Contacts of the helix formed by residues 735 - 744 (chain D) in PDB entry 1JFZ
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 PHE 735 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683D LEU* 3.7 44.2 - - + -
686D LYS* 3.7 22.9 - - + -
687D LEU* 4.0 13.2 - - + -
709D PHE* 3.8 17.5 - + - -
713D TRP* 3.5 32.5 - + - -
731D PHE* 2.9 42.3 + + + +
732D TYR* 4.9 0.2 - - - -
734D LEU* 1.3 109.6 - - + +
736D LYS* 1.3 64.0 + - - +
737D GLU 3.4 1.8 - - - -
738D ASP* 3.5 8.7 + - - +
739D ILE* 2.8 32.1 + - + +
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Residues in contact with LYS 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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654D LEU* 3.8 29.4 - - + +
657D GLN* 5.8 0.6 - - - +
658D TYR* 3.3 39.0 + - - -
732D TYR* 2.8 43.4 + - + +
733D LYS 4.8 0.2 - - - -
734D LEU 3.8 0.6 - - - -
735D PHE* 1.3 77.4 - - - +
737D GLU* 1.3 62.5 + - - +
739D ILE* 3.1 4.2 + - - +
740D LEU* 2.8 48.8 + - + +
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Residues in contact with GLU 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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734D LEU 6.2 0.2 - - - +
735D PHE 3.4 0.2 - - - -
736D LYS* 1.3 83.0 - - - +
738D ASP* 1.3 57.9 + - - +
740D LEU* 3.3 23.9 + - - +
741D SER* 2.8 35.9 + - - -
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Residues in contact with ASP 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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679D PHE* 4.4 6.1 - - + -
683D LEU* 4.5 14.3 - - + +
686D LYS* 2.8 41.9 + - - +
734D LEU 3.5 12.3 - - - +
735D PHE* 3.6 9.6 - - - +
736D LYS 3.1 0.4 - - - -
737D GLU* 1.3 77.9 - - - +
739D ILE* 1.3 60.6 + - - +
741D SER* 3.4 5.9 + - - -
742D ALA* 2.9 32.0 + - - +
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Residues in contact with ILE 739 (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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651D ILE* 3.8 29.8 - - + +
654D LEU* 4.2 22.7 - - + -
674D LEU* 3.7 28.7 - - + +
679D PHE* 4.0 24.0 - - + -
731D PHE* 4.1 19.7 - - + -
735D PHE* 2.8 28.6 + - + +
736D LYS 3.6 4.0 - - - +
738D ASP* 1.3 75.0 - - - +
740D LEU* 1.3 52.7 + - - +
742D ALA* 3.3 1.8 + - - +
743D ILE* 2.6 48.9 + - + +
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Residues in contact with LEU 740 (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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654D LEU* 3.9 16.4 - - + -
658D TYR* 3.4 61.4 - - + +
736D LYS* 2.8 29.7 + - + +
737D GLU* 3.5 26.5 - - - +
739D ILE* 1.3 78.5 - - - +
741D SER* 1.3 62.2 + - - +
743D ILE* 3.5 20.8 + - + +
744D LYS* 3.7 6.2 + - - +
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Residues in contact with SER 741 (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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737D GLU 2.8 19.0 + - - -
738D ASP* 3.6 7.0 + - - -
740D LEU* 1.3 71.4 - - - +
742D ALA* 1.3 69.3 + - - +
744D LYS* 3.1 20.5 + - - +
745D GLU* 5.4 0.7 - - - +
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Residues in contact with ALA 742 (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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673D TYR* 4.4 10.3 - - + -
674D LEU* 3.8 17.7 - - + -
679D PHE* 4.1 12.8 - - + -
738D ASP 2.9 17.0 + - - +
739D ILE 3.5 3.6 - - - +
741D SER* 1.3 81.3 + - - +
743D ILE* 1.3 56.1 + - - +
744D LYS 3.0 1.4 + - - -
745D GLU* 3.2 4.4 + - - +
746D GLY* 2.7 34.7 + - - +
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Residues in contact with ILE 743 (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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654D LEU 4.4 0.2 - - - -
655D LEU* 3.9 28.7 - - + +
658D TYR* 2.9 52.7 - - + +
659D SER* 4.2 6.5 - - - -
660D PRO* 4.5 7.4 - - + +
666D PHE* 5.2 2.3 - - - -
670D LEU* 2.9 36.9 - - + +
674D LEU* 4.1 10.7 - - + +
739D ILE* 2.6 32.0 + - + +
740D LEU* 3.5 18.4 - - + +
742D ALA* 1.3 73.4 - - - +
744D LYS* 1.3 60.6 + - + +
745D GLU 2.7 8.0 + - - -
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Residues in contact with LYS 744 (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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658D TYR 5.5 0.8 + - - -
660D PRO* 3.2 37.2 - - + +
740D LEU 3.7 6.0 + - - +
741D SER* 3.1 14.7 + - - +
742D ALA 3.0 2.9 + - - -
743D ILE* 1.3 80.5 - - + +
745D GLU* 1.3 64.5 + - - +
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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