Contacts of the helix formed by residues 367 - 379 (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 SER 367 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351F LEU* 3.4 10.8 - - - +
356F LEU* 5.0 1.6 - - - -
359F ILE* 3.7 23.0 - - - +
361F PHE* 4.8 3.1 - - - -
362F ILE 3.1 30.5 + - - -
363F GLU* 3.8 8.7 + - - +
364F ASN* 3.2 13.1 + - - -
366F VAL* 1.3 76.7 - - - +
368F LYS* 1.3 62.0 + - - +
369F LEU* 4.9 0.7 - - - -
370F SER* 2.9 30.1 + - - +
371F LEU* 4.2 0.9 + - - +
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Residues in contact with LYS 368 (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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363F GLU* 4.5 22.4 - - + +
364F ASN 3.4 15.2 + - - +
365F ASN 4.9 4.0 - - - +
366F VAL 2.9 2.2 + - - +
367F SER* 1.3 76.7 - - - +
369F LEU* 1.3 65.8 + - - +
371F LEU* 3.0 17.9 + - + +
372F LEU* 3.0 27.9 + - + +
408F GLU* 6.5 0.9 - - + -
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Residues in contact with LEU 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328F PHE* 4.4 24.2 - - + -
335F LEU* 5.1 4.9 - - + -
350F LEU* 4.8 11.9 - - + -
351F LEU* 4.1 19.5 - - + +
356F LEU* 5.5 1.3 - - + -
366F VAL* 2.8 43.0 + - + +
367F SER* 4.3 1.3 - - - +
368F LYS* 1.3 73.3 - - - +
370F SER* 1.3 52.5 + - - +
372F LEU* 2.9 6.8 + - + -
373F LEU* 2.2 41.9 + - - +
407F ILE* 4.9 7.9 - - + -
411F LEU* 3.6 42.1 - - + +
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Residues in contact with SER 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356F LEU* 3.1 38.6 - - - +
361F PHE* 5.8 4.6 - - - -
367F SER* 2.9 16.9 + - - -
369F LEU* 1.3 75.3 - - - +
371F LEU* 1.3 58.3 + - - -
373F LEU* 2.8 16.9 - - - +
374F ASN* 2.4 38.4 + - - +
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Residues in contact with LEU 371 (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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363F GLU* 3.1 42.6 - - + +
367F SER 5.3 0.7 - - - +
368F LYS* 3.0 15.2 + - + +
370F SER* 1.3 81.4 - - - +
372F LEU* 1.3 52.8 + - - +
374F ASN* 2.9 16.4 + - + +
375F ASP* 2.4 44.3 + - - +
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Residues in contact with LEU 372 (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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368F LYS* 3.0 27.2 + - + +
369F LEU* 2.9 9.3 + - + +
371F LEU* 1.3 73.3 - - - +
373F LEU* 1.3 55.0 + - - +
375F ASP* 3.0 28.3 + - + +
376F ILE* 2.4 50.7 + - + +
408F GLU 5.2 0.7 - - - +
411F LEU* 3.4 46.4 - - + -
412F GLN* 3.8 7.2 - - + +
415F SER* 4.2 17.0 - - - +
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Residues in contact with LEU 373 (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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324F ALA* 3.9 13.5 - - + +
328F PHE* 3.4 58.8 - - + +
331F TYR* 3.9 16.2 - - + -
353F LEU* 4.7 3.4 - - + -
356F LEU* 4.7 7.6 - - + -
369F LEU* 2.2 29.5 + - + +
370F SER* 2.8 21.3 - - - +
372F LEU* 1.3 65.2 - - - +
374F ASN* 1.3 49.3 + - + +
376F ILE* 2.9 7.6 + - - +
377F SER* 2.3 59.8 + - - +
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Residues in contact with ASN 374 (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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324F ALA* 5.5 1.8 - - + -
370F SER 2.4 21.3 + - - +
371F LEU* 3.2 20.9 - - + +
373F LEU* 1.3 74.1 - - + +
375F ASP* 1.3 50.8 + - - +
377F SER* 3.8 9.2 - - - +
378F ARG* 2.2 54.4 + - - +
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Residues in contact with ASP 375 (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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371F LEU* 2.4 32.2 + - - +
372F LEU* 3.0 43.3 + - + +
374F ASN* 1.3 67.2 - - - +
376F ILE* 1.3 55.1 + - + +
378F ARG* 2.9 52.7 + - - +
379F LYS* 4.3 4.3 + - - +
415F SER* 4.8 6.1 - - - +
418F VAL* 5.9 0.9 - - - +
419F ASP* 5.7 0.7 - - - +
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Residues in contact with ILE 376 (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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327F ILE* 4.4 0.2 - - - +
331F TYR* 3.2 38.4 + - + +
372F LEU* 2.4 48.6 + - + +
373F LEU* 2.9 6.5 - - - +
375F ASP* 1.3 65.3 - - - +
377F SER* 1.3 51.4 + - - +
380F SER* 2.1 28.0 + - - -
411F LEU* 3.3 33.4 - - + +
414F LEU* 4.3 12.8 - - + -
415F SER* 3.7 24.2 - - - +
418F VAL* 4.1 22.9 - - + -
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Residues in contact with SER 377 (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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324F ALA* 3.7 28.7 - - - +
327F ILE* 3.8 14.0 - - - +
373F LEU* 2.3 47.6 + - - +
374F ASN* 2.9 10.7 - - - +
376F ILE* 1.3 74.6 + - - +
378F ARG* 1.3 65.5 + - - +
379F LYS 3.5 1.6 - - - -
380F SER* 3.2 16.0 + - - -
381F GLU* 4.4 3.3 + - - +
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Residues in contact with ARG 378 (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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374F ASN* 2.2 36.8 + - - +
375F ASP* 2.9 37.8 + - - +
377F SER* 1.3 73.5 - - - +
379F LYS* 1.3 63.1 + - + +
381F GLU* 4.7 6.8 + - - +
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Residues in contact with LYS 379 (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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375F ASP 4.3 3.3 + - - +
378F ARG* 1.3 81.5 - - + +
380F SER* 1.3 61.4 + - - +
381F GLU* 3.0 13.9 + - - +
418F VAL* 3.4 24.0 - - + -
419F ASP* 2.8 48.3 + - - +
422F PHE* 3.2 47.5 + - + +
423F GLU* 4.0 3.6 - - - +
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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