Contacts of the helix formed by residues 417 - 439 (chain C) in PDB entry 5FLZ
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 GLN 417 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C PHE* 4.7 20.6 - - - -
404C LEU* 4.6 10.4 - - - +
408C ASN* 3.9 26.0 + - - +
413C PHE* 3.8 4.5 - - - +
414C GLN 5.1 0.6 + - - -
416C MET* 1.4 70.6 - - - +
418C ASN* 1.4 58.2 + - - +
419C VAL* 3.2 3.1 - - - -
420C GLN* 3.2 34.3 + - - +
421C ASP* 2.8 22.3 + - - +
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Residues in contact with ASN 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C SER 5.3 0.4 + - - -
416C MET* 3.8 28.7 - - + +
417C GLN* 1.4 78.8 - - - +
419C VAL* 1.4 63.4 + - - +
421C ASP* 3.1 15.9 + - - +
422C GLU* 3.1 34.2 + - + +
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Residues in contact with VAL 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C LEU* 6.5 0.2 - - + -
192C ARG* 3.1 31.0 + - - +
412C LEU 5.2 3.1 - - - +
413C PHE* 4.2 24.9 - - + -
416C MET* 3.9 33.2 - - + +
417C GLN 4.5 1.3 - - - -
418C ASN* 1.4 72.8 - - + +
420C GLN* 1.3 67.7 + - + +
422C GLU* 3.5 17.2 + - - +
423C PHE* 3.2 9.9 + - - +
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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
----------------------------------------------------------
185C TYR* 3.2 39.6 + - + +
188C ILE* 5.3 1.5 - - + +
189C LEU* 5.7 7.4 - - + -
394C PHE* 3.9 26.7 - - + -
398C PHE* 3.6 22.1 - - + -
404C LEU* 4.1 11.4 - - - +
408C ASN* 4.4 3.3 + - - +
413C PHE* 4.4 8.2 - - + -
417C GLN* 3.2 38.6 + - - +
419C VAL* 1.3 83.1 - - + +
421C ASP* 1.4 68.3 + - - +
423C PHE* 3.2 7.9 + - - +
424C ALA* 3.1 26.5 + - - +
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Residues in contact with ASP 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C PHE* 5.4 1.4 - - - -
398C PHE* 3.2 40.9 - - - -
417C GLN* 2.8 25.0 + - - +
418C ASN* 3.2 16.8 - - - +
420C GLN* 1.4 77.5 - - - +
422C GLU* 1.4 63.9 + - + +
424C ALA* 3.3 7.6 + - - +
425C GLU* 3.0 29.1 + - - +
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Residues in contact with GLU 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ARG* 4.8 13.9 + - - +
418C ASN* 3.1 22.7 + - + +
419C VAL* 3.7 27.2 + - - +
420C GLN 3.3 0.2 - - - -
421C ASP* 1.4 77.1 - - + +
423C PHE* 1.4 55.8 + - - +
425C GLU* 3.4 14.1 + - - +
426C SER* 3.0 27.6 + - - -
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Residues in contact with PHE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 3.5 45.8 - - + -
189C LEU* 5.6 1.3 - - + -
191C LEU* 4.2 8.5 - - + -
192C ARG* 3.4 62.5 - - + +
195C ILE* 3.4 32.1 - - + -
196C GLU* 5.9 1.1 - - + -
419C VAL 3.2 8.2 + - - +
420C GLN* 3.2 8.9 + - - +
422C GLU* 1.4 73.1 - - - +
424C ALA* 1.3 58.9 + - - +
426C SER* 3.2 12.1 + - - -
427C ARG* 2.8 53.4 + - + +
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Residues in contact with ALA 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C PHE* 3.8 22.2 - - + -
395C ASP* 4.8 3.4 - - - +
420C GLN 3.1 6.9 + - - +
421C ASP* 3.3 9.2 + - - +
423C PHE* 1.3 74.1 - - - +
425C GLU* 1.4 58.1 + - - +
427C ARG* 3.3 31.7 - - - +
428C GLU* 3.0 38.1 + - - +
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Residues in contact with GLU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C ASP* 3.0 19.7 + - - +
422C GLU* 3.5 13.5 - - - +
423C PHE 3.2 0.2 - - - -
424C ALA* 1.4 76.1 - - - +
426C SER* 1.3 60.2 + - - +
428C GLU* 3.3 18.3 + - - +
429C VAL* 3.4 18.6 + - + +
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Residues in contact with SER 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ILE* 5.0 3.1 - - - +
422C GLU 3.0 14.7 + - - -
423C PHE* 3.5 20.7 - - - -
425C GLU* 1.3 72.3 - - - +
427C ARG* 1.3 59.6 + - - +
429C VAL* 3.1 15.4 + - - +
430C VAL* 3.0 34.1 + - - +
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Residues in contact with ARG 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 3.2 51.1 - - - +
191C LEU* 5.3 9.9 - - + -
387C PHE* 4.9 7.6 - - + -
390C ALA* 5.7 0.7 - - - -
391C CYS* 3.4 32.5 - - - +
394C PHE* 3.3 11.5 - - - +
395C ASP* 3.4 18.0 + - - -
423C PHE* 2.8 37.0 + - + +
424C ALA* 3.3 26.7 - - - +
426C SER* 1.3 75.3 - - - +
428C GLU* 1.4 80.7 + - - +
430C VAL* 3.2 13.1 + - + +
431C GLN* 3.1 35.3 + - + +
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Residues in contact with GLU 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C GLU* 4.7 1.2 - - - +
391C CYS* 3.2 34.7 - - - +
