Contacts of the helix formed by residues 413 - 424 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319J TYR* 3.1 27.4 - - - -
411J ALA* 3.7 1.7 - - - +
412J GLY* 1.3 78.0 - - - +
414J LEU* 1.3 62.2 + - - +
415J GLU* 3.8 7.7 + - - +
416J GLU* 3.3 25.1 + - - +
417J ALA 3.5 12.1 + - - -
450J ASP* 6.0 0.4 - - - -
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Residues in contact with LEU 414 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D TYR* 4.5 3.4 - - - +
310J ALA* 5.1 1.6 - - - -
313J ASN 3.6 24.2 - - - +
314J PRO* 3.8 25.8 - - + +
316J THR* 4.0 19.7 - - + +
319J TYR* 3.4 19.0 - - + +
413J SER* 1.3 73.9 - - - +
415J GLU* 1.3 56.7 + - - +
416J GLU 3.1 1.6 - - - -
417J ALA* 3.1 5.3 + - + +
418J LEU* 2.8 52.1 + - + +
446J ARG* 4.2 12.6 - - + +
450J ASP* 3.8 33.5 + - + +
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Residues in contact with GLU 415 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413J SER* 4.2 7.7 + - - +
414J LEU* 1.3 77.2 - - - +
416J GLU* 1.3 58.5 + - - +
418J LEU* 3.3 7.4 + - - +
419J ASN* 2.8 34.6 + - + +
447J ARG* 3.7 19.0 + - - +
450J ASP* 4.3 19.7 + - - +
454J ARG* 4.2 18.5 - - - -
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Residues in contact with GLU 416 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306J LYS* 3.3 34.6 + - + -
411J ALA* 4.0 7.2 - - + -
412J GLY* 3.2 26.1 + - - -
413J SER* 3.3 20.5 + - - +
415J GLU* 1.3 77.8 - - - +
417J ALA* 1.3 65.7 + - - +
418J LEU 2.8 1.9 + - - -
419J ASN* 2.9 11.3 + - - +
420J ALA* 2.8 22.5 + - + +
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Residues in contact with ALA 417 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306J LYS 3.2 18.6 - - - +
309J ASN* 3.6 0.2 - - + -
310J ALA* 3.3 28.5 - - - +
319J TYR* 3.0 28.7 - - - +
411J ALA* 3.6 14.8 - - + +
413J SER 3.5 2.7 + - - +
414J LEU* 3.1 8.0 + - + +
416J GLU* 1.3 78.5 - - - +
418J LEU* 1.3 60.4 + - - +
420J ALA* 3.6 1.7 - - - +
421J LEU 3.1 16.3 + - - -
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Residues in contact with LEU 418 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310J ALA* 4.0 18.2 - - + +
414J LEU* 2.8 35.6 + - + +
415J GLU* 3.5 4.9 - - - +
416J GLU 2.8 0.8 + - - -
417J ALA* 1.3 73.8 - - - +
419J ASN* 1.3 67.0 + - - +
420J ALA 3.0 1.3 - - - -
421J LEU* 2.8 17.2 + - - +
422J ASP* 2.8 11.2 + - - +
442J TYR* 4.5 4.7 - - + -
443J ILE* 4.0 23.6 - - + +
446J ARG* 3.9 35.7 - - + -
447J ARG* 3.7 44.4 - - + +
450J ASP* 5.4 1.6 - - + -
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Residues in contact with ASN 419 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415J GLU* 2.8 23.6 + - + +
416J GLU* 3.6 8.0 - - - +
418J LEU* 1.3 72.2 - - - +
420J ALA* 1.3 61.2 + - - +
422J ASP* 2.9 31.7 + - - +
423J LEU* 3.1 31.7 + - - +
447J ARG* 3.5 14.6 - - - +
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Residues in contact with ALA 420 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306J LYS* 3.6 37.2 - - + -
307J ALA* 3.9 4.3 - - + +
416J GLU* 2.8 16.2 + - + +
417J ALA 3.6 6.1 - - - +
419J ASN* 1.3 79.0 + - - +
421J LEU* 1.3 60.9 + - - +
422J ASP 3.2 0.2 + - - -
423J LEU* 3.3 5.9 + - - +
424J ASP* 2.8 35.7 + - + +
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Residues in contact with LEU 421 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307J ALA* 3.7 21.0 - - + +
310J ALA* 3.9 20.2 - - + -
311J LEU* 4.5 11.7 - - + -
417J ALA 3.1 10.3 + - - +
418J LEU 2.8 10.4 + - - +
420J ALA* 1.3 75.8 - - - +
422J ASP* 1.3 64.8 + - - +
424J ASP 4.9 0.2 - - - -
425J ARG* 3.2 19.9 + - - +
428J LEU* 3.5 31.9 - - + -
434J PHE* 6.4 0.7 - - + -
439J ILE* 4.1 20.9 - - + +
442J TYR* 4.4 14.6 - - + -
443J ILE* 3.8 25.6 - - + -
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Residues in contact with ASP 422 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418J LEU 2.8 8.3 + - - +
419J ASN* 2.9 28.2 + - - +
421J LEU* 1.3 79.2 - - - +
423J LEU* 1.3 72.6 + - - +
425J ARG* 2.7 60.6 + - - +
443J ILE* 4.0 14.6 - - + +
447J ARG* 5.7 3.7 + - - +
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Residues in contact with LEU 423 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419J ASN* 3.1 32.6 + - - +
420J ALA* 3.9 5.2 - - - +
422J ASP* 1.3 86.9 - - - +
424J ASP* 1.3 54.7 + - + +
425J ARG* 2.5 24.4 + - - +
426J GLU* 4.1 6.2 + - - +
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Residues in contact with ASP 424 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303J LYS* 4.2 4.3 - - - +
304J HIS* 2.8 50.3 + - - +
307J ALA* 4.0 8.1 + - + +
420J ALA* 2.8 18.7 + - + +
421J LEU* 4.0 4.7 - - - -
423J LEU* 1.3 70.3 - - + +
425J ARG* 1.3 55.6 + - - +
426J GLU* 3.1 7.5 + - - +
427J PHE* 3.0 26.8 + - - -
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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