Contacts of the helix formed by residues 398 - 412 (chain C) in PDB entry 5G04
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 398 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365C LEU* 3.8 19.5 - - + +
369C THR* 4.2 12.8 - - - +
391C ALA* 3.9 6.7 - - - +
392C ILE* 3.3 10.2 - - - +
395C ASN* 3.4 25.9 + - + +
396C LYS 3.4 1.6 - - - -
397C ARG* 1.3 74.0 - - - +
399C TYR* 1.3 65.1 + - - +
400C ARG* 3.0 36.3 + - - +
401C ALA* 3.3 22.0 + - + +
402C TRP* 3.2 20.0 + - - -
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Residues in contact with TYR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C ARG 3.2 4.5 + - - +
398C ASP* 1.3 73.2 + - - +
400C ARG* 1.3 97.2 + - + +
401C ALA 3.3 0.4 - - - -
402C TRP* 3.3 7.7 - - - +
403C TYR* 2.8 30.7 + - - +
425C ALA* 4.1 8.8 - - - +
428C LEU* 3.7 30.1 - - + -
429C ARG* 3.3 62.8 + - + +
432C ASP* 4.5 13.4 + - - -
434C ARG* 3.7 17.7 + - - -
435C MET* 5.0 7.9 - - - -
80R ILE* 3.4 21.0 - - + +
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Residues in contact with ARG 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LEU* 4.3 5.5 - - - +
366C GLY* 3.4 33.7 - - - +
369C THR* 3.5 24.9 + - - +
398C ASP* 3.4 20.2 + - - +
399C TYR* 1.3 112.3 - - + +
401C ALA* 1.3 51.2 + - - +
403C TYR* 3.1 3.8 + - - +
404C GLY* 2.5 34.0 + - - -
79R TYR* 3.7 49.8 + - + +
80R ILE* 3.8 13.7 - - + +
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Residues in contact with ALA 401 (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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369C THR* 3.9 12.3 + - - -
388C TYR* 3.7 20.2 - - + +
391C ALA* 3.4 32.1 - - + -
392C ILE* 3.9 10.5 - - + -
398C ASP* 3.3 14.6 + - - +
399C TYR 3.3 0.6 - - - -
400C ARG* 1.3 75.4 - - - +
402C TRP* 1.3 62.4 + - - +
404C GLY* 3.2 1.1 + - - +
405C LEU* 2.8 30.0 + - - +
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Residues in contact with TRP 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.2 12.3 - - + -
389C ARG* 4.7 4.5 - - - -
392C ILE* 3.5 39.0 - - + +
396C LYS* 2.9 26.9 + - + -
398C ASP 3.2 20.7 + - - -
399C TYR* 3.3 10.3 + - - +
401C ALA* 1.3 77.1 - - - +
403C TYR* 1.3 64.1 + - - +
405C LEU* 2.8 17.1 + - + +
406C GLY 3.1 9.2 + - - -
420C TYR* 4.1 11.9 - - - -
421C TYR* 3.5 41.9 - + + +
424C ARG* 3.7 51.7 - - + +
425C ALA* 3.6 17.5 - - + -
428C LEU* 3.9 17.8 - - + +
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Residues in contact with TYR 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C TYR 2.8 16.3 + - - +
400C ARG 3.3 7.4 - - - +
402C TRP* 1.3 71.7 - - - +
404C GLY* 1.3 55.2 + - - +
406C GLY 3.1 1.6 + - - -
407C GLN* 2.7 65.7 + - + -
422C TYR* 3.3 17.6 + + - -
425C ALA* 3.8 7.3 - - - +
434C ARG* 4.5 10.5 + - - +
435C MET* 3.0 39.7 - - + -
438C ALA* 4.4 7.6 - - + +
79R TYR 5.2 0.2 - - - -
80R ILE* 3.4 37.8 - - + +
81R PRO* 3.6 29.8 + - + -
83R ARG* 4.1 14.9 + - - -
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Residues in contact with GLY 404 (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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373C HIS* 4.7 5.6 - - - -
388C TYR* 3.6 25.6 - - - -
400C ARG 2.5 20.8 + - - -
401C ALA 3.5 3.1 - - - -
402C TRP 3.1 0.2 - - - -
403C TYR* 1.3 76.2 - - - +
405C LEU* 1.3 51.0 + - - +
407C GLN* 2.9 7.4 + - - +
408C THR* 2.6 38.7 + - - +
79R TYR 5.6 0.4 - - - -
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ILE* 3.6 42.6 - - + +
388C TYR* 3.5 15.0 - - + -
389C ARG* 4.0 22.4 - - - +
392C ILE* 4.6 7.6 - - + -
401C ALA 2.8 9.1 + - - +
402C TRP* 2.8 10.0 + - - +
404C GLY* 1.3 75.9 - - - +
406C GLY* 1.3 56.8 + - - +
408C THR* 3.1 13.5 - - + +
409C TYR* 3.0 37.2 + - + -
421C TYR* 3.6 25.6 - - + -
