Contacts of the helix formed by residues 423 - 439 (chain C) in PDB entry 4WCX
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 ASP 423 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364C ASN* 3.6 20.9 + - - +
368C ARG* 4.7 4.7 + - - -
421C TYR 3.6 3.0 + - - +
422C GLY* 1.3 76.5 - - - -
424C GLU* 1.3 60.3 + - - +
425C LYS* 4.0 10.4 + - - +
426C THR* 2.6 31.6 + - - -
427C LYS* 2.8 29.1 + - - +
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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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423C ASP* 1.3 75.8 - - - +
425C LYS* 1.3 62.5 + - - +
427C LYS* 3.6 29.2 + - - +
428C LYS* 3.1 24.4 + - - +
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Residues in contact with LYS 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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368C ARG* 4.4 17.3 - - - +
423C ASP* 3.3 10.7 + - - +
424C GLU* 1.3 78.9 - - - +
426C THR* 1.3 61.5 + - - +
428C LYS* 3.6 5.5 + - - +
429C ILE* 3.4 27.9 + - - +
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Residues in contact with THR 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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364C ASN* 3.6 26.4 + - - +
367C LEU* 4.8 9.4 - - + -
368C ARG* 3.9 23.9 + - + +
414C PHE* 5.6 2.5 - - + -
417C PHE* 4.2 15.5 - - + -
418C LEU* 3.6 16.9 - - + +
422C GLY* 4.8 2.0 - - - -
423C ASP* 2.6 28.4 + - - -
425C LYS* 1.3 76.2 - - - +
427C LYS* 1.3 59.9 + - - +
429C ILE* 3.3 1.1 + - + +
430C GLY* 2.8 29.1 + - - -
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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
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418C LEU* 3.1 44.4 - - + +
419C ILE* 4.3 13.5 + - - +
422C GLY 3.5 14.3 + - - +
423C ASP* 2.8 19.8 + - - +
424C GLU* 3.6 31.7 + - - +
426C THR* 1.3 76.3 - - - +
428C LYS* 1.3 63.5 + - - +
431C GLU* 2.9 42.6 + - - +
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Residues in contact with LYS 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 3.1 13.8 + - - +
425C LYS* 3.8 7.0 - - - +
426C THR 3.2 0.2 - - - -
427C LYS* 1.3 81.4 - - - +
429C ILE* 1.3 65.4 + - + +
431C GLU* 3.5 10.5 + - - +
432C LYS* 3.4 31.0 + - - +
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Residues in contact with ILE 429 (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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368C ARG* 4.1 31.0 - - + +
371C CYS* 3.6 26.0 - - + +
372C GLU* 4.3 22.9 - - + +
425C LYS 3.4 16.1 + - - +
426C THR 3.3 4.6 + - - +
427C LYS 3.2 0.4 - - - -
428C LYS* 1.3 78.8 - - + +
430C GLY* 1.3 64.7 - - - +
432C LYS* 3.3 28.1 + - + +
433C ALA* 3.3 17.2 + - - +
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Residues in contact with GLY 430 (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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371C CYS* 4.3 3.3 - - - -
414C PHE* 3.6 25.5 - - - -
418C LEU* 3.6 11.4 - - - -
426C THR* 2.8 20.4 + - - -
429C ILE* 1.3 70.1 - - - +
431C GLU* 1.3 60.4 + - - +
433C ALA* 3.0 6.2 + - - +
434C ILE* 2.9 31.5 + - - +
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Residues in contact with GLU 431 (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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415C LYS* 4.1 21.9 + - - +
418C LEU* 4.3 12.1 - - + +
427C LYS* 2.9 33.3 + - - +
428C LYS* 3.8 8.9 - - - +
429C ILE 3.2 0.2 - - - -
430C GLY* 1.3 77.6 - - - +
432C LYS* 1.3 63.5 + - + +
434C ILE* 3.4 10.2 + - + +
435C ALA* 3.1 22.0 + - - +