395C ASP* 5.5 2.0 - - - -
424C ALA* 3.0 30.1 + - - +
425C GLU* 3.5 10.3 - - - +
426C SER 3.2 0.2 - - - -
427C ARG* 1.4 89.6 + - - +
429C VAL* 1.3 52.0 - - + +
431C GLN* 3.4 19.4 + - - +
432C SER* 2.9 32.5 + - - -
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Residues in contact with VAL 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C GLU* 3.6 16.6 - - + +
426C SER* 3.2 14.4 - - - +
428C GLU* 1.3 75.3 - - + +
430C VAL* 1.3 61.4 + - + +
432C SER* 2.9 24.2 + - - +
433C LEU* 3.1 29.6 + - + +
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Residues in contact with VAL 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C ILE* 4.1 25.4 - - + -
264C GLU* 4.7 8.5 - - + +
267C PHE* 4.4 24.0 - - + -
387C PHE* 5.3 5.8 - - + -
426C SER* 3.0 18.8 + - - +
427C ARG* 3.2 13.9 + - + +
429C VAL* 1.3 71.3 - - + +
431C GLN* 1.3 67.5 + - + +
433C LEU* 3.4 10.3 + - - +
434C MET* 3.2 34.3 + - + +
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Residues in contact with GLN 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C VAL* 4.0 23.3 - - + -
387C PHE* 3.5 37.6 + - + +
388C GLU* 2.8 31.7 - - - +
391C CYS* 3.6 16.4 - - - +
427C ARG* 3.1 21.4 + - + +
428C GLU* 3.4 23.4 + - - +
430C VAL* 1.3 78.2 - - + +
432C SER* 1.4 60.5 + - - +
434C MET* 3.4 5.0 + - - +
435C GLU* 2.7 35.6 + - - +
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Residues in contact with SER 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C GLU 2.9 14.1 + - - -
429C VAL* 2.9 28.1 + - - +
431C GLN* 1.4 74.1 - - - +
433C LEU* 1.3 57.9 + - - +
435C GLU* 3.3 8.7 + - - +
436C ASP* 3.1 26.0 + - - +
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Residues in contact with LEU 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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264C GLU* 4.6 15.0 - - + -
429C VAL* 3.1 38.2 + - + +
430C VAL* 3.7 9.0 - - - +
432C SER* 1.3 75.3 + - - +
434C MET* 1.4 56.3 + - - +
436C ASP* 3.2 17.1 + - + +
437C TYR* 3.0 62.8 + - + +
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Residues in contact with MET 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C GLU 5.3 1.8 - - - +
265C LEU* 4.0 21.8 - - + -
267C PHE* 4.4 12.1 - - + -
380C MET 4.8 0.7 - - - +
381C SER* 4.1 18.7 + - - +
383C VAL* 3.6 31.4 - - + -
384C VAL* 3.8 26.7 - - + -
387C PHE* 4.0 15.7 - - + -
430C VAL* 3.2 25.4 + - + +
431C GLN* 3.4 6.7 + - - +
433C LEU* 1.4 75.7 - - - +
435C GLU* 1.3 68.3 + - - +
437C TYR* 3.4 25.8 - - + +
438C VAL* 3.6 12.0 + - - +
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Residues in contact with GLU 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C SER* 4.7 5.2 - - - +
384C VAL* 3.6 33.8 - - - +
388C GLU* 4.4 6.4 - - - +
431C GLN* 2.7 27.8 + - - +
432C SER* 3.3 10.3 + - - +
434C MET* 1.3 80.6 - - - +
436C ASP* 1.4 63.7 + - - +
438C VAL* 3.2 25.6 + - + +
439C ALA* 3.9 2.6 + - - +
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Residues in contact with ASP 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C SER 3.1 12.7 + - - +
433C LEU* 3.2 20.1 + - + +
435C GLU* 1.4 73.5 - - - +
437C TYR* 1.3 67.3 + - - +
439C ALA* 3.0 28.9 + - - +
441C GLU* 3.6 15.2 - - - +
442C GLN* 3.5 29.7 + - - +
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Residues in contact with TYR 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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262C SER* 5.1 4.4 + - - -
264C GLU* 3.5 29.3 + - + +
265C LEU* 3.7 39.5 - - + -
315C TYR* 3.4 23.3 - - + -
381C SER* 5.5 2.2 - - - +
433C LEU* 3.0 52.5 + - + +
434C MET* 3.4 18.6 - - + +
436C ASP* 1.3 85.2 - - - +
438C VAL* 1.3 63.8 + - + +
439C ALA 3.3 6.3 + - - +
442C GLN* 3.5 35.6 + - + +
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Residues in contact with VAL 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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315C TYR* 3.1 54.1 - - + -
346C SER* 5.1 8.7 - - - +
347C TRP 4.8 1.0 - - - -
348C SER* 3.9 5.2 + - - -
381C SER* 3.8 13.2 - - - +
434C MET 3.8 10.5 - - - +
435C GLU* 3.2 19.4 + - + +
437C TYR* 1.3 76.6 - - - +
439C ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C SER* 3.8 4.0 - - - -
435C GLU 3.9 2.3 + - - +
436C ASP* 3.0 14.5 + - - +
437C TYR 3.4 0.3 - - - +
438C VAL* 1.3 84.6 - - - +
440C ALA* 1.4 63.3 - - - +
441C GLU* 3.2 24.4 + - + +
442C GLN* 3.0 27.0 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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