Contacts of the helix formed by residues 730 - 738 (chain D) in PDB entry 4AY6
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 ASP 730 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570A MET* 5.5 4.6 - - - +
1000A LYS* 3.5 49.4 + - + +
728D GLY* 3.2 0.6 - - - -
729D ILE* 1.3 94.1 - - - +
731D LEU* 1.3 64.2 + - - +
732D LYS 3.3 3.3 + - - -
733D ALA* 3.4 14.0 + - + +
734D PHE* 3.3 19.9 + - - +
792D PHE* 4.3 6.6 - - + -
815D ARG* 4.2 12.5 - - - +
816D THR* 5.5 3.0 + - - +
817D ILE* 4.4 9.0 - - + +
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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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707D LYS* 4.7 8.7 - - + +
708D LYS* 4.0 9.0 - - - +
709D ALA* 3.7 23.6 - - + +
726D LEU* 3.5 42.4 - - + +
727D ASN* 4.3 3.6 - - - -
728D GLY* 3.3 21.4 + - - +
729D ILE 3.3 1.0 + - - -
730D ASP* 1.3 77.9 - - - +
732D LYS* 1.3 58.5 + - - +
734D PHE* 3.2 15.5 + - + +
735D LEU* 2.9 40.9 + - + +
765D PRO* 6.0 0.4 - - + -
817D ILE* 4.3 21.0 - - + +
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Residues in contact with LYS 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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707D LYS* 6.2 7.6 - - + +
729D ILE 4.9 2.6 + - - +
730D ASP 3.3 0.8 - - - -
731D LEU* 1.3 78.4 - - - +
733D ALA* 1.3 62.1 + - - +
735D LEU* 3.1 15.9 + - + +
736D ASP* 2.9 51.0 + - - +
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Residues in contact with ALA 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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1000A LYS* 6.0 3.4 - - + -
730D ASP* 3.4 15.2 + - + +
732D LYS* 1.3 79.0 - - - +
734D PHE* 1.3 58.7 + - - +
736D ASP* 3.5 12.9 + - - +
737D SER* 3.3 15.4 + - - -
792D PHE* 3.5 21.4 - - + -
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Residues in contact with PHE 734 (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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726D LEU* 4.6 9.6 - - + -
730D ASP 3.3 3.3 + - - +
731D LEU* 3.2 18.5 + - + +
733D ALA* 1.3 76.3 - - - +
735D LEU* 1.3 69.4 + - + +
737D SER* 2.7 25.4 + - - -
738D LEU* 3.5 30.5 + - + +
767D ILE* 4.5 11.2 - - + -
772D ILE* 5.1 4.5 - - + -
776D VAL* 5.8 2.7 - - + -
789D ILE* 3.4 41.7 - - + -
792D PHE* 3.6 35.8 - + + -
794D ILE* 4.2 18.6 - - + -
817D ILE* 3.7 26.7 - - + -
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Residues in contact with LEU 735 (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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709D ALA* 4.1 15.9 - - + -
731D LEU* 2.9 29.0 + - + +
732D LYS* 3.1 14.8 + - + +
734D PHE* 1.3 81.8 - - + +
736D ASP* 1.3 63.9 + - - +
738D LEU* 3.2 25.2 + - + +
741D VAL* 3.4 23.9 - - + +
743D ILE* 5.9 0.7 - - + -
765D PRO* 3.4 34.5 - - + -
767D ILE* 3.8 35.0 - - + -
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Residues in contact with ASP 736 (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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732D LYS* 2.9 43.6 + - - +
733D ALA* 3.6 12.7 - - - +
734D PHE 3.1 0.4 - - - -
735D LEU* 1.3 77.1 - - - +
737D SER* 1.3 62.8 + - - +
738D LEU 3.5 4.8 + - - +
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Residues in contact with SER 737 (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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733D ALA 3.3 6.4 + - - -
734D PHE* 2.7 26.2 + - - -
736D ASP* 1.3 76.5 - - - +
738D LEU* 1.3 61.0 + - - +
739D PRO* 4.0 2.8 - - - +
790D ASN* 2.8 36.0 + - - +
792D PHE* 4.0 18.4 - - - -
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Residues in contact with LEU 738 (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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734D PHE* 3.5 31.4 - - + +
735D LEU* 3.2 24.6 + - + +
736D ASP 3.9 5.0 - - - +
737D SER* 1.3 90.7 + - - +
739D PRO* 1.3 76.7 - - + +
740D ASP 3.6 1.1 + - - +
741D VAL* 3.9 11.4 - - + +
767D ILE* 3.7 42.8 - - + -
772D ILE* 3.9 32.3 - - + -
789D ILE* 4.7 0.2 - - + -
790D ASN* 4.2 7.9 - - - +
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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