Contacts of the helix formed by residues 522 - 548 (chain I) 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 LEU 522 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521I SER* 3.8 28.9 - - - +
523I HIS* 3.8 26.0 - - - +
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Residues in contact with HIS 523 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522I LEU* 3.8 25.1 - - - +
524I PHE* 3.8 28.5 - - - +
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Residues in contact with PHE 524 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523I HIS* 3.8 26.2 - - - +
525I VAL* 3.8 29.4 - - - +
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Residues in contact with VAL 525 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524I PHE* 3.8 26.2 - - - +
526I LYS* 3.8 28.7 - - - +
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Residues in contact with LYS 526 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525I VAL* 3.8 29.2 - - - +
527I ARG* 3.9 25.8 - - - +
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Residues in contact with ARG 527 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526I LYS* 3.9 24.5 - - - +
528I ARG* 3.8 28.5 - - - +
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Residues in contact with ARG 528 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527I ARG* 3.8 29.6 - - - +
529I MET* 3.9 25.6 - - - +
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Residues in contact with MET 529 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392I ALA* 4.7 19.7 - - - +
528I ARG* 3.9 26.9 - - - +
530I GLU* 3.8 28.7 - - - +
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Residues in contact with GLU 530 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529I MET* 3.8 28.5 - - - +
531I ASN* 3.8 26.5 - - - +
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Residues in contact with ASN 531 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530I GLU* 3.8 26.7 - - - +
532I ILE* 3.8 28.0 - - - +
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Residues in contact with ILE 532 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531I ASN* 3.8 28.5 - - - +
533I ILE* 3.8 26.0 - - - +
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Residues in contact with ILE 533 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532I ILE* 3.8 28.7 - - - +
534I ASP* 3.8 25.6 - - - +
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Residues in contact with ASP 534 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533I ILE* 3.8 26.5 - - - +
535I GLN* 3.8 28.9 - - - +
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Residues in contact with GLN 535 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534I ASP* 3.8 28.9 - - - +
536I CYS* 3.8 24.7 - - - +
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Residues in contact with CYS 536 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535I GLN* 3.8 26.5 - - - +
537I LEU* 3.8 29.4 - - - +
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Residues in contact with LEU 537 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536I CYS* 3.8 28.9 - - - +
538I GLN* 3.9 26.5 - - - +
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Residues in contact with GLN 538 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537I LEU* 3.9 26.2 - - - +
539I LYS* 3.8 28.5 - - - +
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Residues in contact with LYS 539 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538I GLN* 3.8 28.0 - - - +
540I PRO* 3.9 26.9 - - - -
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Residues in contact with PRO 540 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380I GLY* 4.5 20.9 - - - -
539I LYS* 3.9 26.0 - - - -
541I ALA* 3.8 29.6 - - - -
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Residues in contact with ALA 541 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196I ALA* 4.1 25.8 - - - +
540I PRO* 3.8 28.5 - - - -
542I ASP* 3.8 25.8 - - - +
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Residues in contact with ASP 542 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541I ALA* 3.8 28.3 - - - +
543I VAL* 3.8 26.7 - - - +
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Residues in contact with VAL 543 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542I ASP* 3.8 26.2 - - - +
544I ILE* 3.8 28.3 - - - +
----------------------------------------------------------
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Residues in contact with ILE 544 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543I VAL* 3.8 26.0 - - - +
545I GLY* 3.8 28.7 - - - +
547I SER* 4.6 17.3 - - - +
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Residues in contact with GLY 545 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544I ILE* 3.8 26.5 - - - +
546I LYS* 3.8 29.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 546 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545I GLY* 3.8 28.9 - - - +
547I SER* 3.8 24.7 - - - +
549I ASN* 4.6 16.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 547 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544I ILE* 4.6 18.4 - - - +
546I LYS* 3.8 27.1 - - - +
548I MET* 3.8 28.0 - - - +
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Residues in contact with MET 548 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238I THR* 4.0 27.4 - - - +
547I SER* 3.8 28.7 - - - +
549I ASN* 3.8 27.1 - - - +
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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
------------------------------------------------------------
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