Contacts of the helix formed by residues 719 - 734 (chain F) in PDB entry 6NYY
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 719 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580F VAL* 4.7 4.9 - - + -
584F TYR* 3.6 36.5 + - + -
715F LEU* 3.2 25.4 + - + +
716F LEU* 3.2 8.2 + - + +
718F GLU* 1.3 97.2 + - + +
720F LYS* 1.3 60.8 + - - +
721F ALA 3.4 2.5 - - - -
722F ASP* 3.2 35.9 + - + +
723F VAL* 3.3 16.5 + - - +
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Residues in contact with LYS 720 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637F ILE* 3.7 32.2 + - + +
638F PHE* 3.6 31.8 - - + -
716F LEU 2.9 13.4 + - - +
717F THR* 4.0 16.2 - - - +
718F GLU 3.3 3.6 + - - -
719F LYS* 1.3 75.9 - - - +
721F ALA* 1.3 63.3 + - - +
723F VAL* 3.3 12.7 + - - +
724F GLU* 3.5 8.9 + - - +
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Residues in contact with ALA 721 (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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718F GLU 5.3 0.4 + - - -
719F LYS 3.4 0.4 - - - -
720F LYS* 1.3 79.1 - - - +
722F ASP* 1.3 65.5 + - - +
724F GLU* 3.6 10.3 + - - +
725F LYS* 3.3 36.0 + - - +
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Residues in contact with ASP 722 (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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580F VAL* 4.5 3.8 - - + -
584F TYR* 3.2 23.8 + - + +
719F LYS* 3.2 37.9 + - + +
720F LYS 3.2 0.8 - - - -
721F ALA* 1.3 81.6 - - - +
723F VAL* 1.3 63.5 + - - +
725F LYS* 3.6 17.0 + - - +
726F VAL* 3.3 27.5 + - - +
745F LEU* 3.7 19.1 - - + +
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Residues in contact with VAL 723 (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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573F TYR* 4.8 1.3 - - + +
576F ALA* 3.5 19.5 - - + +
577F GLY* 4.4 1.1 - - - -
580F VAL* 3.9 15.7 - - + -
634F SER* 3.6 23.8 - - - +
638F PHE* 3.6 15.7 - - + -
716F LEU* 3.7 30.7 - - + -
719F LYS 3.3 16.4 + - - +
720F LYS* 3.3 9.4 + - - +
722F ASP* 1.3 77.2 - - - +
724F GLU* 1.3 63.0 + - - +
726F VAL* 3.4 4.0 + - - +
727F ALA* 3.1 22.6 + - + +
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Residues in contact with GLU 724 (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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573F TYR* 4.2 20.2 + - - +
638F PHE* 3.9 24.4 - - + -
720F LYS* 3.5 5.9 + - - +
721F ALA* 4.0 11.6 - - - +
722F ASP 3.3 0.4 - - - -
723F VAL* 1.3 80.1 - - - +
725F LYS* 1.3 62.2 + - + +
727F ALA* 3.3 4.1 + - - +
728F LEU* 3.2 40.4 + - + +
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Residues in contact with LYS 725 (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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721F ALA* 3.3 26.9 + - - +
722F ASP* 4.0 18.3 + - - +
723F VAL 3.3 0.8 - - - -
724F GLU* 1.3 78.2 - - + +
726F VAL* 1.3 62.7 + - + +
727F ALA 3.6 0.2 + - - -
728F LEU* 3.8 12.8 + - - +
729F LEU* 4.0 7.4 + - - +
744F LEU* 3.6 35.2 - - + +
745F LEU* 5.7 3.4 - - + -
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Residues in contact with VAL 726 (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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576F ALA* 3.8 13.5 - - + -
579F ALA* 4.3 6.3 - - + -
580F VAL* 3.8 15.7 - - + -
722F ASP 3.3 15.5 - - - +
723F VAL 3.4 7.3 + - - +
724F GLU 3.3 0.2 - - - -
725F LYS* 1.3 79.0 - - + +
727F ALA* 1.3 62.5 + - - +
728F LEU 3.4 0.3 + - - -
729F LEU* 3.6 3.1 + - - +
730F LEU* 3.2 18.2 + - - +
736F LEU* 3.8 14.5 - - + +
741F MET* 3.7 39.3 - - + -
744F LEU* 3.8 11.6 - - + +
