Contacts of the helix formed by residues 404 - 427 (chain C) in PDB entry 5Q14
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 404 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ASP* 5.9 2.2 - - + -
319C ASP* 3.2 13.8 + - - +
402C ILE* 3.6 3.7 - - - +
403C LYS* 1.4 76.6 - - + +
405C ARG* 1.3 61.4 + - - +
406C GLU* 3.5 10.2 + - - +
407C ALA* 3.2 40.6 + - + +
408C VAL* 3.6 12.6 - - - +
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Residues in contact with ARG 405 (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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397C PRO* 3.1 36.8 + - + +
398C ASP* 5.3 2.4 - - - +
399C ARG 5.0 5.7 + - - -
400C GLN* 6.1 0.4 - - - +
401C TYR* 5.3 4.2 - - - +
402C ILE* 3.1 37.9 + - + +
403C LYS* 3.9 10.0 + - - +
404C ASP* 1.3 70.9 + - - +
406C GLU* 1.4 60.1 + - - +
408C VAL 3.1 3.3 + - - -
409C GLU* 2.9 25.6 + - - +
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Residues in contact with GLU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C ASP* 3.4 7.7 + - - +
405C ARG* 1.4 73.9 - - - +
407C ALA* 1.3 59.5 + - - +
409C GLU* 3.2 18.3 + - + +
410C LYS* 3.0 58.0 + - + +
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Residues in contact with ALA 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 3.8 19.8 - - + +
404C ASP* 3.2 37.3 + - + +
405C ARG 3.3 0.2 - - - -
406C GLU* 1.3 75.3 - - - +
408C VAL* 1.3 59.9 + - - +
410C LYS* 3.6 9.9 + - - +
411C LEU* 3.4 24.9 + - - +
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Residues in contact with VAL 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 4.4 12.8 - - + -
319C ASP* 5.3 3.1 - - + +
323C LEU* 3.9 26.5 - - + -
395C LEU* 3.5 35.8 - - + +
396C SER 3.9 3.6 - - - +
397C PRO* 3.8 14.6 - - + -
402C ILE* 4.1 17.9 - - + -
404C ASP 3.6 14.6 - - - +
405C ARG 3.1 6.3 + - - +
407C ALA* 1.3 75.0 - - - +
409C GLU* 1.4 64.5 + - - +
411C LEU* 3.1 8.6 + - - +
412C GLN* 3.0 19.9 + - - +
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Residues in contact with GLU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C PRO* 3.8 21.4 - - + +
405C ARG 2.9 13.9 + - - +
406C GLU* 3.5 21.1 + - + +
408C VAL* 1.4 74.8 - - - +
410C LYS* 1.3 57.7 + - + +
412C GLN* 3.2 8.3 + - - +
413C GLU* 2.9 54.0 + - + +
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Residues in contact with LYS 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C GLU* 3.0 47.7 + - + +
407C ALA* 3.7 10.1 - - - +
408C VAL 3.3 0.2 - - - -
409C GLU* 1.3 74.8 - - + +
411C LEU* 1.3 61.5 + - + +
413C GLU* 4.0 14.1 - - - +
414C PRO* 3.2 20.4 - - - +
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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
----------------------------------------------------------
310C PRO 3.6 18.2 - - - +
311C GLY* 3.4 38.1 - - - +
312C PHE* 3.8 3.6 - - - +
314C THR* 5.0 2.5 - - - +
315C LEU* 3.8 29.6 - - + -
395C LEU* 3.9 19.9 - - + +
407C ALA 3.4 11.0 - - - +
408C VAL* 3.1 8.0 + - - +
410C LYS* 1.3 80.2 - - + +
412C GLN* 1.3 64.0 + - - +
413C GLU 3.5 0.2 - - - -
414C PRO* 3.4 15.4 - - - +
415C LEU* 3.8 12.8 - - - +
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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
----------------------------------------------------------
392C ILE* 3.1 39.9 - - + +
395C LEU* 3.2 30.5 - - + +
396C SER* 3.9 3.8 + - - -
