Contacts of the helix formed by residues 374 - 379 (chain A) 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 VAL 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.8 28.3 - - + -
301A SER* 4.8 2.2 - - - +
326A LYS* 3.9 39.3 - - + +
329A VAL* 5.5 2.5 - - + -
330A VAL* 4.6 5.2 - - + -
369A ALA* 3.0 16.7 + - + +
372A TYR* 4.1 16.4 - - + +
373A GLU* 1.3 73.2 - - - +
375A LYS* 1.3 64.3 + - - +
376A LYS 4.9 0.7 - - - +
377A PHE* 3.7 25.3 - - + +
378A VAL* 3.3 24.4 + - - +
744A PHE* 4.3 0.8 - - - -
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Residues in contact with LYS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A LYS* 5.4 1.4 - - - +
373A GLU* 3.6 38.5 + - - +
374A VAL* 1.3 74.4 - - - +
376A LYS* 1.3 59.3 + - + +
378A VAL* 3.4 2.4 + - - +
379A ALA* 2.9 31.2 + - - +
740A VAL* 3.7 20.4 - - + +
741A GLU* 4.8 18.3 - - + +
744A PHE* 3.9 40.8 - - + -
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A MET* 4.3 19.3 - - + +
327A ASP* 5.0 11.2 - - - +
330A VAL* 3.7 32.0 - - + +
374A VAL* 3.5 0.6 - - - +
375A LYS* 1.3 76.4 - - + +
377A PHE* 1.3 63.1 + - - +
379A ALA* 3.9 4.4 - - - +
380A HIS* 3.4 23.6 + - - +
736A ASP* 6.0 3.6 - - - -
737A ASP* 5.3 9.8 - - - +
740A VAL* 3.9 31.9 - - + +
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Residues in contact with PHE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A VAL* 5.2 0.9 - - + -
298A LEU* 5.9 2.5 - - + -
329A VAL* 3.6 38.8 - - + -
330A VAL* 3.5 10.1 - - + +
333A LEU* 3.7 31.7 - - + +
345A ILE* 3.9 27.8 - - + -
346A LEU* 3.7 21.1 - - + -
365A ARG* 5.0 9.4 - - + -
366A LEU* 3.8 24.0 - - + -
369A ALA* 3.7 24.2 - - + -
374A VAL* 3.7 24.3 + - + +
375A LYS 3.3 0.6 - - - -
376A LYS* 1.3 79.6 - - - +
378A VAL* 1.3 58.4 + - - +
379A ALA 3.5 0.2 - - - -
380A HIS* 4.0 0.9 - - - +
383A CYS* 3.5 17.2 - - - +
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU* 4.6 6.3 - - + -
369A ALA* 3.9 25.8 - - + +
370A ILE* 4.1 18.6 - - + -
374A VAL 3.3 18.6 - - - +
375A LYS 3.4 1.2 + - - +
377A PHE* 1.3 81.7 - - + +
379A ALA* 1.3 55.6 + - - +
380A HIS 3.3 4.4 + - - -
383A CYS* 4.0 17.9 - - - +
384A GLN* 2.9 22.0 - - - +
387A LEU* 4.6 4.0 - - + -
743A LYS 5.2 1.2 - - - +
744A PHE* 4.0 19.7 - - + -
747A ALA* 3.7 27.5 - - + +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A LYS 2.9 19.2 + - - +
376A LYS* 4.0 4.0 - - - -
377A PHE 3.5 0.2 - - - -
378A VAL* 1.3 75.5 - - - +
380A HIS* 1.3 58.9 + - - +
381A PRO* 4.1 4.5 - - - +
384A GLN* 4.5 5.7 - - - +
740A VAL* 3.9 29.4 - - + +
743A LYS* 3.7 40.0 + - + +
744A PHE 4.6 2.0 - - - +
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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