Contacts of the helix formed by residues 555 - 579 (chain N) in PDB entry 5KHR
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 HIS 555 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554N MET* 3.8 28.9 - - - +
556N PHE* 3.8 24.5 - - - +
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Residues in contact with PHE 556 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555N HIS* 3.8 28.3 - - - +
557N CYS* 3.9 24.9 - - - +
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Residues in contact with CYS 557 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556N PHE* 3.9 28.3 - - - +
558N GLU* 3.9 26.7 - - - +
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Residues in contact with GLU 558 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557N CYS* 3.9 26.9 - - - +
559N VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 559 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558N GLU* 3.8 29.4 - - - +
560N MET* 3.8 25.6 - - - +
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Residues in contact with MET 560 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559N VAL* 3.8 25.6 - - - +
561N LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 561 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560N MET* 3.8 26.5 - - - +
562N LYS* 3.8 28.7 - - - +
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Residues in contact with LYS 562 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561N LEU* 3.8 28.5 - - - +
563N ASP* 3.9 24.9 - - - +
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Residues in contact with ASP 563 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562N LYS* 3.9 28.3 - - - +
564N MET* 4.4 17.9 - - - +
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Residues in contact with MET 564 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563N ASP* 4.4 19.5 - - - +
565N ALA* 3.9 28.3 - - - +
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Residues in contact with ALA 565 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564N MET* 3.9 26.9 - - - +
566N ASP* 3.8 28.3 - - - +
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Residues in contact with ASP 566 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565N ALA* 3.8 28.5 - - - +
567N SER* 3.8 25.6 - - - +
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Residues in contact with SER 567 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566N ASP* 3.8 24.7 - - - +
568N ARG* 3.8 28.5 - - - +
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Residues in contact with ARG 568 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567N SER* 3.8 29.2 - - - +
569N ARG* 3.8 25.4 - - - +
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Residues in contact with ARG 569 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568N ARG* 3.8 28.5 - - - +
570N ILE* 3.8 27.4 - - - +
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Residues in contact with ILE 570 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569N ARG* 3.8 26.2 - - - +
571N ASN* 3.8 28.7 - - - +
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Residues in contact with ASN 571 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570N ILE* 3.8 26.2 - - - +
572N ALA* 3.8 28.5 - - - +
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Residues in contact with ALA 572 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571N ASN* 3.8 28.7 - - - +
573N ASN* 3.8 26.2 - - - +
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Residues in contact with ASN 573 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572N ALA* 3.8 28.7 - - - +
574N ILE* 3.8 26.7 - - - +
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Residues in contact with ILE 574 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573N ASN* 3.8 28.5 - - - +
575N ARG* 3.9 25.8 - - - +
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Residues in contact with ARG 575 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574N ILE* 3.9 25.8 - - - +
576N GLU* 3.8 28.5 - - - +
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Residues in contact with GLU 576 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575N ARG* 3.8 26.0 - - - +
577N GLU* 3.8 29.2 - - - +
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Residues in contact with GLU 577 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576N GLU* 3.8 28.7 - - - +
578N ASP* 3.9 26.5 - - - +
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Residues in contact with ASP 578 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577N GLU* 3.9 25.1 - - - +
579N GLU* 3.8 28.7 - - - +
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Residues in contact with GLU 579 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578N ASP* 3.8 24.7 - - - +
580N LYS* 3.8 28.5 - - - +
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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
------------------------------------------------------------
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