745F LEU* 3.9 15.9 - - + -
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Residues in contact with ALA 727 (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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572F ALA* 3.3 24.7 - - + +
573F TYR* 3.5 28.9 - - + -
576F ALA* 3.8 10.5 - - + -
723F VAL* 3.1 16.4 + - + +
724F GLU 3.9 1.8 - - - +
725F LYS 3.3 0.2 - - - -
726F VAL* 1.3 78.0 - - - +
728F LEU* 1.3 60.4 + - - +
730F LEU* 3.3 5.7 + - - +
731F LEU* 2.8 28.1 + - - +
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Residues in contact with LEU 728 (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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573F TYR* 4.8 14.8 - - + +
724F GLU* 3.2 33.0 + - + +
725F LYS* 4.3 7.6 - - + +
726F VAL 3.3 0.2 - - - -
727F ALA* 1.3 77.9 - - - +
729F LEU* 1.3 60.0 + - + +
731F LEU* 2.9 32.8 + - + +
732F GLU* 3.0 23.7 + - + +
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Residues in contact with LEU 729 (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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725F LYS 4.0 4.1 + - - +
726F VAL 3.6 6.5 + - - +
728F LEU* 1.3 76.7 - - + +
730F LEU* 1.3 64.2 + - - +
732F GLU* 4.1 13.9 - - + +
733F LYS* 3.3 38.7 + - + +
736F LEU* 4.1 11.9 - - + -
740F ASP* 5.5 6.1 - - + +
744F LEU* 3.7 37.7 - - + -
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Residues in contact with LEU 730 (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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572F ALA* 3.6 25.1 - - + +
575F GLN* 4.1 1.1 - - + -
576F ALA* 3.8 17.7 - - + +
594F VAL* 3.6 42.6 - - + +
596F ILE* 3.8 34.1 - - + +
726F VAL 3.2 15.8 + - - +
727F ALA 3.3 9.0 - - - +
728F LEU 3.2 0.2 - - - -
729F LEU* 1.3 77.7 - - - +
731F LEU* 1.3 59.7 + - - +
734F GLU* 3.2 34.7 + - - +
736F LEU* 3.8 14.7 - - + +
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Residues in contact with LEU 731 (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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568F LYS* 3.6 39.7 - - + +
569F LYS* 4.4 13.0 - - + +
572F ALA* 4.2 8.3 - - + -
573F TYR* 6.6 0.2 - - + -
596F ILE* 4.8 6.3 - - + +
727F ALA 2.8 16.3 + - - +
728F LEU* 2.9 25.7 + - + +
730F LEU* 1.3 74.4 - - - +
732F GLU* 1.3 68.9 + - + +
734F GLU* 4.6 7.2 - - - +
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Residues in contact with GLU 732 (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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728F LEU* 3.0 21.8 + - + +
729F LEU* 3.5 16.6 + - + +
730F LEU 3.3 0.4 - - - -
731F LEU* 1.3 89.6 - - - +
733F LYS* 1.3 62.8 + - + +
734F GLU* 3.6 5.2 - - - +
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Residues in contact with LYS 733 (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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729F LEU* 3.3 24.1 + - + +
732F GLU* 1.3 77.9 - - + +
734F GLU* 1.3 60.0 - - - +
735F VAL* 2.9 42.3 + - - +
736F LEU* 5.0 3.4 - - + -
737F ASP* 5.6 0.4 - - - +
740F ASP* 3.1 27.8 + - - +
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Residues in contact with GLU 734 (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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568F LYS* 4.2 18.4 + - - +
595F SER* 3.2 28.9 + - - -
596F ILE* 3.6 24.0 + - + +
597F ILE* 3.4 32.0 - - + +
730F LEU* 3.2 24.7 + - - +
731F LEU 4.6 6.3 - - - +
732F GLU 4.6 7.2 - - - +
733F LYS* 1.3 77.4 - - - +
735F VAL* 1.3 58.0 + - + +
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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