Contacts of the helix formed by residues 414 - 437 (chain C) in PDB entry 5YL4
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 GLU 414 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409C VAL* 5.0 2.9 - - - -
413C MET* 1.3 74.5 - - - +
415C GLU* 1.3 66.7 + - - +
416C GLY* 4.0 9.0 - - - +
417C GLU* 2.9 36.2 + - - +
418C PHE* 3.8 10.1 + - - -
107E SER* 4.1 11.5 + - - -
111E ASN* 3.4 33.6 + - - +
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Residues in contact with GLU 415 (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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399C TYR* 3.3 18.9 + - - +
402C ARG* 2.8 42.2 + - - +
405C VAL* 4.6 16.0 - - + +
409C VAL* 4.9 8.0 - - + +
414C GLU* 1.3 72.2 - - - +
416C GLY* 1.3 62.4 + - - +
418C PHE* 2.9 18.1 + - - +
419C SER* 3.1 12.2 + - - -
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Residues in contact with GLY 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C GLU* 3.2 8.2 - - - +
415C GLU* 1.3 77.0 - - - +
417C GLU* 1.3 55.0 + - - +
419C SER* 3.1 9.3 + - - -
420C GLU* 2.8 36.8 + - - +
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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
----------------------------------------------------------
103C TYR* 5.6 1.0 - - - -
108C TYR* 2.6 30.1 + - - -
189C LEU* 3.9 5.8 - - + +
192C HIS* 4.8 2.1 - - - -
412C GLY 4.6 0.9 - - - +
413C MET* 3.3 30.3 - - + +
414C GLU* 2.9 43.2 + - + +
416C GLY* 1.3 72.1 - - - +
418C PHE* 1.3 59.7 + - - +
420C GLU* 4.0 11.7 - - - +
421C ALA* 3.1 28.4 + - - +
104E LYS* 4.5 10.6 + - + +
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Residues in contact with PHE 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 3.6 37.7 - + + -
189C LEU* 4.3 11.9 - - + -
395C PHE* 3.6 21.8 - + + -
399C TYR* 3.3 39.3 - + + -
405C VAL* 4.4 14.4 - - + -
408C TYR* 3.7 44.2 - + + -
409C VAL* 5.9 0.9 - - + -
413C MET* 4.2 17.0 - - + -
414C GLU 3.9 13.0 - - - -
415C GLU* 2.9 9.2 + - - +
417C GLU* 1.3 78.2 - - - +
419C SER* 1.3 58.8 + - - +
421C ALA* 3.4 2.1 + - - +
422C ARG* 2.9 28.9 + - - +
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Residues in contact with SER 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C TYR* 4.6 15.0 - - - -
415C GLU 3.1 9.0 + - - -
416C GLY* 3.1 17.3 + - - -
418C PHE* 1.3 76.6 - - - +
420C GLU* 1.3 59.3 + - - +
422C ARG* 3.8 6.3 - - - +
423C GLU* 2.9 30.5 + - - +
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Residues in contact with GLU 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C HIS* 3.1 27.7 + - + +
416C GLY 2.8 22.3 + - - +
417C GLU* 4.0 10.8 - - - +
419C SER* 1.3 74.2 + - - +
421C ALA* 1.3 65.3 + - - +
423C GLU* 3.2 5.7 + - - +
424C ASP* 3.1 22.3 + - - +
100E LYS* 4.6 13.1 + - - -
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Residues in contact with ALA 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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188C ILE* 3.7 18.6 - - + +
189C LEU* 4.1 13.2 - - + -
192C HIS* 3.4 33.8 - - + +
417C GLU 3.1 20.2 + - - +
418C PHE 3.7 4.0 - - - +
419C SER 3.4 0.2 - - - -
420C GLU* 1.3 75.6 - - - +
422C ARG* 1.3 62.2 + - - +
424C ASP* 3.2 5.5 + - - +
425C MET* 3.2 24.1 + - - +
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Residues in contact with ARG 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 4.0 5.8 - - - +