397C PRO* 3.4 24.7 - - - +
408C VAL 3.0 10.4 + - - +
409C GLU* 3.2 7.9 + - - +
411C LEU* 1.3 76.8 - - - +
413C GLU* 1.4 64.0 + - - +
415C LEU* 3.1 8.9 + - - +
416C LEU* 3.1 45.7 + - + +
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Residues in contact with GLU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C GLU* 2.9 40.7 + - + +
410C LYS* 4.0 17.6 - - - +
412C GLN* 1.4 73.5 - - - +
414C PRO* 1.4 67.5 - - + +
416C LEU* 3.2 14.9 + - + +
417C ASP* 3.1 30.8 + - - +
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Residues in contact with PRO 414 (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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253C GLN* 5.0 0.9 + - - +
256C LEU* 4.3 16.8 - - + -
410C LYS 3.2 20.4 - - - +
411C LEU* 3.4 13.7 - - - +
413C GLU* 1.4 90.6 - - + +
415C LEU* 1.3 57.2 + - + +
417C ASP* 3.3 9.8 + - + +
418C VAL* 3.0 33.9 + - + +
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Residues in contact with LEU 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C LEU* 4.1 19.5 - - + -
260C ILE* 3.9 24.7 - - + -
309C LEU* 4.9 3.1 - - + -
310C PRO* 5.5 3.8 - - + -
388C LEU* 4.0 22.6 - - + +
391C ALA* 3.7 24.2 - - + -
392C ILE* 3.8 16.1 - - + +
395C LEU* 3.6 31.6 - - + -
411C LEU 3.8 10.1 - - - +
412C GLN* 3.1 9.3 + - - +
414C PRO* 1.3 74.7 - - + +
416C LEU* 1.3 60.0 + - - +
418C VAL* 3.4 4.3 + - - +
419C LEU* 2.9 29.6 + - - +
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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
----------------------------------------------------------
392C ILE* 3.8 26.2 - - + +
412C GLN* 3.1 46.4 + - + +
413C GLU* 3.2 13.7 + - + +
415C LEU* 1.3 75.5 - - - +
417C ASP* 1.4 58.6 + - - +
419C LEU* 3.4 2.1 + - - +
420C GLN* 2.9 32.2 + - - +
434C PHE* 3.8 15.6 - - + -
438C LEU* 3.7 32.1 - - + -
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Residues in contact with ASP 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C GLN* 4.2 14.4 - - - +
413C GLU* 3.1 22.9 + - - +
414C PRO* 3.7 11.2 - - + +
415C LEU 3.3 0.2 - - - -
416C LEU* 1.4 75.6 - - - +
418C VAL* 1.4 64.8 + - - +
420C GLN* 3.5 14.1 + - - +
421C LYS* 3.2 28.7 + - + +
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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
----------------------------------------------------------
249C LEU* 4.0 18.6 - - + -
253C GLN* 3.8 35.0 - - + +
256C LEU* 4.1 18.6 - - + -
257C LEU* 4.4 16.6 - - + -
388C LEU* 3.7 24.9 - - + -
414C PRO* 3.0 21.1 + - + +
415C LEU 3.8 3.8 - - - +
417C ASP* 1.4 71.1 - - - +
419C LEU* 1.3 66.0 + - - +
421C LYS* 3.2 4.0 + - - +
422C LEU* 3.0 28.1 + - + +
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Residues in contact with LEU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU* 3.9 31.9 - - + +
388C LEU* 3.9 17.9 - - + +
389C LEU* 3.8 24.0 - - + -
392C ILE* 3.7 24.2 - - + -
415C LEU 2.9 17.1 + - - +
416C LEU 3.8 4.3 - - - +
418C VAL* 1.3 76.2 - - - +
420C GLN* 1.4 56.0 + - - +
422C LEU* 3.2 4.1 + - + +
423C CYS* 2.9 29.0 + - - -
434C PHE* 3.9 17.7 - - + -
437C LEU* 3.8 27.6 - - + -
438C LEU* 5.1 2.0 - - + -
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Residues in contact with GLN 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C LEU 2.9 17.3 + - - +
417C ASP* 3.8 15.3 - - - +
418C VAL 3.3 0.2 - - - -
419C LEU* 1.4 75.1 - - - +
421C LYS* 1.3 63.1 + - + +
