Contacts of the helix formed by residues 719 - 731 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580E VAL* 4.5 5.2 - - + -
584E TYR* 3.5 44.5 - - + +
715E LEU* 3.1 27.4 + - + +
716E LEU* 3.2 5.3 + - - +
718E GLU* 1.3 94.5 - - + +
720E LYS* 1.3 61.8 + - - +
721E ALA 3.4 2.7 - - - -
722E ASP* 3.4 27.1 + - + +
723E VAL* 3.3 24.1 + - - +
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Residues in contact with LYS 720 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637E ILE* 3.8 30.2 + - + +
638E PHE* 3.5 31.7 - - + -
716E LEU 3.0 12.3 + - - +
717E THR* 4.1 14.4 - - - +
718E GLU 3.5 2.8 + - - -
719E LYS* 1.3 75.1 - - - +
721E ALA* 1.3 66.9 + - - +
723E VAL* 3.3 7.7 + - - +
724E GLU* 3.2 24.8 + - - +
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Residues in contact with ALA 721 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719E LYS 3.4 0.4 - - - -
720E LYS* 1.3 78.1 - - - +
722E ASP* 1.3 60.0 + - - +
724E GLU* 3.4 12.6 + - - +
725E LYS* 3.1 40.5 + - - +
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Residues in contact with ASP 722 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580E VAL* 4.2 8.5 - - + -
584E TYR* 3.3 22.1 + - - +
719E LYS* 3.4 33.1 + - + +
720E LYS 3.2 0.8 - - - -
721E ALA* 1.3 77.4 - - - +
723E VAL* 1.3 64.5 + - - +
725E LYS* 3.5 20.9 + - - +
726E VAL* 3.3 26.7 + - - +
745E LEU* 3.8 21.3 - - + +
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Residues in contact with VAL 723 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573E TYR 4.8 0.2 - - - +
576E ALA* 3.9 19.5 - - + +
577E GLY 4.3 0.4 - - - +
580E VAL* 3.8 17.5 - - + -
634E SER* 3.4 25.4 - - - +
638E PHE* 3.6 16.8 - - + -
716E LEU* 3.7 30.3 - - + +
719E LYS 3.3 15.9 - - - +
720E LYS* 3.3 8.9 + - - +
722E ASP* 1.3 75.7 - - - +
724E GLU* 1.3 62.9 + - - +
726E VAL* 3.2 11.8 + - - +
727E ALA* 3.2 14.0 + - - +
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Residues in contact with GLU 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573E TYR* 4.4 17.3 + - - +
638E PHE* 4.0 17.6 - - + -
720E LYS* 3.2 15.4 + - - +
721E ALA* 3.8 13.1 - - - +
722E ASP 3.3 0.2 - - - -
723E VAL* 1.3 76.1 - - - +
725E LYS* 1.3 63.6 + - + +
726E VAL 3.5 0.2 + - - -
727E ALA* 4.8 0.2 - - - +
728E LEU* 3.3 42.5 + - + +
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Residues in contact with LYS 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721E ALA* 3.1 26.1 + - + +
722E ASP* 3.7 26.5 + - - +
723E VAL 3.3 0.2 - - - -
724E GLU* 1.3 78.4 - - - +
726E VAL* 1.3 61.9 + - + +
728E LEU* 4.0 8.0 + - - +
729E LEU* 4.0 8.1 + - - +
744E LEU* 4.0 44.4 + - + +
745E LEU* 5.2 1.1 - - + -
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Residues in contact with VAL 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576E ALA* 3.8 22.4 - - + -
579E ALA* 4.6 2.9 - - + -
580E VAL* 3.8 15.0 - - + -
722E ASP 3.3 15.7 - - - +
723E VAL 3.2 7.7 + - - +
725E LYS* 1.3 78.5 - - - +
727E ALA* 1.3 64.2 + - - +
729E LEU* 3.3 16.5 + - - +
730E LEU* 3.5 9.9 + - + +
736E LEU* 3.7 26.0 - - + +
741E MET* 4.0 22.4 - - + -
744E LEU* 3.8 16.7 - - + +
745E LEU* 4.3 8.7 - - + -
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Residues in contact with ALA 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572E ALA* 3.3 27.5 - - + +
573E TYR* 3.5 30.3 - - + -
576E ALA* 3.7 7.9 - - + -
723E VAL 3.2 5.2 + - - +
724E GLU 4.8 0.2 - - - +
725E LYS 3.5 0.2 - - - -
726E VAL* 1.3 76.7 - - - +
728E LEU* 1.3 61.1 + - - +
729E LEU 3.2 0.2 - - - -
730E LEU* 3.1 13.7 + - - +
731E LEU* 2.9 30.1 + - - +
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Residues in contact with LEU 728 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573E TYR* 4.2 16.2 - - + +
724E GLU* 3.3 37.1 + - + +
725E LYS* 4.5 5.4 - - - +
726E VAL 3.3 1.2 - - - -
727E ALA* 1.3 77.4 - - - +
729E LEU* 1.3 64.2 + - + +
731E LEU* 3.3 28.4 + - + +
732E GLU* 3.3 23.3 + - - +
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Residues in contact with LEU 729 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725E LYS 4.0 8.6 + - - +
726E VAL 3.3 7.9 + - - +
727E ALA 3.2 0.4 - - - -
728E LEU* 1.3 77.3 - - + +
730E LEU* 1.3 55.2 + - - +
732E GLU* 2.9 22.2 + - + +
733E LYS* 2.4 69.4 + - + +
736E LEU* 4.6 13.2 - - + -
740E ASP* 5.4 2.9 - - + +
744E LEU* 3.7 37.5 - - + -
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Residues in contact with LEU 730 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572E ALA* 3.9 29.4 - - + +
575E GLN* 4.5 5.4 - - + -
576E ALA 4.6 1.6 - - - +
594E VAL* 3.8 31.2 - - + +
596E ILE* 3.4 19.7 - - + +
726E VAL* 3.5 7.3 + - + +
727E ALA* 3.1 18.0 + - - +
729E LEU* 1.3 76.2 - - - +
731E LEU* 1.3 58.7 + - - +
732E GLU 3.1 0.4 - - - -
734E GLU* 3.3 50.7 + - - +
735E VAL 4.0 0.9 - - - +
736E LEU* 3.7 34.5 - - + -
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Residues in contact with LEU 731 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568E LYS* 3.4 51.0 + - + +
569E LYS* 4.0 30.5 - - + +
572E ALA* 4.1 8.3 - - + -
573E TYR* 5.4 7.4 - - + +
596E ILE* 5.0 0.2 - - + -
727E ALA 2.9 15.9 + - - +
728E LEU* 3.7 27.4 - - + +
729E LEU 3.2 0.6 - - - -
730E LEU* 1.3 77.3 - - - +
732E GLU* 1.3 62.0 + - + +
734E GLU* 5.2 3.1 - - - -
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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