392C ASP* 3.6 39.6 + - - +
395C PHE* 3.6 33.9 - - + -
396C ASP* 2.9 37.6 + - - +
418C PHE 2.9 18.4 + - - +
419C SER* 3.9 7.4 - - - +
421C ALA* 1.3 76.3 - - - +
423C GLU* 1.3 57.2 + - - +
425C MET* 3.3 1.9 + - - +
426C ALA* 3.0 47.3 + - - +
429C GLU* 4.7 3.8 + - - -
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Residues in contact with GLU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C SER 2.9 18.9 + - - +
420C GLU* 3.2 7.4 + - - +
422C ARG* 1.3 72.8 - - - +
424C ASP* 1.3 60.5 + - - +
426C ALA* 3.2 14.5 + - - +
427C ALA* 3.0 34.7 + - + +
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Residues in contact with ASP 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C HIS* 2.8 48.4 + - + +
195C LEU* 3.7 15.4 - - - +
264C ARG* 2.8 33.1 + - - -
420C GLU 3.1 10.2 + - - +
421C ALA 3.5 5.6 - - - +
423C GLU* 1.3 75.8 - - - +
425C MET* 1.3 58.0 + - - +
427C ALA* 3.4 4.4 + - - +
428C LEU* 2.8 24.3 + - - +
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Residues in contact with MET 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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188C ILE* 4.0 21.1 - - + +
191C THR* 3.4 33.0 - - + -
192C HIS* 4.6 7.2 - - - -
195C LEU* 5.8 2.0 - - - -
388C TRP* 3.5 42.6 - - + -
392C ASP* 3.4 33.0 - - - +
421C ALA 3.2 14.7 + - - +
422C ARG* 3.6 7.9 - - - +
423C GLU 3.2 0.2 - - - -
424C ASP* 1.3 74.7 - - - +
426C ALA* 1.3 60.2 + - - +
428C LEU* 3.2 12.6 + - + +
429C GLU* 2.9 33.1 + - - +
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Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ARG* 3.0 29.3 + - - +
423C GLU* 3.2 24.4 + - - +
425C MET* 1.3 75.0 - - - +
427C ALA* 1.3 58.1 + - - +
429C GLU* 3.4 8.7 + - - +
430C LYS* 3.0 27.0 + - - +
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Residues in contact with ALA 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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264C ARG* 3.8 11.2 - - - +
423C GLU* 3.0 21.0 + - + +
424C ASP* 3.4 12.1 - - - +
425C MET 3.2 0.2 - - - -
426C ALA* 1.3 74.9 - - - +
428C LEU* 1.3 54.3 + - - +
430C LYS* 3.1 13.6 + - + +
431C ASP* 2.7 40.4 + - - +
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Residues in contact with LEU 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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191C THR* 4.8 1.1 - - + -
195C LEU* 4.4 13.7 - - + -
264C ARG* 3.3 47.0 - - + +
265C ILE* 4.8 1.3 - - + -
267C PHE* 4.4 7.0 - - + -
388C TRP* 3.5 36.8 - - + +
424C ASP 2.8 17.1 + - - +
425C MET* 3.2 24.0 + - + +
427C ALA* 1.3 75.3 - - - +
429C GLU* 1.3 62.4 + - - +
431C ASP* 3.2 4.9 + - - +
432C TYR* 3.1 49.0 + - + -
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Residues in contact with GLU 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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385C ALA* 4.5 10.1 - - + +
388C TRP* 4.1 15.3 - - + -
389C ALA* 3.5 32.8 - - - +
392C ASP* 2.7 31.1 - - - +
422C ARG* 4.7 4.5 + - - -
425C MET 2.9 15.3 + - - +
426C ALA* 3.6 10.8 - - - +
428C LEU* 1.3 76.0 - - - +
430C LYS* 1.3 62.3 + - - +
432C TYR* 3.4 7.0 + - - +
433C GLU* 3.2 26.1 + - - +
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Residues in contact with LYS 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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426C ALA 3.0 15.6 + - - +
