Contacts of the helix formed by residues 719 - 734 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580B VAL* 4.4 7.4 - - + -
584B TYR* 3.6 51.3 + - + -
715B LEU* 3.1 27.0 + - + +
716B LEU* 4.2 5.4 - - - -
717B THR 3.2 0.2 - - - -
718B GLU* 1.3 98.4 + - + +
720B LYS* 1.3 61.5 + - - +
721B ALA 3.4 2.2 - - - -
722B ASP* 3.3 23.5 + - - +
723B VAL* 3.3 15.6 + - - +
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Residues in contact with LYS 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637B ILE* 3.8 33.5 + - + +
638B PHE* 3.8 28.3 - - + -
716B LEU 3.8 10.5 - - - +
717B THR* 3.4 21.5 + - + +
718B GLU 3.3 4.6 + - - -
719B LYS* 1.3 78.0 - - - +
721B ALA* 1.3 62.4 + - - +
723B VAL* 3.3 7.1 + - - +
724B GLU* 3.2 18.1 + - + +
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Residues in contact with ALA 721 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B GLU 5.2 0.4 + - - -
719B LYS 3.4 0.4 - - - -
720B LYS* 1.3 79.6 - - - +
722B ASP* 1.3 65.2 + - - +
724B GLU* 3.4 9.7 + - - +
725B LYS* 3.3 33.0 + - - +
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Residues in contact with ASP 722 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B VAL* 3.8 7.7 - - + +
584B TYR* 3.2 19.6 + - - +
719B LYS* 3.3 27.5 + - + +
720B LYS 3.2 0.8 - - - -
721B ALA* 1.3 78.7 - - - +
723B VAL* 1.3 64.7 + - - +
724B GLU 3.3 0.2 - - - -
725B LYS* 3.6 21.4 + - - +
726B VAL* 3.3 28.1 + - - +
745B LEU* 3.7 24.5 - - + +
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Residues in contact with VAL 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B ALA* 3.7 25.9 - - + +
577B GLY* 4.0 1.8 - - - +
580B VAL* 3.7 27.4 - - + -
634B SER* 3.5 25.8 - - - +
638B PHE* 3.6 18.7 - - + -
716B LEU* 3.9 18.8 - - + +
719B LYS 3.3 17.0 - - - +
720B LYS* 3.3 3.9 + - - +
722B ASP* 1.3 74.6 - - - +
724B GLU* 1.3 65.3 + - - +
726B VAL 3.6 0.4 + - - +
727B ALA* 3.2 24.1 + - - +
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Residues in contact with GLU 724 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B TYR* 3.3 26.9 + - - -
638B PHE* 3.9 22.6 - - - -
720B LYS 3.2 11.6 + - - +
721B ALA* 3.5 14.6 - - + +
723B VAL* 1.3 78.9 - - - +
725B LYS* 1.3 60.6 + - + +
727B ALA* 4.2 1.7 - - - +
728B LEU* 3.3 48.2 + - + +
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Residues in contact with LYS 725 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721B ALA* 3.3 23.8 + - - +
722B ASP* 3.6 23.3 + - - +
723B VAL 3.3 0.4 - - - -
724B GLU* 1.3 77.1 - - + +
726B VAL* 1.3 64.7 + - - +
728B LEU* 3.7 2.6 + - - +
729B LEU* 3.4 18.5 + - - +
744B LEU* 3.6 45.9 + - + +
745B LEU* 5.3 1.3 - - + -
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Residues in contact with VAL 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B ALA* 4.0 20.4 - - + +
579B ALA* 4.2 11.2 - - + -
580B VAL* 4.1 9.6 - - + -
594B VAL* 6.2 0.7 - - + -
722B ASP 3.3 18.2 + - - +
725B LYS* 1.3 76.4 - - - +
727B ALA* 1.3 62.4 + - - +
729B LEU* 3.6 0.3 + - - +
730B LEU* 3.2 21.0 + - + +
736B LEU* 3.5 15.3 - - + +
741B MET* 3.8 39.3 - - + -
744B LEU* 3.8 18.4 - - + -
745B LEU* 4.1 9.6 - - + -