279O ASP* 3.4 22.4 - - - +
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Residues in contact with GLY 406 (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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402C TRP 3.1 10.1 + - - -
403C TYR 3.5 3.1 - - - -
405C LEU* 1.3 75.3 - - - +
407C GLN* 1.3 54.4 + - - +
409C TYR 3.4 0.3 + - - -
410C GLU* 2.8 35.9 + - - +
418C CYS* 3.4 15.6 - - - +
421C TYR* 3.6 18.7 - - - +
422C TYR* 3.6 16.3 - - - -
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Residues in contact with GLN 407 (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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388C TYR* 5.9 0.2 - - - +
403C TYR* 2.7 36.9 + - + +
404C GLY* 3.4 9.0 - - - +
406C GLY* 1.3 72.3 - - - +
408C THR* 1.3 57.6 + - - +
410C GLU* 3.3 4.1 + - - +
411C ILE* 2.9 55.0 + - - +
422C TYR* 2.9 27.8 + - - +
81R PRO* 4.1 20.7 + - + +
83R ARG* 3.2 18.4 + - - +
87R GLN* 4.2 9.2 + - - +
88R MET* 4.3 3.8 - - - +
131R LEU* 3.8 28.2 - - + +
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Residues in contact with THR 408 (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 MET* 3.5 26.8 - - - +
381C THR* 3.0 26.2 + - - -
384C ALA* 4.4 0.3 - - - +
385C ILE* 3.8 13.4 - - + +
388C TYR* 3.6 16.1 + - + -
404C GLY 2.6 21.4 + - - +
405C LEU* 3.1 37.0 - - + +
407C GLN* 1.3 72.9 - - - +
409C TYR* 1.3 60.4 + - - +
411C ILE* 3.3 4.9 + - - +
412C LEU* 3.1 22.7 + - - +
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Residues in contact with TYR 409 (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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385C ILE* 3.8 29.3 - - + +
405C LEU* 3.0 27.3 + - + +
408C THR* 1.3 77.5 + - - +
410C GLU* 1.3 59.9 + - - +
412C LEU* 3.1 28.3 + - + +
413C LYS 3.4 0.5 + - - -
414C MET* 3.4 44.5 + - + +
417C TYR* 3.5 31.6 + + - -
418C CYS* 3.5 22.4 - - + +
421C TYR* 3.3 29.8 - + - -
278O PHE 4.4 5.5 + - - -
279O ASP* 3.2 17.6 + - - -
300O LEU* 3.9 19.3 - - + +
303O ALA* 4.8 2.8 - - + +
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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
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406C GLY 2.8 21.0 + - - +
407C GLN* 3.4 7.3 + - - +
409C TYR* 1.3 69.8 - - - +
411C ILE* 1.3 57.3 + - - +
413C LYS* 2.8 26.1 + - - +
414C MET 4.9 1.6 - - - +
415C PRO* 5.0 3.2 - - + +
418C CYS* 3.4 21.9 - - - +
422C TYR* 2.8 27.1 + - - -
441C GLU* 3.8 4.9 - - - +
442C CYS* 4.3 6.1 - - - -
445C LYS* 3.6 15.9 + - - +
83R ARG* 2.8 33.4 + - - -
88R MET* 3.4 29.1 - - + +
92R SER* 5.7 0.2 - - - -
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Residues in contact with ILE 411 (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 MET* 3.8 12.8 - - + -
407C GLN* 2.9 46.8 + - - +
408C THR 3.5 6.5 - - - +
410C GLU* 1.3 71.0 - - + +
412C LEU* 1.3 56.2 + - - +
413C LYS* 2.9 32.5 + - - +
87R GLN* 4.9 0.4 - - - +
88R MET* 3.6 23.8 - - + -
91R ALA* 3.8 33.9 - - + -
92R SER* 3.7 6.1 - - - +
95R LEU* 3.6 17.7 - - + -
130R ILE* 3.8 15.7 - - + -
131R LEU* 4.2 7.6 - - + -
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Residues in contact with LEU 412 (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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381C THR* 3.7 19.3 - - + +
385C ILE* 3.6 30.1 - - + -
408C THR 3.1 19.6 + - - +
409C TYR* 3.1 24.1 + - + +
411C ILE* 1.3 74.1 - - - +
413C LYS* 1.3 69.8 + - - +
414C MET* 3.0 28.0 + - - +
296O TYR* 3.7 21.1 - - + -
300O LEU* 3.7 17.3 - - + -
329O ARG* 5.3 0.3 - - - +
330O ILE* 3.8 11.1 - - + +
333O GLU* 4.1 0.5 - - - +
95R LEU* 3.7 20.6 - - + -
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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