Contacts of the helix formed by residues 537 - 548 (chain F) in PDB entry 5KRA
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 SER 537 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347F THR 5.9 0.6 + - - -
351F ASP* 2.6 42.4 + - - +
536F LEU* 1.3 77.8 - - - +
538F ASP* 1.3 60.6 + - - +
539F LEU 3.7 1.4 + - - -
540F LEU* 3.1 25.4 + - - +
541F LEU* 2.9 26.9 + - - +
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Residues in contact with ASP 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536F LEU 4.5 3.6 - - - +
537F SER* 1.3 76.0 - - - +
539F LEU* 1.3 57.9 + - - +
541F LEU* 3.4 14.2 + - - +
542F GLU* 3.0 34.2 + - + +
689H ILE* 3.8 18.3 - - + +
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Residues in contact with LEU 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351F ASP* 4.0 17.9 - - - +
354F LEU* 4.2 28.9 - - + -
355F VAL* 4.5 8.7 - - + -
358F ILE* 4.2 7.4 - - + -
537F SER* 3.3 1.0 + - - -
538F ASP* 1.3 78.6 - - - +
540F LEU* 1.3 58.7 + - - +
542F GLU* 3.3 5.2 + - + +
543F MET* 3.0 51.0 + - + +
689H ILE* 3.6 31.6 - - + +
690H LEU* 4.1 15.9 - - + +
693H LEU* 4.0 22.0 - - + -
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Residues in contact with LEU 540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F THR* 3.8 29.8 - - + +
350F ALA* 4.7 6.3 - - + -
351F ASP* 4.7 10.8 - - - +
354F LEU* 3.7 16.2 - - + -
383F TRP* 3.6 37.3 - - + -
525F LEU* 5.4 6.5 - - + +
536F LEU* 4.2 25.8 - - + -
537F SER* 3.1 28.1 + - - +
539F LEU* 1.3 76.8 - - - +
541F LEU* 1.3 58.3 + - - +
543F MET* 3.4 3.8 + - - +
544F LEU* 3.0 28.6 + - - +
601F 6WT 5.0 4.0 - - + -
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Residues in contact with LEU 541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529F LYS* 4.2 35.7 - - + +
536F LEU* 3.8 45.1 - - + +
537F SER 2.9 17.7 + - - +
538F ASP* 3.7 13.7 - - - +
539F LEU 3.2 0.2 - - - -
540F LEU* 1.3 76.6 - - - +
542F GLU* 1.3 58.0 + - + +
544F LEU* 3.3 6.5 + - + +
545F ASP* 2.9 36.9 + - - +
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Residues in contact with GLU 542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380F GLU* 5.1 0.6 - - - +
538F ASP* 3.0 19.0 + - + +
539F LEU* 3.7 7.0 - - + +
541F LEU* 1.3 75.2 - - + +
543F MET* 1.3 65.2 + - + +
545F ASP* 3.4 8.8 + - - +
546F ALA* 3.2 21.0 + - - +
687H HIS* 3.2 37.2 - - + +
688H LYS* 3.5 20.3 + - - -
689H ILE* 3.2 38.0 + - - +
690H LEU 4.5 0.5 + - - -
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Residues in contact with MET 543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F LEU* 4.0 19.7 - - + -
358F ILE* 6.0 0.7 - - + -
379F LEU* 3.6 16.4 - - + +
380F GLU* 4.0 11.8 - - - +
383F TRP* 3.4 56.0 + - + +
539F LEU* 3.0 38.1 + - + +
540F LEU* 3.8 4.7 - - - +
542F GLU* 1.3 76.7 - - - +
544F LEU* 1.3 64.2 + - - +
546F ALA* 3.3 17.7 + - - +
547F HIS* 3.7 16.1 - - - -
687H HIS* 6.4 0.9 - - - -
690H LEU* 3.7 30.7 - - + -
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Residues in contact with LEU 544 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F TRP* 4.7 2.4 - - + -
522F MET* 3.6 43.3 - - + +
525F LEU* 3.4 39.3 - - + +
526F TYR* 3.8 17.9 - - + +
529F LYS* 4.1 21.8 - - + -
536F LEU* 4.8 4.0 - - + -
540F LEU 3.0 18.8 + - - +
541F LEU* 3.5 13.0 - - + +
542F GLU 3.2 0.2 - - - -
543F MET* 1.3 77.4 - - - +
545F ASP* 1.3 64.2 + - - +
547F HIS* 3.4 10.9 + - - +
548F ARG* 3.6 13.5 + - + +
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Residues in contact with ASP 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529F LYS* 4.4 22.1 + - - +
541F LEU* 2.9 19.9 + - - +
542F GLU* 3.7 10.0 - - - +
543F MET 3.3 0.2 - - - -
544F LEU* 1.3 80.1 - - - +
546F ALA* 1.3 62.2 + - - +
547F HIS 3.2 0.9 + - - -
548F ARG* 3.5 7.2 + - - +
549F LEU* 3.4 30.1 + - + +
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Residues in contact with ALA 546 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380F GLU* 3.6 44.2 - - + +
542F GLU 3.2 12.2 + - - +
543F MET 3.5 11.7 - - - +
544F LEU 3.2 0.6 - - - -
545F ASP* 1.3 78.3 - - - +
547F HIS* 1.3 61.5 + - - +
549F LEU* 3.9 16.1 + - - +
687H HIS 5.8 1.1 - - - +
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Residues in contact with HIS 547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516E HIS* 4.9 15.5 - + - -
520E LYS* 3.2 28.8 + - - +
380F GLU 2.7 29.5 + - - -
381F CYS* 3.7 27.5 + - - -
383F TRP* 3.9 3.8 + - - -
384F LEU 6.0 0.2 + - - -
518F SER* 5.3 2.2 - - - -
519F ASN* 5.2 6.0 + - - -
522F MET* 3.4 52.1 - - + +
543F MET 3.7 11.7 - - - -
544F LEU 3.4 7.0 + - - +
545F ASP 3.1 0.6 - - - -
546F ALA* 1.3 77.9 - - - +
548F ARG* 1.3 58.7 + - + +
549F LEU 3.0 11.6 + - - -
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Residues in contact with ARG 548 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520E LYS* 4.9 4.0 - - - +
523E GLU* 4.9 5.7 + - - -
522F MET* 6.3 1.1 - - + -
523F GLU* 3.1 30.3 + - - +
526F TYR* 3.6 65.2 + - + +
544F LEU* 3.6 11.5 + - + +
545F ASP* 3.5 8.0 + - - +
547F HIS* 1.3 77.4 - - + +
549F LEU* 1.3 61.4 + - - +
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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