423C CYS* 3.4 4.2 + - - +
424C LYS* 3.2 37.1 + - + +
434C PHE* 3.6 46.7 - - + +
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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
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247C MET* 3.5 42.3 - - + +
248C GLU 2.8 30.7 + - - +
249C LEU* 3.7 12.3 - - + -
250C THR* 4.0 11.5 - - - +
253C GLN* 2.8 38.1 + - - +
417C ASP* 3.2 15.4 + - - +
418C VAL 3.6 7.2 - - - +
420C GLN* 1.3 74.6 - - + +
422C LEU* 1.3 61.0 + - - +
424C LYS* 3.2 14.2 + - - +
425C ILE* 3.1 29.6 + - + +
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Residues in contact with LEU 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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249C LEU* 4.0 25.4 - - + -
257C LEU* 3.8 10.1 - - + -
384C GLU* 3.6 34.8 - - + +
385C GLU* 4.3 6.7 - - + +
388C LEU* 3.5 28.0 - - + -
418C VAL* 3.0 17.6 + - + +
419C LEU* 3.6 8.5 - - - +
421C LYS* 1.3 74.7 - - - +
423C CYS* 1.4 53.3 + - - +
425C ILE* 3.2 10.3 + - + -
426C HIS* 2.8 60.1 + - + +
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Residues in contact with CYS 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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385C GLU* 4.3 4.9 - - - -
419C LEU* 2.9 21.4 + - - +
420C GLN 3.5 8.7 - - - +
422C LEU* 1.4 75.0 - - - +
424C LYS* 1.3 56.9 + - + +
427C GLN* 3.0 35.4 + - - +
430C ASN 5.7 0.2 - - - -
433C HIS* 3.2 31.7 + - + +
434C PHE* 3.8 31.4 - - + +
437C LEU* 3.6 24.2 - - - -
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Residues in contact with LYS 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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358A ASN* 5.1 3.6 - - - +
247C MET* 3.3 42.3 + - - +
420C GLN* 3.2 32.9 + - + +
421C LYS* 3.2 14.3 + - - +
423C CYS* 1.3 76.5 - - + +
425C ILE* 1.4 59.2 + - + +
427C GLN 4.6 3.4 - - - -
428C PRO* 3.4 28.7 - - - +
431C PRO* 6.5 0.7 - - + -
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Residues in contact with ILE 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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247C MET 3.9 20.4 - - - +
248C GLU* 4.4 13.9 - - + -
249C LEU* 4.6 13.0 - - + +
421C LYS* 3.1 24.0 + - + +
422C LEU* 3.2 11.9 + - + +
424C LYS* 1.4 77.7 - - + +
426C HIS* 1.3 77.3 + - + +
427C GLN 3.3 0.4 - - - -
428C PRO* 3.4 13.7 - - - +
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Residues in contact with HIS 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C THR* 3.7 33.5 + - + +
384C GLU* 3.9 19.2 + - - -
385C GLU* 3.2 27.4 - - - +
422C LEU* 2.8 36.6 + - + +
425C ILE* 1.3 83.4 - - + +
427C GLN* 1.3 71.9 + - - +
428C PRO* 3.7 3.7 - - - +
429C GLU* 4.4 1.9 - - - +
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Residues in contact with GLN 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C LEU 2.9 28.7 + - - +
380C LYS* 4.4 13.9 + - - +
382C THR* 5.7 0.7 - - - +
385C GLU* 4.3 1.0 - - - +
423C CYS 3.0 20.9 + - - +
424C LYS* 4.3 1.7 - - - +
426C HIS* 1.3 99.5 - - - +
428C PRO* 1.4 63.7 - - - +
429C GLU* 3.2 26.5 + - - +
430C ASN* 3.2 24.6 + - + +
431C PRO* 5.1 0.2 - - - +
433C HIS* 3.3 35.6 + - + -
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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
------------------------------------------------------------
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