Contacts of the helix formed by residues 409 - 428 (chain C) 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 GLY 409 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C VAL* 5.4 4.0 - - - -
406C THR* 3.8 1.9 + - - -
407C ILE 3.1 5.7 + - - -
408C GLU* 1.3 75.7 - - - +
410C PHE* 1.3 61.2 + - - +
411C LEU 3.1 2.2 - - - -
412C GLN* 3.3 20.0 + - - +
413C ALA* 2.8 30.8 + - - +
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Residues in contact with PHE 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 3.8 24.0 - - + -
338C LEU* 4.0 19.3 - - + -
344C ILE* 4.1 16.6 - - + -
392C PRO* 4.1 31.2 - - + -
395C ALA* 5.5 2.7 - - + -
396C HIS* 4.4 19.1 - + + -
400C VAL* 4.1 17.7 - - + -
405C VAL* 4.3 13.1 - - + +
406C THR 3.1 26.5 + - - +
407C ILE* 3.9 6.3 - - + +
408C GLU 4.1 0.2 - - - +
409C GLY* 1.3 77.2 - - - +
411C LEU* 1.3 69.3 + - + +
413C ALA* 3.1 8.2 - - + +
414C LEU* 2.9 35.9 + - + +
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Residues in contact with LEU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 5.0 11.2 - - + -
369C LEU* 4.0 38.6 - - + +
372C LEU* 4.6 15.3 - - + -
373C LEU* 4.3 13.9 - - + -
376C ILE* 4.0 25.6 - - + +
407C ILE* 4.5 12.8 - - + -
408C GLU* 4.3 22.0 - - - +
409C GLY 3.1 0.8 - - - +
410C PHE* 1.3 86.8 - - + +
412C GLN* 1.3 67.9 + - - +
413C ALA 3.0 1.3 - - - -
414C LEU* 2.9 11.6 + - + +
415C SER* 2.9 19.8 + - - -
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Residues in contact with GLN 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C LEU* 4.9 12.1 - - + +
408C GLU 4.0 9.9 + - - +
409C GLY* 3.3 25.8 + - - +
411C LEU* 1.3 77.8 - - - +
413C ALA* 1.3 59.8 + - - +
415C SER* 3.2 11.4 + - - -
416C LEU* 2.9 40.6 + - + +
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Residues in contact with ALA 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395C ALA* 4.7 7.4 - - + +
399C TYR* 4.4 23.7 - - + -
400C VAL* 5.1 12.1 - - + +
409C GLY 2.8 21.0 + - - +
410C PHE* 3.1 12.6 - - + +
411C LEU 3.0 0.2 - - - -
412C GLN* 1.3 75.7 - - - +
414C LEU* 1.3 65.8 + - - +
416C LEU* 3.2 12.0 + - - +
417C ALA* 2.9 22.3 + - - +
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Residues in contact with LEU 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C TYR* 3.5 46.0 - - + +
373C LEU* 5.2 2.7 - - + -
376C ILE* 3.9 14.4 - - + -
391C LEU* 3.6 32.1 - - + -
392C PRO* 4.2 15.9 - - + -
395C ALA* 4.5 9.5 - - + +
410C PHE* 2.9 24.4 + - + +
411C LEU* 3.3 12.3 - - + +
413C ALA* 1.3 74.8 - - - +
415C SER* 1.3 56.4 + - - +
417C ALA* 3.1 6.4 + - + +
418C VAL* 2.9 31.1 + - + +
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Residues in contact with SER 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C LEU* 6.5 1.6 - - - -
376C ILE* 4.6 9.8 - - - +
379C LYS* 2.0 41.9 + - - +
411C LEU 2.9 11.3 + - - -
412C GLN* 3.2 15.9 - - - -
414C LEU* 1.3 77.1 - - - +
416C LEU* 1.3 64.9 + - - +
418C VAL* 3.1 6.1 + - - +
419C ASP* 2.9 30.9 + - - +
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Residues in contact with LEU 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C TYR* 4.6 28.7 + - + -
412C GLN* 2.9 29.2 + - + +
413C ALA* 3.6 10.1 - - - +
415C SER* 1.3 76.6 - - - +
417C ALA* 1.3 61.7 + - - +
419C ASP* 3.3 17.1 + - + +
420C LYS* 2.9 23.4 + - - +
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Residues in contact with ALA 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C LEU* 4.4 13.0 - - + -
395C ALA* 3.9 23.8 - - + -
398C LEU* 5.1 8.3 - - + -
399C TYR* 4.7 10.0 - - + -
413C ALA 2.9 13.5 + - - +
414C LEU* 3.1 11.4 + - + +
416C LEU* 1.3 76.1 - - - +
418C VAL* 1.3 58.0 + - - +
420C LYS* 3.1 10.9 + - - +
421C GLN* 2.9 30.8 + - - +
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Residues in contact with VAL 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C TYR* 3.8 10.8 - - - +
376C ILE* 4.9 1.8 - - + -
379C LYS* 4.6 7.9 - - + +
380C SER* 3.9 19.5 - - - +
383C LEU* 3.9 11.9 - - + -
391C LEU* 3.6 27.4 - - + -
414C LEU* 2.9 25.5 + - + +
415C SER* 3.7 5.8 - - - +
417C ALA* 1.3 72.6 - - - +
419C ASP* 1.3 68.0 + - - +
421C GLN* 2.9 8.3 + - - +
422C PHE* 2.9 46.5 + - + -
