Contacts of the helix formed by residues 408 - 426 (chain C) in PDB entry 6V3O
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 408 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C PHE* 3.5 2.5 - - - +
407C THR* 1.3 82.9 + - - +
409C ILE* 1.3 62.7 + - - +
410C GLU* 2.9 17.7 + - - +
411C GLU* 2.8 34.6 + - - +
412C PHE* 3.4 15.9 + - - +
448C LEU* 3.7 12.0 - - - +
527C ASP* 5.0 3.8 - - - -
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Residues in contact with ILE 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ARG* 5.4 9.4 - - - +
408C SER* 1.3 74.1 - - - +
410C GLU* 1.3 65.1 + - - +
412C PHE* 3.5 2.9 + - - +
413C LEU* 3.0 38.7 + - + +
443C VAL* 3.8 32.8 - - + +
444C PHE* 5.7 3.1 - - + -
447C GLY* 4.3 15.3 - - - -
448C LEU* 3.5 21.5 - - + +
452C LYS* 5.6 4.3 - - - +
527C ASP* 4.0 23.5 + - + +
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Residues in contact with GLU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C SER* 3.3 19.6 + - - +
409C ILE* 1.3 88.3 + - - +
411C GLU* 1.3 56.2 + - - +
413C LEU* 3.2 10.2 + - + +
414C GLU* 3.1 26.7 + - - +
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Residues in contact with GLU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C LYS* 4.7 6.4 + - - -
402C ALA 4.8 0.5 - - - +
403C GLU 5.3 1.2 - - - +
405C SER 3.5 14.9 - - - +
406C PHE* 3.3 22.4 - - + -
407C THR* 2.7 39.2 + - - +
408C SER* 2.8 29.5 + - - +
410C GLU* 1.3 70.5 - - - +
412C PHE* 1.3 65.0 - - - +
414C GLU* 4.0 7.9 + - - +
415C PRO* 3.5 12.6 - - - +
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Residues in contact with PHE 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C TYR* 4.0 36.3 - + + -
323C ILE* 4.8 4.7 - - + -
378C VAL* 3.6 24.0 - - + -
382C LEU* 4.3 10.5 - - + -
406C PHE* 3.6 36.3 - + + -
408C SER 3.4 14.1 + - - +
409C ILE 3.7 7.0 - - - +
410C GLU 3.3 0.4 - - - -
411C GLU* 1.3 79.2 - - - +
413C LEU* 1.3 56.2 + - - +
415C PRO* 3.2 14.9 - - - +
416C LEU* 3.2 22.6 - - + +
439C LEU* 5.5 0.4 - - + -
443C VAL* 3.6 39.5 - - + -
448C LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C ILE* 3.0 35.3 + - + +
410C GLU* 3.2 10.2 + - + +
412C PHE* 1.3 76.1 - - - +
414C GLU* 1.3 67.1 + - - +
416C LEU* 3.1 5.6 + - + -
417C GLU* 2.8 40.7 + - + +
440C LEU* 3.8 23.8 - - + -
443C VAL* 3.6 24.9 - - + -
444C PHE* 3.4 46.7 - - + -
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Residues in contact with GLU 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C GLU* 5.0 1.9 - - - +
342C ARG* 2.5 43.6 + - - -
410C GLU 3.1 14.8 + - - +
411C GLU* 4.1 8.1 - - - +
413C LEU* 1.3 75.9 - - - +
415C PRO* 1.3 74.0 - - + +
417C GLU* 3.5 6.3 + - - +
418C LEU* 3.1 24.3 + - - +
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Residues in contact with PRO 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C ARG* 5.0 3.1 - - - +
374C ILE* 4.5 10.8 - - + +
375C LEU* 6.0 0.4 - - + -
377C HIS* 6.2 3.1 - - + -
378C VAL* 3.6 31.6 - - + -
406C PHE* 4.9 6.5 - - + -
411C GLU 3.5 10.3 - - - +
412C PHE 3.2 16.6 - - - +
414C GLU* 1.3 104.4 - - + +
416C LEU* 1.3 60.0 + - - +
418C LEU* 3.3 9.1 + - + +
419C CYS* 3.1 29.1 + - - -
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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
----------------------------------------------------------
323C ILE* 4.7 4.0 - - + -
375C LEU* 5.1 5.4 - - + -
378C VAL* 4.3 17.5 - - + -
412C PHE* 3.2 41.5 - - + +
413C LEU* 3.1 8.1 + - + +
415C PRO* 1.3 80.5 - - - +
417C GLU* 1.3 58.8 + - - +
419C CYS* 3.2 12.4 + - - +
420C TYR* 3.1 24.3 + - - +
436C LEU* 4.3 10.8 - - + +
439C LEU* 3.5 35.9 - - + -
440C LEU* 3.6 26.6 - - + +
443C VAL* 4.1 15.7 - - + -
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Residues in contact with GLU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C TYR* 2.5 44.3 + - + +
413C LEU* 2.8 35.9 + - + +
414C GLU* 4.2 5.4 + - - +
416C LEU* 1.3 73.7 - - - +
418C LEU* 1.3 64.2 + - - +
420C TYR* 3.2 9.4 + - - +
421C LYS* 3.1 24.4 + - - +
440C LEU* 4.3 8.3 - - + -
