Contacts of the helix formed by residues 563 - 575 (chain A) in PDB entry 1HK3
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 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561A ALA 3.7 0.2 - - - -
562A ASP* 1.3 81.2 - - + +
564A LYS* 1.3 67.0 + - - +
565A GLU* 3.3 8.2 + - - +
566A THR* 2.7 43.8 + - - +
567A CYS* 3.3 4.3 + - - -
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Residues in contact with LYS 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A PHE* 4.1 24.2 - - + -
511A ALA* 5.6 2.0 + - - +
514A CYS* 4.3 19.3 - - - +
515A THR* 5.9 0.6 + - - -
558A CYS 3.4 19.5 - - - +
559A CYS* 3.3 15.4 + - - -
561A ALA* 3.3 32.5 - - + +
562A ASP 3.6 1.8 - - - +
563A ASP* 1.3 71.9 - - - +
565A GLU* 1.3 58.1 + - + +
567A CYS* 2.6 27.9 + - - +
568A PHE* 2.8 17.9 + - + +
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Residues in contact with GLU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A PHE* 3.5 40.2 - - + +
563A ASP* 3.0 10.9 + - - +
564A LYS* 1.3 77.4 - - + +
566A THR* 1.3 49.8 + - - +
568A PHE* 4.0 1.7 - - - +
569A ALA* 2.6 42.5 + - + +
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Residues in contact with THR 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A ASP* 2.7 41.0 + - - -
565A GLU* 1.3 70.1 - - - +
567A CYS* 1.3 58.6 + - - -
569A ALA* 4.2 4.7 - - - -
570A GLU* 2.4 51.2 + - + +
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Residues in contact with CYS 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A LYS* 4.6 2.5 - - - -
558A CYS* 2.0 55.9 - - + +
561A ALA 5.5 5.8 - - - +
563A ASP 3.3 2.9 + - - +
564A LYS* 2.6 20.2 + - - +
566A THR* 1.3 74.5 - - - +
568A PHE* 1.3 56.6 - - - +
570A GLU* 4.7 2.2 - - - -
571A GLU* 2.7 41.6 + - - +
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Residues in contact with PHE 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A PHE 5.9 0.4 - - - -
509A PHE* 3.2 52.9 - + + -
513A ILE* 4.7 1.8 - - + -
514A CYS* 4.2 0.2 - - - -
554A PHE* 3.4 24.6 - + - -
555A VAL* 3.3 53.6 - - + -
558A CYS* 3.3 33.3 - - + -
559A CYS* 3.9 8.1 - - - -
564A LYS* 2.8 18.6 + - + +
565A GLU 4.0 0.9 - - - +
567A CYS* 1.3 73.7 - - - +
569A ALA* 1.3 53.9 + - - +
572A GLY* 2.7 31.2 + - - -
3003A T44 4.0 15.9 - - + -
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Residues in contact with ALA 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A PHE* 5.7 0.4 - - - +
565A GLU* 2.6 27.5 + - + +
566A THR* 3.8 4.0 - - - +
568A PHE* 1.3 70.5 - - - +
570A GLU* 1.3 59.0 + - - +
573A LYS* 2.8 36.3 + - - +
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Residues in contact with GLU 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A THR* 2.4 47.3 + - + +
567A CYS* 4.0 1.6 - - - +
569A ALA* 1.3 71.4 - - - +
571A GLU* 1.3 62.0 + - - +
573A LYS* 3.4 3.8 + - - +
574A LYS* 3.3 17.3 + - - +
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Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A PHE* 3.5 20.7 - - + -
558A CYS* 4.6 2.9 - - - -
567A CYS* 2.7 24.7 + - - +
570A GLU* 1.3 75.0 - - - +
572A GLY* 1.3 60.3 + - - +
574A LYS* 3.1 10.9 - - - +
575A LEU* 3.0 20.4 + - - +
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Residues in contact with GLY 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A PHE* 6.0 1.9 - - - -
554A PHE* 3.8 14.3 - - - -
568A PHE 2.7 27.5 + - - -
571A GLU* 1.3 70.9 - - - +
573A LYS* 1.3 66.8 + - - +
574A LYS 2.9 1.1 - - - -
575A LEU* 2.8 25.7 + - - +
3004A T44 5.3 1.2 - - - +
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Residues in contact with LYS 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A ALA* 2.8 23.2 + - - +
570A GLU* 3.8 4.7 - - - +
572A GLY* 1.3 72.3 - - - +
574A LYS* 1.3 62.2 + - - +
575A LEU 4.3 3.5 - - - -
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Residues in contact with LYS 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A GLU 3.3 9.7 + - - +
571A GLU* 3.1 15.7 + - - +
573A LYS* 1.3 81.7 - - - +
575A LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A PHE* 5.4 4.3 - - - -
550A ASP* 5.9 1.6 - - + -
551A PHE* 3.7 37.2 - - + +
554A PHE* 4.7 21.1 - - + -
571A GLU 3.0 10.5 + - - +
572A GLY* 2.8 23.7 + - - +
573A LYS 4.3 2.9 - - - -
574A LYS* 1.3 77.0 - - - +
3004A T44 3.4 61.3 + - + +
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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