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Residues in contact with ASP 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C LYS* 4.3 15.9 + - - +
415C SER* 2.9 30.9 + - - +
416C LEU* 3.4 21.5 - - + +
418C VAL* 1.3 77.1 - - - +
420C LYS* 1.3 63.2 + - - +
422C PHE* 3.3 8.3 + - - +
423C GLU* 3.0 36.3 + - - +
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Residues in contact with LYS 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C LEU* 4.1 36.2 - - + +
399C TYR* 4.2 20.0 + - + +
416C LEU 2.9 12.7 + - - +
417C ALA* 3.1 11.4 + - - +
419C ASP* 1.3 77.4 - - - +
421C GLN* 1.3 58.5 + - + +
423C GLU* 3.2 10.1 + - + +
424C GLU* 2.8 64.0 + - + +
143D VAL* 5.8 6.3 - - - +
148D HIS* 4.8 12.9 + - - +
315D ILE* 5.9 4.4 - - - +
316D LYS 5.4 1.9 + - - -
317D GLN* 4.8 13.1 + - - -
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Residues in contact with GLN 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C LEU* 4.5 16.2 - - + -
387C VAL* 3.5 25.6 - - + +
391C LEU* 3.7 24.0 - - + +
398C LEU* 5.9 4.6 - - - +
417C ALA 2.9 18.1 + - - +
418C VAL* 2.9 10.3 + - - +
420C LYS* 1.3 77.7 - - - +
422C PHE* 1.3 62.7 + - - +
424C GLU* 2.9 28.1 + - - +
425C ARG* 3.0 33.6 + - - +
313D ALA 5.1 5.9 + - - +
314D ASP 4.4 15.4 + - - -
315D ILE* 5.8 0.2 - - - +
316D LYS* 5.5 5.7 - - - +
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Residues in contact with PHE 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C LYS 3.1 27.1 - - - -
380C SER 3.7 0.7 - - - -
381C GLU 3.7 14.8 - - - -
382C GLY* 4.2 7.2 - - - -
383C LEU* 3.4 45.3 - - + -
418C VAL* 2.9 32.6 + - + -
419C ASP* 3.8 9.2 - - - +
421C GLN* 1.3 76.8 - - - +
423C GLU* 1.3 65.3 + - + +
424C GLU 3.1 0.2 + - - -
425C ARG* 3.3 6.8 + - + +
426C LYS* 2.9 23.1 + - - +
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Residues in contact with GLU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C ASP* 3.0 27.4 + - - +
420C LYS* 3.8 8.8 - - - +
422C PHE* 1.3 75.5 - - + +
424C GLU* 1.3 59.3 + - - +
426C LYS* 3.4 8.7 - - - +
427C LYS* 2.9 29.5 + - - +
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Residues in contact with GLU 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C LYS* 2.8 59.7 + - + +
421C GLN* 2.9 40.0 + - - +
422C PHE 3.0 0.2 - - - -
423C GLU* 1.3 74.3 - - + +
425C ARG* 1.3 55.2 + - - +
426C LYS 3.0 0.9 - - - -
427C LYS* 3.1 5.8 + - - +
428C LEU* 2.6 36.0 + - - +
178D HIS* 5.6 1.0 + - - -
315D ILE* 6.1 0.2 - - - -
316D LYS* 3.8 42.3 + - + +
317D GLN* 6.1 0.9 - - - -
318D TYR 6.4 0.2 - - - +
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Residues in contact with ARG 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C GLY 5.4 1.3 - - - -
383C LEU* 4.0 28.1 - - - +
384C SER* 4.3 13.1 + - - +
387C VAL* 3.7 28.7 - - - +
421C GLN* 3.0 21.4 + - - +
422C PHE* 3.9 5.4 - - + +
424C GLU* 1.3 75.4 - - - +
426C LYS* 1.3 64.1 + - - +
428C LEU* 3.2 12.5 - - - +
429C ALA 3.9 3.1 + - - +
310D VAL* 4.4 24.3 + - - +
311D ASP* 4.5 6.9 - - - +
316D LYS* 2.9 33.7 - - - +
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Residues in contact with LYS 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C PHE 2.9 14.0 + - - +
423C GLU* 3.4 13.7 - - - +
424C GLU 3.0 0.2 - - - -
425C ARG* 1.3 72.9 - - - +
427C LYS* 1.3 65.8 + - - +
428C LEU 3.0 1.1 - - - -
429C ALA* 2.9 15.9 + - - -
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Residues in contact with LYS 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C GLU 2.9 20.8 + - - +
424C GLU* 3.7 5.6 - - - +
426C LYS* 1.3 72.9 - - - +
428C LEU* 1.3 57.9 + - - +
429C ALA* 2.8 14.1 + - - +
178D HIS* 4.6 2.9 - - + -
318D TYR* 4.2 39.8 - - + -
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Residues in contact with LEU 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C GLU 2.6 17.9 + - - +
425C ARG* 3.2 15.3 - - - +
426C LYS 3.0 0.6 - - - -
427C LYS* 1.3 71.5 - - - +
429C ALA* 1.3 67.3 + - - +
178D HIS* 4.6 15.9 - - + +
303D GLU* 3.0 10.7 - - - +
305D ILE* 4.2 12.7 - - + +
316D LYS* 3.6 22.9 - - + +
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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