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Residues in contact with ALA 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B ALA* 3.4 27.4 - - - +
573B TYR* 3.4 28.3 - - + -
576B ALA* 3.7 9.2 - - + -
638B PHE* 5.4 0.2 - - + -
723B VAL 3.2 19.0 + - - +
724B GLU 4.2 0.7 - - - +
725B LYS 3.2 0.2 - - - -
726B VAL* 1.3 77.9 - - - +
728B LEU* 1.3 61.6 + - - +
730B LEU* 3.0 8.6 + - - +
731B LEU* 2.9 25.0 + - - +
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Residues in contact with LEU 728 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B TYR* 4.1 20.9 - - + +
724B GLU* 3.3 40.6 + - + +
725B LYS* 4.4 2.7 - - - +
726B VAL 3.6 0.2 - - - -
727B ALA* 1.3 76.3 - - - +
729B LEU* 1.3 57.1 + - - +
731B LEU* 3.1 39.5 + - + +
732B GLU* 3.4 17.3 + - - +
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Residues in contact with LEU 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725B LYS 3.4 16.2 + - - +
726B VAL 3.9 4.9 - - - +
727B ALA 3.2 0.8 - - - -
728B LEU* 1.3 78.6 - - - +
730B LEU* 1.3 57.6 + - - +
732B GLU* 3.4 23.8 - - + +
733B LYS* 3.1 38.8 + - + +
736B LEU* 3.7 27.2 - - + +
740B ASP* 4.7 12.1 - - + +
744B LEU* 4.0 24.2 - - + -
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Residues in contact with LEU 730 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B ALA* 4.4 21.3 - - + +
575B GLN 4.7 1.6 - - - +
576B ALA 4.7 7.2 - - - +
594B VAL* 3.6 47.1 - - + +
595B SER* 4.3 2.5 - - - -
596B ILE* 3.4 26.8 - - + +
726B VAL* 3.2 20.4 + - + +
727B ALA* 3.0 11.0 + - - +
729B LEU* 1.3 75.4 - - - +
731B LEU* 1.3 60.0 + - - +
732B GLU 3.2 0.9 - - - -
734B GLU* 3.2 43.2 + - - +
736B LEU* 3.8 19.9 - - + +
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Residues in contact with LEU 731 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B PRO 5.9 0.7 - - - +
568B LYS* 4.2 21.3 - - + +
569B LYS* 4.2 25.6 - - + +
572B ALA* 4.0 18.6 - - + -
573B TYR* 5.8 1.6 - - + -
596B ILE* 4.9 3.6 - - + -
727B ALA 2.9 11.0 + - - +
728B LEU* 3.1 36.0 + - + +
730B LEU* 1.3 77.7 - - - +
732B GLU* 1.3 57.4 + - - +
734B GLU* 5.1 5.2 - - - +
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Residues in contact with GLU 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728B LEU 3.4 14.3 + - - +
729B LEU* 3.4 29.0 - - + +
731B LEU* 1.3 80.4 - - - +
733B LYS* 1.3 63.2 + - + +
734B GLU* 3.8 4.9 - - - +
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Residues in contact with LYS 733 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B ILE* 5.6 0.5 - - - +
729B LEU* 3.1 22.5 + - + +
732B GLU* 1.3 80.0 - - + +
734B GLU* 1.3 66.5 + - - +
735B VAL* 3.1 38.0 + - - +
736B LEU* 4.7 6.5 - - + -
740B ASP* 5.4 5.6 + - - +
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Residues in contact with GLU 734 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568B LYS* 3.8 25.3 + - - +
595B SER* 2.8 27.2 + - - -
596B ILE* 3.1 29.0 + - + -
597B ILE* 3.6 26.7 - - + +
730B LEU* 3.2 31.7 + - - +
731B LEU 5.1 4.9 - - - +
732B GLU 4.8 4.0 - - - -
733B LYS* 1.3 79.8 - - - +
735B VAL* 1.3 51.9 + - - +
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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