Contacts of the helix formed by residues 413 - 424 (chain E) in PDB entry 1FPY
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 SER 413 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319E TYR* 3.1 29.6 - - - -
411E ALA* 3.7 1.7 - - - +
412E GLY* 1.3 77.3 - - - +
414E LEU* 1.3 62.8 + - - +
415E GLU* 3.8 7.5 + - - +
416E GLU* 3.3 25.5 + - - +
417E ALA 3.5 11.6 + - - -
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Residues in contact with LEU 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ALA* 5.1 1.8 - - - -
313E ASN 3.6 24.0 - - - +
314E PRO* 3.8 25.1 - - + +
316E THR* 4.0 18.8 - - + +
319E TYR* 3.4 18.6 - - + +
413E SER* 1.3 73.7 - - - +
415E GLU* 1.3 56.5 + - - +
416E GLU 3.1 2.2 - - - -
417E ALA* 3.1 5.5 + - + +
418E LEU* 2.8 52.8 + - + +
446E ARG* 4.2 12.8 - - + +
450E ASP* 3.8 32.9 + - + +
465K TYR* 4.5 3.6 - - - +
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Residues in contact with GLU 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413E SER* 4.2 7.7 + - - +
414E LEU* 1.3 76.1 - - - +
416E GLU* 1.3 57.8 + - - +
418E LEU* 3.3 8.2 + - - +
419E ASN* 2.8 34.9 + - + +
447E ARG* 3.7 20.0 + - - +
450E ASP* 4.3 18.4 + - - +
454E ARG* 4.2 19.5 + - - -
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Residues in contact with GLU 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E LYS* 3.3 34.4 + - + +
411E ALA* 4.0 7.6 - - + -
412E GLY* 3.2 25.9 + - - -
413E SER* 3.3 21.3 + - - +
415E GLU* 1.3 78.1 - - - +
417E ALA* 1.3 65.3 + - - +
418E LEU 2.8 2.3 + - - -
419E ASN* 2.9 10.9 + - - +
420E ALA* 2.8 24.1 + - + +
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Residues in contact with ALA 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E LYS 3.2 18.5 - - - +
309E ASN* 3.6 0.4 - - + -
310E ALA* 3.3 28.4 - - - +
319E TYR* 3.0 28.7 - - - +
411E ALA* 3.6 14.8 - - + +
413E SER 3.5 2.7 + - - +
414E LEU* 3.1 7.5 + - + +
416E GLU* 1.3 78.4 - - - +
418E LEU* 1.3 61.5 + - - +
420E ALA* 3.9 1.8 - - - -
421E LEU 3.1 16.3 + - - -
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Residues in contact with LEU 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ALA* 4.0 18.4 - - + +
414E LEU* 2.8 35.6 + - + +
415E GLU* 3.5 4.7 - - - +
416E GLU 2.8 0.6 + - - -
417E ALA* 1.3 72.5 - - - +
419E ASN* 1.3 67.5 + - - +
420E ALA 3.0 0.9 - - - -
421E LEU* 2.8 16.9 + - - +
422E ASP* 2.8 11.0 + - - +
442E TYR* 4.5 4.5 - - + -
443E ILE* 4.0 25.0 - - + +
446E ARG* 3.9 34.8 - - + +
447E ARG* 3.6 43.5 - - + +
450E ASP* 5.4 1.8 - - + -
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Residues in contact with ASN 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E GLU* 2.8 22.9 + - + +
416E GLU* 3.6 8.1 - - - +
418E LEU* 1.3 73.1 - - - +
420E ALA* 1.3 61.1 + - - +
422E ASP* 2.9 30.3 + - - +
423E LEU* 3.1 31.1 + - - +
447E ARG* 3.5 15.1 - - - +
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Residues in contact with ALA 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E LYS* 3.6 37.5 - - + -
307E ALA* 3.9 3.4 - - + +
416E GLU* 2.8 16.6 + - + +
417E ALA 3.6 6.1 - - - +
419E ASN* 1.3 78.4 + - - +
421E LEU* 1.3 61.1 + - - +
422E ASP 3.2 0.2 + - - -
423E LEU* 3.3 5.7 + - - +
424E ASP* 2.8 34.8 + - + +
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Residues in contact with LEU 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E ALA* 3.7 21.7 - - + +
310E ALA* 3.9 20.9 - - + -
311E LEU* 4.5 11.7 - - + -
417E ALA 3.1 10.5 + - - +
418E LEU* 2.8 10.4 + - + +
420E ALA* 1.3 75.5 - - - +
422E ASP* 1.3 65.8 + - - +
424E ASP 4.9 0.2 - - - -
425E ARG* 3.2 19.5 + - - +
428E LEU* 3.5 32.5 - - + -
434E PHE* 6.4 0.7 - - + -
439E ILE* 4.1 20.9 - - + +
442E TYR* 4.4 14.1 - - + -
443E ILE* 3.8 25.4 - - + -
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Residues in contact with ASP 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E LEU 2.8 8.5 + - - +
419E ASN* 2.9 27.1 + - - +
421E LEU* 1.3 79.0 - - - +
423E LEU* 1.3 71.1 + - + +
425E ARG* 2.7 60.5 + - - +
443E ILE* 4.0 14.8 - - + -
447E ARG* 5.7 4.1 + - - +
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Residues in contact with LEU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419E ASN* 3.1 33.1 + - - +
420E ALA* 3.9 5.2 - - - +
422E ASP* 1.3 86.9 - - - +
424E ASP* 1.3 54.8 + - + +
425E ARG* 2.5 24.2 + - - +
426E GLU* 4.1 6.4 + - - +
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Residues in contact with ASP 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E LYS* 4.2 4.7 - - - +
304E HIS* 2.8 50.9 + - - +
307E ALA* 4.0 8.3 + - + +
420E ALA* 2.8 19.6 + - + +
421E LEU* 4.0 4.7 - - - -
423E LEU* 1.3 70.9 - - + +
425E ARG* 1.3 54.4 + - - +
426E GLU* 3.1 7.5 + - - +
427E PHE* 3.0 26.9 + - - -
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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