Contacts of the helix formed by residues 565 - 573 (chain D) in PDB entry 2JAZ
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 THR 565 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468D ALA* 3.2 3.2 + - + -
469D GLY* 3.7 19.7 - - - +
529D THR* 4.6 0.4 - - + -
533D ASP* 3.7 37.8 + - + +
541D PHE* 3.6 24.7 - - + -
564D VAL* 1.3 76.9 - - - +
566D PRO* 1.3 68.9 - - - +
567D LYS* 3.7 3.8 + - - +
568D ARG* 3.1 23.4 + - - +
569D HIS* 2.9 27.6 + - - +
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Residues in contact with PRO 566 (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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529D THR* 3.6 16.6 - - + +
533D ASP 3.5 9.0 - - - +
535D SER* 3.9 12.1 - - - +
538D ARG* 3.3 44.6 + - + +
539D THR 4.5 0.4 - - - -
540D SER 3.3 23.8 - - - +
542D GLU* 3.9 18.2 - - - +
565D THR* 1.3 87.6 - - - +
567D LYS* 1.3 61.5 + - - +
569D HIS* 3.2 2.1 + - - +
570D ILE* 3.0 29.1 + - - +
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Residues in contact with LYS 567 (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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469D GLY 6.1 0.7 - - - -
532D GLN* 3.1 29.1 + - - +
533D ASP* 3.3 25.8 + - - +
534D VAL 3.9 9.0 - - - +
535D SER* 4.1 9.5 - - - -
565D THR* 3.3 3.5 - - - +
566D PRO* 1.3 79.9 - - - +
568D ARG* 1.3 62.1 + - - +
570D ILE* 3.5 6.4 + - - +
571D ASP* 3.3 29.2 + - - +
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Residues in contact with ARG 568 (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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468D ALA 3.9 8.1 - - - +
469D GLY* 3.6 35.9 - - - +
470D LYS* 3.8 2.2 - - - +
471D ASP* 2.6 47.4 + - - +
472D LEU* 5.8 0.6 - - - +
564D VAL* 4.7 2.2 - - + -
565D THR* 3.1 18.6 + - - +
567D LYS* 1.3 77.9 - - - +
569D HIS* 1.3 66.6 - - - +
571D ASP* 3.1 18.0 + - - +
572D ILE* 2.9 43.6 + - + +
576D LYS* 2.9 41.2 + - - +
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Residues in contact with HIS 569 (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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538D ARG* 3.6 7.8 + - - +
542D GLU* 2.5 34.8 + - + +
543D LEU 4.2 8.5 - - - -
544D HIS* 3.5 14.6 + + + +
564D VAL* 3.6 11.9 - - + +
565D THR 2.9 19.6 + - - +
566D PRO 3.5 2.2 - - - +
568D ARG* 1.3 76.7 - - - +
570D ILE* 1.3 62.0 + - - +
572D ILE* 3.3 13.6 + - + +
573D HIS* 3.2 20.2 + + - -
600D ZN 2.1 36.0 - - - -
601D PO4 3.5 16.6 + - - -
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Residues in contact with ILE 570 (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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535D SER* 3.0 31.9 - - - +
538D ARG* 3.6 31.6 - - - +
566D PRO 3.0 16.4 + - - +
567D LYS* 3.7 6.1 - - - +
569D HIS* 1.3 77.9 - - - +
571D ASP* 1.3 64.8 + - - +
572D ILE 3.3 0.2 + - - -
573D HIS* 3.4 6.0 + - - +
574D ARG* 3.3 36.0 + - - +
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Residues in contact with ASP 571 (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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567D LYS* 3.3 19.1 + - - +
568D ARG* 3.1 29.6 + - - +
570D ILE* 1.3 81.9 - - - +
572D ILE* 1.3 60.9 + - - +
574D ARG* 2.8 40.4 + - - +
575D GLY 3.3 0.2 + - - -
576D LYS* 2.8 39.5 + - + +
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Residues in contact with ILE 572 (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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471D ASP 3.2 27.8 - - - +
472D LEU* 4.0 24.7 - - + -
544D HIS* 4.0 31.6 - - + +
564D VAL* 4.1 18.4 - - + -
568D ARG* 2.9 29.5 + - + +
569D HIS* 3.5 11.7 - - - +
570D ILE 3.2 0.2 - - - -
571D ASP* 1.3 72.1 - - - +
573D HIS* 1.3 60.5 + - + +
574D ARG 2.9 9.3 + - - -
575D GLY* 3.0 14.7 + - - -
576D LYS 4.1 5.8 + - - -
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Residues in contact with HIS 573 (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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544D HIS* 3.2 15.8 + + - -
545D HIS 5.0 0.7 - - - -
569D HIS* 3.3 31.9 + + - +
570D ILE* 3.4 4.9 + - - +
572D ILE* 1.3 78.6 - - + +
574D ARG* 1.3 57.6 + - - +
575D GLY 3.5 0.9 - - - -
600D ZN 2.0 36.0 - - - -
601D PO4 3.2 14.1 + - - -
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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