427C ALA* 3.2 15.5 - - + +
429C GLU* 1.3 76.3 - - - +
431C ASP* 1.3 51.8 + - - +
433C GLU* 3.1 18.4 + - + +
434C GLU* 2.8 59.5 + - + +
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Residues in contact with ASP 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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264C ARG* 2.9 41.8 + - - +
265C ILE* 4.0 18.2 - - + -
427C ALA* 2.7 19.1 + - - +
428C LEU* 3.4 10.1 - - + +
430C LYS* 1.3 74.6 - - - +
432C TYR* 1.3 57.8 + - - +
434C GLU* 3.3 17.8 + - - +
435C VAL* 3.1 34.2 + - + +
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Residues in contact with TYR 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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265C ILE* 3.6 41.0 - - + +
267C PHE* 3.3 33.9 + + - +
313C MET* 4.7 2.0 - - + -
380C ASN* 4.5 4.4 + - - -
381C THR 4.2 5.2 - - - -
382C THR* 3.4 39.9 - - + +
384C ILE* 4.0 18.6 - - + -
385C ALA* 3.8 27.4 - - + -
388C TRP* 4.0 12.1 - + - -
428C LEU* 3.1 48.1 + - + +
429C GLU 3.9 3.6 - - - +
431C ASP* 1.3 72.6 - - - +
433C GLU* 1.3 65.7 + - - +
435C VAL* 3.3 17.2 - - + +
436C GLY* 4.6 0.3 - - - -
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Residues in contact with GLU 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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429C GLU* 3.2 16.2 + - - +
430C LYS* 3.1 21.1 + - + +
432C TYR* 1.3 77.9 - - - +
434C GLU* 1.3 61.8 + - + +
436C GLY* 3.4 11.1 + - - -
437C VAL* 3.5 18.4 + - + +
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Residues in contact with GLU 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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391B ARG* 3.0 17.6 + - - -
430C LYS* 2.8 54.8 + - + +
431C ASP* 3.3 18.8 + - - +
433C GLU* 1.3 70.7 - - + +
435C VAL* 1.3 66.0 + - + +
437C VAL* 3.1 18.9 + - + +
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Residues in contact with VAL 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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391B ARG* 3.6 7.1 + - - +
262C TYR* 3.8 33.4 - - + -
265C ILE* 4.3 11.7 - - + -
313C MET* 3.7 28.9 - - + -
344C VAL* 3.5 6.1 - - - +
346C TRP* 2.9 29.6 + - + +
382C THR* 3.7 8.1 - - + -
431C ASP* 3.1 14.1 + - + +
432C TYR* 3.3 22.9 - - + +
434C GLU* 1.3 76.0 - - + +
436C GLY* 1.3 62.3 + - - +
437C VAL 3.5 1.0 + - - +
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Residues in contact with GLY 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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311C LYS* 2.9 37.1 + - - +
344C VAL* 3.8 14.9 - - - +
382C THR* 4.4 11.7 - - - -
432C TYR 3.8 1.0 + - - -
433C GLU 3.4 7.4 + - - -
434C GLU 3.2 1.0 - - - -
435C VAL* 1.3 80.6 - - - +
437C VAL* 1.3 62.2 + - - +
438C ASP* 4.5 0.3 - - - +
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Residues in contact with VAL 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ARG* 2.8 34.4 + - - +
311C LYS* 5.0 0.2 - - - +
344C VAL* 5.7 0.7 - - - +
346C TRP* 4.7 1.0 - - - -
433C GLU* 3.5 18.8 - - + +
434C GLU* 3.1 15.6 + - + +
435C VAL 3.7 1.6 - - - +
436C GLY* 1.3 78.7 - - - +
438C ASP* 1.3 68.2 + - + +
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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