Contacts of the helix formed by residues 406 - 424 (chain F) in PDB entry 6F0X
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 THR 406 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345F TYR 4.0 15.5 - - - +
405F VAL* 1.3 95.0 - - + +
407F ILE* 1.3 67.5 + - - +
408F GLU* 3.0 17.8 + - - +
409F GLY 3.2 9.5 + - - -
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Residues in contact with ILE 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F LEU* 3.9 33.4 - - + -
339F MET* 3.6 31.2 - - + -
344F ILE* 3.6 22.5 - - + +
345F TYR 4.6 4.9 - - - -
348F GLN* 5.1 14.1 - - + +
350F LEU* 4.5 4.3 - - + -
369F LEU* 4.9 5.2 - - + -
405F VAL 3.5 1.2 + - - -
406F THR* 1.3 73.4 - - - +
408F GLU* 1.3 78.3 + - + +
410F PHE* 2.9 7.7 + - + +
411F LEU* 2.8 49.7 + - + +
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Residues in contact with GLU 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F GLN* 4.7 10.7 - - - +
365F ASN 4.8 11.2 - - - +
368F LYS* 6.5 0.9 - - + -
372F LEU* 5.2 0.2 - - - +
406F THR* 3.3 24.7 + - - +
407F ILE* 1.3 91.0 + - + +
409F GLY* 1.3 62.6 + - - +
411F LEU* 3.1 16.3 + - + +
412F GLN* 3.0 27.8 + - - +
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Residues in contact with GLY 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399F TYR* 5.6 0.2 - - - +
400F VAL* 5.9 0.4 - - - -
405F VAL* 4.5 11.9 - - - -
406F THR* 3.2 11.5 + - - -
408F GLU* 1.3 78.5 - - - +
410F PHE* 1.3 57.2 + - - +
412F GLN* 3.0 23.9 + - - +
413F ALA* 2.9 30.1 + - - +
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Residues in contact with PHE 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F LEU* 3.9 26.7 - - + -
338F LEU* 4.7 2.2 - - + -
344F ILE* 3.4 33.4 - - + -
392F PRO* 3.1 51.6 - - + -
395F ALA* 3.6 8.1 - - + -
396F HIS* 3.5 22.7 - - + -
400F VAL* 4.3 5.8 - - + -
405F VAL* 3.8 16.4 - - + +
406F THR 3.6 3.6 + - - -
407F ILE* 2.9 13.8 + - + +
409F GLY* 1.3 77.0 - - - +
411F LEU* 1.3 64.3 + - + +
413F ALA* 3.3 5.8 - - + +
414F LEU* 2.8 36.4 + - + +
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Residues in contact with LEU 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335F LEU* 4.6 8.5 - - + -
369F LEU* 3.6 33.4 - - + +
372F LEU* 3.4 21.8 - - + -
376F ILE* 3.3 17.8 - - + +
407F ILE* 2.8 39.3 + - + +
408F GLU* 3.1 26.2 + - + +
410F PHE* 1.3 84.2 - - + +
412F GLN* 1.3 62.3 + - - +
414F LEU* 3.2 3.4 + - + -
415F SER* 2.9 23.9 + - - -
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Residues in contact with GLN 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F LEU* 3.8 9.7 - - + +
408F GLU 3.0 12.3 + - - +
409F GLY* 3.0 32.3 + - - +
411F LEU* 1.3 76.0 - - - +
413F ALA* 1.3 55.7 + - - +
415F SER* 3.2 9.8 - - - -
416F LEU* 2.9 39.3 + - + +
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Residues in contact with ALA 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395F ALA* 4.0 11.9 - - + +
399F TYR* 3.5 41.8 - - + -
400F VAL* 5.5 2.5 - - + +
409F GLY 2.9 19.7 + - - +
410F PHE* 3.3 11.0 - - - +
411F LEU 3.1 0.2 - - - -
412F GLN* 1.3 77.6 - - + +
414F LEU* 1.3 58.3 + - - +
416F LEU* 3.1 6.2 + - - +
417F ALA* 2.8 26.9 + - - +
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Residues in contact with LEU 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F TYR* 4.3 22.2 - - + -
376F ILE* 4.3 17.0 - - + -
391F LEU* 3.4 39.7 - - + +
392F PRO* 4.0 26.2 - - + -
395F ALA* 3.4 15.7 - - + +
410F PHE* 2.8 24.0 + - + +
411F LEU* 3.2 4.9 + - + +
413F ALA* 1.3 72.5 - - - +
415F SER* 1.3 65.5 + - - +
417F ALA* 3.9 7.6 - - + -
418F VAL* 2.9 28.1 + - + +
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Residues in contact with SER 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F LEU* 4.2 12.4 - - - +
375F ASP* 4.8 6.1 - - - +
