Contacts of the helix formed by residues 452 - 478 (chain F) in PDB entry 5L9U
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 PHE 452 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451F ALA* 3.9 25.4 - - - +
453F ASN* 3.8 28.9 - - - +
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Residues in contact with ASN 453 (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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452F PHE* 3.8 28.7 - - - +
454F LEU* 3.8 24.9 - - - +
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Residues in contact with LEU 454 (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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453F ASN* 3.8 27.8 - - - +
455F GLN* 3.9 26.9 - - - +
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Residues in contact with GLN 455 (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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454F LEU* 3.9 26.0 - - - +
456F LYS* 3.8 28.7 - - - +
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Residues in contact with LYS 456 (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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455F GLN* 3.8 29.2 - - - +
457F ALA* 3.9 27.4 - - - +
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Residues in contact with ALA 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456F LYS* 3.9 28.5 - - - +
458F ALA* 3.8 28.3 - - - +
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Residues in contact with ALA 458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457F ALA* 3.8 28.5 - - - +
459F ALA* 3.9 25.6 - - - +
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Residues in contact with ALA 459 (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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458F ALA* 3.9 25.8 - - - +
460F GLU* 3.8 28.9 - - - +
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Residues in contact with GLU 460 (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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459F ALA* 3.8 25.4 - - - +
461F GLY* 3.8 29.2 - - - +
463F MET* 4.7 17.3 - - - +
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Residues in contact with GLY 461 (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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460F GLU* 3.8 25.4 - - - +
462F LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 462 (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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461F GLY* 3.8 28.5 - - - +
463F MET* 3.8 25.4 - - - +
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Residues in contact with MET 463 (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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460F GLU* 4.7 14.4 - - - +
462F LEU* 3.8 28.7 - - - +
464F SER* 3.9 25.6 - - - +
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Residues in contact with SER 464 (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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463F MET* 3.9 26.2 - - - +
465F LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 465 (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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464F SER* 3.8 25.8 - - - +
466F LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 466 (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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465F LEU* 3.8 29.2 - - - +
467F ARG* 3.8 25.6 - - - +
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Residues in contact with ARG 467 (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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466F LEU* 3.8 26.9 - - - +
468F GLU* 3.8 28.5 - - - +
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Residues in contact with GLU 468 (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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467F ARG* 3.8 24.9 - - - +
469F MET* 3.8 28.9 - - - +
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Residues in contact with MET 469 (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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468F GLU* 3.8 26.7 - - - +
470F GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 470 (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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469F MET* 3.8 29.4 - - - +
471F LYS* 3.8 26.9 - - - +
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Residues in contact with LYS 471 (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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470F GLY* 3.8 25.6 - - - +
472F GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 472 (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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471F LYS* 3.8 27.4 - - - +
473F TYR* 3.8 28.9 - - - +
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Residues in contact with TYR 473 (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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472F GLY* 3.8 28.9 - - - +
474F LEU* 3.8 26.0 - - - +
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Residues in contact with LEU 474 (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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473F TYR* 3.8 25.8 - - - +
475F ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 475 (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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474F LEU* 3.8 28.5 - - - +
476F LEU* 3.8 26.0 - - - +
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Residues in contact with LEU 476 (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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475F ALA* 3.8 26.0 - - - +
477F CYS* 3.8 29.6 - - - +
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Residues in contact with CYS 477 (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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476F LEU* 3.8 29.2 - - - +
478F SER* 3.9 25.1 - - - +
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Residues in contact with SER 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477F CYS* 3.9 28.7 - - - +
479F TYR* 3.9 24.5 - - - +
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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
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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