Contacts of the helix formed by residues 719 - 733 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580D VAL* 4.3 15.0 - - + -
584D TYR* 3.6 44.8 + - + -
715D LEU* 3.1 25.5 + - + +
716D LEU* 4.0 5.8 - - + -
718D GLU* 1.3 95.6 + - + +
720D LYS* 1.3 62.4 + - - +
721D ALA 3.4 3.1 - - - +
722D ASP* 3.5 24.0 + - - +
723D VAL* 3.3 23.7 + - - +
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Residues in contact with LYS 720 (chain D).
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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637D ILE* 3.7 31.2 + - + +
638D PHE* 3.6 31.7 - - + -
716D LEU 3.4 15.4 + - - +
717D THR* 3.5 21.1 + - + +
718D GLU 3.4 3.4 + - - -
719D LYS* 1.3 77.7 - - - +
721D ALA* 1.3 62.3 + - - +
723D VAL* 3.4 10.6 + - - -
724D GLU* 3.5 10.4 + - - +
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Residues in contact with ALA 721 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718D GLU 5.3 0.4 + - - -
719D LYS 3.4 0.6 - - - -
720D LYS* 1.3 79.2 - - - +
722D ASP* 1.3 62.3 + - - +
724D GLU* 3.3 13.0 + - - +
725D LYS* 3.1 35.8 + - - +
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Residues in contact with ASP 722 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580D VAL* 4.1 12.3 - - + -
584D TYR* 3.1 16.8 + - - +
719D LYS* 3.5 28.1 + - - +
720D LYS 3.3 1.0 - - - -
721D ALA* 1.3 77.4 - - - +
723D VAL* 1.3 65.6 + - - +
725D LYS* 3.4 31.3 + - - +
726D VAL* 3.2 27.9 + - - +
745D LEU* 3.7 21.0 - - + +
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Residues in contact with VAL 723 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D TYR* 4.7 0.4 - - + +
576D ALA* 3.7 24.2 - - + +
580D VAL* 3.8 17.9 - - + -
634D SER* 3.3 27.1 - - - +
638D PHE* 3.6 15.0 - - + -
716D LEU* 3.7 30.5 - - + +
719D LYS 3.3 17.3 - - - +
720D LYS* 3.4 7.6 + - - +
721D ALA 3.3 0.4 - - - -
722D ASP* 1.3 76.7 - - - +
724D GLU* 1.3 62.1 + - - +
726D VAL 3.3 1.0 + - - -
727D ALA* 3.2 20.3 + - - +
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Residues in contact with GLU 724 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D TYR* 4.5 17.9 + - + +
638D PHE* 4.1 16.1 - - + -
720D LYS* 3.5 10.7 + - - +
721D ALA* 3.3 13.1 + - - +
722D ASP 3.2 0.8 - - - -
723D VAL* 1.3 77.4 - - - +
725D LYS* 1.3 64.0 + - + +
727D ALA 4.7 0.2 - - - +
728D LEU* 3.2 50.7 + - + +
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Residues in contact with LYS 725 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721D ALA* 3.1 23.6 + - - +
722D ASP* 3.6 31.6 + - - +
723D VAL 3.3 0.2 - - - -
724D GLU* 1.3 78.2 - - - +
726D VAL* 1.3 61.8 + - + +
728D LEU* 3.8 5.0 + - - +
729D LEU* 3.6 22.3 + - - +
744D LEU* 4.0 33.8 + - + +
745D LEU* 5.0 6.3 - - + -
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Residues in contact with VAL 726 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D ALA* 4.0 16.2 - - + -
579D ALA* 4.3 16.8 - - + -
580D VAL* 3.8 14.4 - - + -
594D VAL* 6.0 0.7 - - + -
722D ASP 3.2 17.6 + - - +
723D VAL 3.8 4.3 - - - +
724D GLU 3.3 0.2 - - - -
725D LYS* 1.3 77.9 - - - +
727D ALA* 1.3 58.3 + - - +
729D LEU* 3.3 6.8 + - - +
730D LEU* 3.1 29.4 + - + +
736D LEU* 3.7 18.9 - - + +
741D MET* 4.6 6.3 - - + -
744D LEU* 4.0 20.2 - - + -
745D LEU* 4.1 15.9 - - + -
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Residues in contact with ALA 727 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D ALA* 3.3 28.2 - - + +
573D TYR* 3.5 30.5 - - + -
576D ALA* 3.8 1.8 - - + -
723D VAL 3.2 11.5 + - - +
724D GLU 4.6 0.2 - - - +
726D VAL* 1.3 76.9 - - - +
728D LEU* 1.3 62.2 + - - +
729D LEU 3.3 0.2 - - - -
730D LEU* 3.2 12.5 + - - +
731D LEU* 3.1 31.9 + - - +
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Residues in contact with LEU 728 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D TYR* 4.9 11.4 - - + +
724D GLU* 3.2 42.9 + - + +
725D LYS* 4.3 4.9 - - - +
726D VAL 3.3 0.2 - - - -
727D ALA* 1.3 75.8 - - + +
729D LEU* 1.3 64.1 + - + +
731D LEU* 3.6 19.9 + - + +
732D GLU* 3.4 28.1 + - - +
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Residues in contact with LEU 729 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725D LYS 3.6 9.0 + - - +
726D VAL 3.3 9.0 + - - +
727D ALA 3.3 0.4 - - - -
728D LEU* 1.3 76.4 - - + +
730D LEU* 1.3 57.3 + - - +
732D GLU* 3.4 23.3 - - + +
733D LYS* 2.6 42.3 + - + +
736D LEU* 4.0 20.6 - - + -
740D ASP* 4.8 5.4 - - + +
744D LEU* 3.7 38.6 - - + -
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Residues in contact with LEU 730 (chain D).
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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572D ALA* 3.8 23.6 - - + +
575D GLN* 4.4 0.7 - - + -
576D ALA 4.2 8.3 - - - +
594D VAL* 3.8 28.5 - - + +
596D ILE* 3.5 42.8 - - + +
726D VAL* 3.1 31.1 + - + +
727D ALA* 3.2 11.2 + - - +
729D LEU* 1.3 76.8 - - - +
731D LEU* 1.3 60.7 + - - +
733D LYS 3.3 11.6 - - - +
734D GLU* 3.5 16.7 - - - +
736D LEU* 3.7 24.9 - - + -
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Residues in contact with LEU 731 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D LYS* 3.4 44.0 - - + +
569D LYS* 4.2 20.4 - - + +
572D ALA* 3.8 8.5 - - + -
573D TYR* 6.1 3.6 - - + +
596D ILE* 5.2 4.9 - - + -
727D ALA* 3.1 16.8 + - + +
728D LEU* 4.0 21.8 - - + +
729D LEU 3.2 0.4 - - - -
730D LEU* 1.3 77.7 - - - +
732D GLU* 1.3 63.8 + - + +
734D GLU* 4.7 6.6 - - - +
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Residues in contact with GLU 732 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728D LEU* 3.4 16.5 + - - +
729D LEU* 3.1 27.3 + - + +
731D LEU* 1.3 82.3 - - + +
733D LYS* 1.3 62.0 + - + +
734D GLU* 3.9 13.5 + - - +
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Residues in contact with LYS 733 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729D LEU* 2.6 29.1 + - + +
730D LEU* 3.3 9.0 - - - +
732D GLU* 1.3 74.1 - - + +
734D GLU* 1.3 68.4 + - - +
735D VAL* 3.1 33.0 + - + +
736D LEU* 4.7 4.4 - - + +
740D ASP* 4.1 21.6 + - - +
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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