Contacts of the helix formed by residues 769 - 774 (chain F) in PDB entry 6M04
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 LYS 769 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768F PRO* 1.3 75.3 - - - +
770F GLN* 1.3 57.0 + - + +
771F LEU 2.7 17.2 + - - -
772F PHE* 3.0 48.2 + - + +
791F PRO* 3.5 17.3 - - + +
792F GLU* 3.2 25.1 - - - +
793F LYS* 3.0 42.9 - - + +
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Residues in contact with GLN 770 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746F ILE* 3.3 30.5 - - + +
748F ILE* 2.8 24.1 - - + +
749F GLY* 3.3 28.6 + - - +
769F LYS* 1.3 75.6 - - + +
771F LEU* 1.3 54.1 + - - +
772F PHE* 3.0 20.6 - - + -
773F LYS* 2.9 24.2 + - + +
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Residues in contact with LEU 771 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748F ILE* 3.3 24.5 - - + +
751F LEU* 4.8 4.9 - - + -
757F LEU* 3.8 39.0 - - + -
767F LEU* 3.8 21.8 - - + -
769F LYS 2.7 5.1 + - - -
770F GLN* 1.3 67.8 - - - +
772F PHE* 1.3 58.5 + - - +
773F LYS 3.1 5.2 - - - -
774F CYS* 3.2 27.0 - - - -
777F LEU* 4.0 10.5 - - + -
780F LEU* 3.8 10.5 - - + -
793F LYS* 3.7 29.1 - - + +
796F GLN* 5.2 0.9 - - - +
797F LEU* 3.9 25.8 - - + -
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Residues in contact with PHE 772 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769F LYS* 3.0 53.6 + - + -
770F GLN* 3.0 21.5 - - + -
771F LEU* 1.3 75.2 - - - +
773F LYS* 1.3 70.9 + - + +
774F CYS 3.3 1.1 - - - +
793F LYS* 3.7 24.2 - - + +
796F GLN* 3.3 38.8 + - + +
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Residues in contact with LYS 773 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748F ILE 4.3 6.3 - - - +
749F GLY* 4.3 11.7 - - - +
751F LEU 5.7 1.1 - - - +
752F GLN* 3.6 40.6 - - + +
770F GLN* 2.9 18.0 + - + +
772F PHE* 1.3 89.8 - - + +
774F CYS* 1.3 63.4 + - - +
775F ILE* 3.9 2.3 + - - +
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Residues in contact with CYS 774 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748F ILE 5.5 0.2 + - - -
751F LEU* 3.2 26.0 + - + +
752F GLN 3.3 9.4 - - - +
754F LEU* 3.6 13.0 - - + -
771F LEU* 3.2 27.0 + - - +
772F PHE 3.9 5.4 - - - +
773F LYS* 1.3 84.0 - - - +
775F ILE* 1.3 58.4 + - - +
776F LYS 4.7 0.4 - - - +
777F LEU* 3.6 43.4 - - + +
796F GLN* 4.5 13.4 - - - +
797F LEU* 5.9 0.2 - - - -
799F GLN* 5.5 0.7 - - - +
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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