Contacts of the helix formed by residues 688 - 693 (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 GLU 688 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610D LYS* 3.1 20.7 + - - +
684D ALA 2.6 11.6 + - - -
685D GLN* 3.0 18.9 + - - +
686D LYS 4.6 0.4 - - - +
687D LEU* 1.3 77.2 - - - +
689D LEU* 1.3 55.9 + - - +
690D HIS* 3.1 12.3 - - + -
691D LYS* 2.5 66.7 + - - +
692D PHE* 3.0 18.6 - - + -
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Residues in contact with LEU 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607D LEU* 3.3 34.3 - - + -
625D LEU* 4.2 9.0 - - + -
684D ALA* 3.4 22.4 + - + -
687D LEU* 3.2 17.1 - - + -
688D GLU* 1.3 76.7 - - - +
690D HIS* 1.3 63.9 + - - +
691D LYS 3.0 1.6 + - - -
692D PHE* 3.0 11.0 + - + +
693D ILE* 2.9 21.7 + - + +
705D ILE* 4.4 7.2 - - + +
708D VAL* 3.3 32.8 - - + +
709D PHE* 3.7 26.0 - - + +
712D LEU* 3.9 12.6 - - + -
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Residues in contact with HIS 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D ALA* 5.6 1.2 - - - +
685D GLN* 3.9 25.1 + - + -
688D GLU* 4.4 15.1 - - + -
689D LEU* 1.3 79.2 + - - +
691D LYS* 1.3 89.1 + - + +
693D ILE* 3.6 21.5 - - - +
700D ILE* 3.9 18.4 - - + +
705D ILE* 3.6 28.1 - - + +
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Residues in contact with LYS 691 (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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603D MET 5.4 3.3 - - - +
688D GLU* 2.5 44.2 + - + +
690D HIS* 1.3 107.0 - - + +
692D PHE* 1.3 67.8 + - + +
693D ILE 3.2 6.6 + - - +
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Residues in contact with PHE 692 (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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602D LYS 5.6 0.9 - - - -
603D MET 4.9 7.6 - - - -
604D LEU 3.0 29.6 - - - -
605D GLU* 4.7 2.5 - - - -
606D GLN* 4.2 3.4 - - + -
607D LEU* 3.9 29.8 - - + -
610D LYS* 4.2 16.8 - - + -
625D LEU* 3.0 48.5 - - + +
687D LEU 3.1 24.5 - - - -
688D GLU* 3.0 34.5 - - + -
689D LEU* 3.0 6.2 + - - +
691D LYS* 1.3 83.1 - - + +
693D ILE* 1.3 61.9 + - - +
694D ARG* 3.5 6.1 + - - +
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Residues in contact with ILE 693 (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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625D LEU* 3.6 14.6 - - + +
627D HIS* 5.3 0.7 - - + -
689D LEU* 2.9 26.5 - - + +
690D HIS* 3.6 22.4 - - - +
691D LYS 3.2 3.3 - - - +
692D PHE* 1.3 77.1 - - - +
694D ARG* 1.3 63.5 + - - +
695D ILE* 3.3 32.0 + - + +
700D ILE* 4.4 4.7 - - + +
704D ILE* 3.9 17.5 - - + -
705D ILE* 5.0 9.9 - - + -
708D VAL* 3.3 42.6 - - + -
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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