444C PHE* 4.8 5.7 - - - -
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Residues in contact with LEU 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ASN* 4.9 4.7 - - - +
338C GLU* 3.3 46.0 - - + +
339C LEU* 3.8 33.7 - - + +
342C ARG* 4.0 29.2 - - + +
374C ILE* 5.1 7.9 - - + -
414C GLU* 3.1 18.1 + - - +
415C PRO* 3.5 11.2 - - + +
416C LEU 3.2 0.2 - - - -
417C GLU* 1.3 74.8 - - - +
419C CYS* 1.3 65.1 + - - +
421C LYS* 3.5 2.3 + - + +
422C SER* 3.0 26.4 + - - -
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Residues in contact with CYS 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C LEU* 5.3 2.5 - - + -
339C LEU* 4.1 8.7 - - - -
371C TYR* 3.9 11.8 - - + -
374C ILE* 2.9 36.8 - - - -
375C LEU* 4.2 22.9 - - - -
415C PRO 3.1 16.2 + - - -
416C LEU* 3.3 11.0 - - - +
418C LEU* 1.3 77.4 - - - +
420C TYR* 1.3 62.7 + - - +
422C SER* 3.6 1.0 - - - -
423C LEU* 2.9 28.6 + - - +
436C LEU* 3.9 17.0 - - + -
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Residues in contact with TYR 420 (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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275C ARG* 5.9 0.2 - - - -
278C TYR* 4.1 24.2 - + - +
416C LEU 3.1 13.0 + - - +
417C GLU* 3.6 12.1 - - - +
418C LEU 3.2 0.4 - - - -
419C CYS* 1.3 78.3 - - - +
421C LYS* 1.3 75.3 + - + +
423C LEU* 3.5 2.9 + - - +
424C CYS* 3.1 48.7 + - - -
429C LYS* 3.7 16.2 + - - -
432C ALA* 3.7 27.3 - - + +
433C ASP* 2.7 29.0 + - - -
436C LEU* 3.7 11.4 - - + -
437C LEU* 4.6 12.6 - - + +
440C LEU* 3.9 23.3 - - + -
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Residues in contact with LYS 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ASN* 4.0 5.4 - - - +
417C GLU 3.1 14.1 + - - +
418C LEU* 4.5 2.7 - - + +
420C TYR* 1.3 91.5 - - + +
422C SER* 1.3 57.1 + - - +
424C CYS* 4.0 20.2 - - + +
425C ASP* 2.7 54.6 + - - +
429C LYS* 5.6 4.0 - - - +
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Residues in contact with SER 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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335C CYS* 3.8 0.2 - - - -
336C ASN* 3.3 35.7 + - - +
339C LEU* 3.3 18.7 - - - +
371C TYR* 2.5 34.4 + - - -
418C LEU 3.0 19.3 + - - -
419C CYS 3.6 1.6 - - - -
421C LYS* 1.3 78.4 - - - +
423C LEU* 1.3 61.7 + - - +
425C ASP* 3.2 4.2 + - - +
426C CYS* 3.1 23.2 - - - -
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Residues in contact with LEU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C LEU* 4.3 18.6 - - + -
332C MET* 4.7 13.2 - - + -
371C TYR* 3.7 31.2 - - + +
419C CYS 2.9 14.6 + - - +
420C TYR 3.8 4.3 - - - +
422C SER* 1.3 77.2 + - - +
424C CYS* 1.3 60.9 + - - +
426C CYS* 3.5 4.6 + - - -
428C ASP* 2.8 52.3 + - + +
431C ILE* 4.5 10.5 - - + -
432C ALA* 3.8 24.5 - - + +
436C LEU* 3.8 28.5 - - + -
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Residues in contact with CYS 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C TYR* 3.1 49.1 + - - +
421C LYS* 3.7 20.9 - - + +
422C SER 3.2 0.2 - - - -
423C LEU* 1.3 75.0 - - - +
425C ASP* 1.3 66.5 + - - +
427C GLY* 3.1 13.9 + - - -
429C LYS* 3.6 46.0 + - + +
432C ALA* 4.3 1.6 - - - -
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Residues in contact with ASP 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ASN* 3.2 33.8 + - + +
421C LYS* 2.7 40.3 + - - +
422C SER 3.2 4.7 + - - +
424C CYS* 1.3 74.6 - - - +
426C CYS* 1.3 57.7 + - - +
427C GLY 3.3 3.2 + - - -
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Residues in contact with CYS 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ARG* 4.0 16.2 - - + +
335C CYS* 3.4 41.7 - - - -
336C ASN* 3.7 3.4 - - - -
371C TYR* 4.5 0.4 - - - -
422C SER 3.1 19.2 + - - +
423C LEU* 4.3 3.1 - - - +
424C CYS 3.2 1.0 - - - -
425C ASP* 1.3 76.3 - - - +
427C GLY* 1.3 57.4 + - - +
428C ASP* 3.3 10.7 + - - +
52D LEU* 5.1 0.2 - - - +
226D ARG* 2.9 24.9 + - - +
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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