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Residues in contact with LYS 432 (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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428C LYS* 3.4 20.5 - - - +
429C ILE* 3.3 28.9 + - + +
431C GLU* 1.3 79.2 - - + +
433C ALA* 1.3 56.5 + - - +
435C ALA* 3.2 7.3 + - - +
436C VAL* 3.0 33.3 + - + +
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Residues in contact with ALA 433 (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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371C CYS* 3.7 36.8 - - + +
375C TYR 4.6 5.4 - - - +
376C LEU* 4.7 4.3 - - + -
414C PHE* 4.3 5.4 - - + -
429C ILE 3.3 4.0 + - - +
430C GLY 3.0 10.4 + - - +
432C LYS* 1.3 75.7 - - - +
434C ILE* 1.3 65.7 + - - +
436C VAL* 3.4 5.2 + - - +
437C ASN* 2.8 40.0 + - - +
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Residues in contact with ILE 434 (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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376C LEU* 5.1 2.7 - - + -
411C ILE* 3.9 19.6 - - + +
414C PHE* 4.0 12.1 - - + -
415C LYS* 3.9 48.2 - - + +
418C LEU* 4.1 13.9 - - + -
430C GLY 2.9 13.3 + - - +
431C GLU* 3.6 11.2 - - + +
432C LYS 3.3 0.2 - - - -
433C ALA* 1.3 76.4 - - - +
435C ALA* 1.3 57.4 + - - +
437C ASN* 3.2 3.3 + - - +
438C LEU* 2.9 37.4 + - + +
454C LEU* 3.9 27.6 - - + -
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Residues in contact with ALA 435 (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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431C GLU 3.1 10.6 + - - +
432C LYS* 3.2 10.3 + - - +
434C ILE* 1.3 81.7 - - - +
436C VAL* 1.3 64.5 + - + +
438C LEU* 3.7 20.3 + - - +
439C GLU* 3.9 12.6 + - - +
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Residues in contact with VAL 436 (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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76C ASN* 5.6 0.7 - - - +
374C GLY* 6.1 4.9 - - - +
432C LYS* 3.0 20.3 + - + +
433C ALA* 3.8 6.3 - - - +
435C ALA* 1.3 80.6 - - + +
437C ASN* 1.3 68.9 + - - +
439C GLU* 3.4 15.6 + - - +
440C LYS* 4.0 27.7 + - - +
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Residues in contact with ASN 437 (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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76C ASN* 2.5 43.7 + - - +
374C GLY 5.6 1.0 - - - -
375C TYR 4.6 2.4 + - - -
376C LEU* 3.8 21.9 - - + +
407C LEU* 3.9 19.3 - - + +
411C ILE* 3.8 10.4 - - + +
433C ALA* 2.8 36.5 + - - +
434C ILE* 4.1 0.7 - - - +
436C VAL* 1.3 78.8 - - - +
438C LEU* 1.3 68.0 + - - +
439C GLU 3.1 2.2 - - - -
440C LYS* 3.0 30.1 + - - +
441C ILE 3.7 2.8 + - - -
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Residues in contact with LEU 438 (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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411C ILE* 3.7 9.5 - - + +
434C ILE* 2.9 30.6 + - + +
435C ALA* 3.8 11.2 - - - +
437C ASN* 1.3 75.9 - - - +
439C GLU* 1.3 65.5 + - - +
441C ILE* 3.1 29.6 + - + +
447C ARG* 3.2 17.4 - - - +
450C THR* 3.8 30.5 - - + -
451C LYS* 4.0 33.4 - - + -
454C LEU* 3.8 22.9 - - + -
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Residues in contact with GLU 439 (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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435C ALA 4.0 12.0 - - - +
436C VAL* 3.4 8.8 + - - +
437C ASN 3.1 1.4 - - - -
438C LEU* 1.3 79.0 - - - +
440C LYS* 1.3 61.1 + - - +
441C ILE 3.3 5.6 + - - +
447C ARG* 3.7 21.3 + - - +
451C LYS* 2.9 33.4 + - - -
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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