376F ILE* 3.7 24.2 - - - +
411F LEU 2.9 14.2 + - - -
412F GLN* 3.2 15.9 - - - -
414F LEU* 1.3 77.5 - - - +
416F LEU* 1.3 59.7 + - - +
418F VAL* 3.3 3.4 + - - +
419F ASP* 2.8 41.2 + - - +
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Residues in contact with LEU 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398F LEU* 5.6 0.2 - - - -
399F TYR* 3.7 36.1 + - + +
412F GLN* 2.9 20.8 + - + +
413F ALA* 3.6 6.1 - - - +
415F SER* 1.3 76.7 - - - +
417F ALA* 1.3 58.4 + - - +
419F ASP* 3.0 19.9 - - + +
420F LYS* 2.9 27.0 + - - +
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Residues in contact with ALA 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F LEU* 5.1 2.2 - - + +
394F LEU* 5.0 4.7 - - + -
395F ALA* 4.2 11.2 - - - +
398F LEU* 4.2 24.2 - - + -
399F TYR* 4.7 0.4 - - - -
413F ALA 2.8 16.7 + - - +
414F LEU* 3.2 20.8 + - + +
416F LEU* 1.3 76.8 - - - +
418F VAL* 1.3 58.3 + - + +
420F LYS* 3.1 9.5 + - - +
421F GLN* 2.8 33.6 + - + +
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Residues in contact with VAL 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F TYR* 4.6 0.4 - - - +
375F ASP 5.9 0.7 - - - +
376F ILE* 4.1 18.8 - - + +
379F LYS* 3.4 12.6 - - + -
380F SER* 4.1 15.3 - - - +
383F LEU* 4.9 1.6 - - + -
391F LEU* 3.7 31.9 - - + -
414F LEU* 2.9 26.0 + - + +
415F SER* 3.8 3.8 - - - +
417F ALA* 1.3 71.9 - - - +
419F ASP* 1.3 66.5 + - - +
421F GLN* 3.9 7.4 - - + -
422F PHE* 2.9 45.4 + - + -
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Residues in contact with ASP 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F ASP 5.7 0.7 - - - +
379F LYS* 2.8 34.6 + - - +
415F SER* 2.8 34.8 + - - +
416F LEU* 3.0 34.5 - - + +
417F ALA 3.1 0.2 - - - -
418F VAL* 1.3 76.0 - - - +
420F LYS* 1.3 62.9 + - - +
423F GLU* 2.9 25.5 + - - +
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Residues in contact with LYS 420 (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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145A VAL* 5.6 4.4 - - - +
148A HIS* 4.9 14.1 + - - +
317A GLN* 5.8 3.8 + - - +
398F LEU* 5.0 21.0 - - + +
416F LEU 2.9 11.7 + - - +
417F ALA* 3.2 10.3 - - - +
419F ASP* 1.3 74.2 - - - +
421F GLN* 1.3 78.7 + - - +
423F GLU* 2.8 39.8 + - - +
424F GLU* 3.4 15.3 - - + +
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Residues in contact with GLN 421 (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 LEU* 5.4 3.4 - - + -
387F VAL* 4.9 9.2 - - + +
391F LEU* 3.9 23.8 - - + -
394F LEU* 4.2 22.6 - - + +
417F ALA* 2.8 23.7 + - + +
418F VAL* 3.0 9.8 + - - +
420F LYS* 1.3 93.6 - - - +
422F PHE* 1.3 69.7 + - + +
424F GLU* 2.6 57.2 + - - +
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Residues in contact with PHE 422 (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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379F LYS* 3.2 53.2 + - + +
380F SER* 3.7 6.1 - - - -
381F GLU 3.7 10.8 - - - -
382F GLY* 3.8 9.2 - - - -
383F LEU* 3.5 52.0 - - + -
418F VAL* 2.9 25.1 + - + -
419F ASP 3.6 1.8 - - - -
421F GLN* 1.3 80.7 - - + +
423F GLU* 1.3 59.0 + - - +
424F GLU* 3.0 9.6 + - - +
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Residues in contact with GLU 423 (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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379F LYS* 4.6 3.6 - - - +
419F ASP* 2.9 30.6 + - - +
420F LYS* 2.8 22.9 + - - +
422F PHE* 1.3 76.6 - - - +
424F GLU* 1.3 60.7 + - - +
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Residues in contact with GLU 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420F LYS* 3.4 15.9 - - + +
421F GLN* 2.6 60.1 + - - +
422F PHE* 3.0 6.7 - - - +
423F GLU* 1.3 82.2 - - - +
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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