0.2 + - - -
363D LEU* 4.1 23.1 - - + -
364D SER 3.3 0.6 - - - -
365D ARG* 1.3 77.3 - - - +
367D LYS* 1.3 61.9 + - - +
369D ALA* 4.0 2.2 - - + +
370D ILE* 3.6 24.8 + - - +
377D PHE* 3.8 27.1 - - + -
378D VAL* 4.6 8.5 - - + -
383D CYS* 3.7 34.5 - - - -
386D GLN* 4.3 12.8 - - + +
387D LEU* 3.8 22.2 - - + -
751D PHE* 4.0 14.9 - - + -
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Residues in contact with LYS 367 (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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363D LEU* 3.3 32.1 + - - +
364D SER* 4.2 7.7 + - - +
365D ARG 3.3 0.2 - - - -
366D LEU* 1.3 76.8 - - - +
368D LEU* 1.3 59.2 + - - +
369D ALA 3.3 0.2 - - - -
370D ILE* 3.2 7.9 + - - +
371D LYS* 2.9 28.1 + - - +
751D PHE* 3.6 31.0 - - + -
754D PHE* 6.3 2.0 - - - -
755D GLU* 6.0 6.2 - - - +
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Residues in contact with LEU 368 (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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295D MET* 3.7 32.1 - - + -
298D LEU* 4.8 8.7 - - + -
299D GLU* 4.0 2.9 - - - +
364D SER 3.5 12.9 + - - +
365D ARG* 3.1 13.6 + - - +
367D LYS* 1.3 80.9 - - - +
369D ALA* 1.3 56.8 + - - +
371D LYS* 4.3 21.3 - - + +
372D TYR* 2.9 71.4 + - + +
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Residues in contact with ALA 369 (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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298D LEU* 4.8 10.2 - - + +
365D ARG 2.9 14.6 + - - +
366D LEU* 4.2 5.2 - - - +
367D LYS 3.3 0.6 - - - -
368D LEU* 1.3 76.2 - - - +
370D ILE* 1.3 58.6 + - - +
372D TYR 4.2 0.7 - - - -
373D GLU* 4.0 0.2 - - - -
374D VAL* 3.0 48.2 + - + +
377D PHE* 3.7 31.2 - - + -
378D VAL* 3.9 9.6 - - + +
744D PHE* 4.2 0.2 - - - -
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Residues in contact with ILE 370 (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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366D LEU 3.6 12.3 + - - +
367D LYS* 3.2 10.8 + - - +
368D LEU 3.2 0.4 - - - -
369D ALA* 1.3 78.8 - - - +
371D LYS* 1.3 66.1 + - - +
372D TYR 3.4 0.2 - - - -
373D GLU* 3.3 9.5 + - - +
378D VAL* 4.1 15.5 - - + -
744D PHE* 3.7 28.2 - - + -
747D ALA 4.4 7.2 - - - +
748D LYS* 3.8 28.4 - - + +
751D PHE* 3.6 43.7 - - + -
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Residues in contact with LYS 371 (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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367D LYS 2.9 16.3 + - - +
368D LEU* 3.5 18.2 + - + +
370D ILE* 1.3 79.5 - - - +
372D TYR* 1.3 84.0 + - + +
373D GLU* 3.4 3.5 + - - +
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Residues in contact with TYR 372 (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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298D LEU* 3.5 36.1 - - + -
299D GLU* 3.0 24.8 + - - -
301D SER* 4.9 4.7 + - - +
302D ASN* 3.4 44.5 + - + -
305D ALA* 6.0 2.4 - - - +
326D LYS* 4.1 9.5 + - - -
368D LEU* 2.9 49.6 + - + +
371D LYS* 1.3 105.3 + - + +
373D GLU* 1.3 69.1 + - - +
374D VAL* 3.5 14.6 - - + +
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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