Contacts of the helix formed by residues 413 - 424 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319D TYR* 3.1 27.7 - - - -
411D ALA* 3.7 1.9 - - - +
412D GLY* 1.3 77.6 - - - +
414D LEU* 1.3 63.0 + - - +
415D GLU* 3.8 7.5 + - - +
416D GLU* 3.3 24.2 + - - +
417D ALA 3.5 11.4 + - - -
450D ASP* 6.0 0.2 - - - -
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Residues in contact with LEU 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D ALA* 5.1 2.0 - - - -
313D ASN 3.6 24.0 - - - +
314D PRO* 3.8 25.4 - - + +
316D THR* 4.0 19.7 - - + +
319D TYR* 3.4 18.9 - - + +
413D SER* 1.3 73.5 - - - +
415D GLU* 1.3 56.8 + - - +
416D GLU 3.1 1.8 - - - -
417D ALA* 3.1 5.0 + - + +
418D LEU* 2.8 52.3 + - + +
446D ARG* 4.2 12.1 - - + +
450D ASP* 3.8 33.0 + - + +
465J TYR* 4.5 3.4 - - - +
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Residues in contact with GLU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D SER* 4.2 7.5 + - - +
414D LEU* 1.3 77.3 - - - +
416D GLU* 1.3 57.7 + - - +
418D LEU* 3.3 7.9 + - - +
419D ASN* 2.8 35.1 + - + +
447D ARG* 3.7 19.7 + - - +
450D ASP* 4.3 17.7 + - - +
454D ARG* 4.2 19.3 + - - -
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Residues in contact with GLU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D LYS* 3.3 34.5 + - + -
411D ALA* 4.0 7.6 - - + -
412D GLY* 3.2 27.0 + - - -
413D SER* 3.3 19.4 + - - +
415D GLU* 1.3 77.0 - - - +
417D ALA* 1.3 67.4 + - - +
418D LEU 2.8 2.4 + - - -
419D ASN* 2.9 11.4 + - - +
420D ALA* 2.8 22.2 + - + +
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Residues in contact with ALA 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D LYS 3.2 18.0 - - - +
309D ASN* 3.6 0.7 - - + -
310D ALA* 3.3 29.3 - - - +
319D TYR* 3.0 28.7 - - - +
411D ALA* 3.6 14.6 - - + +
413D SER 3.5 2.5 + - - +
414D LEU* 3.1 7.9 + - + +
416D GLU* 1.3 78.7 - - - +
418D LEU* 1.3 62.2 + - - +
420D ALA* 3.6 2.0 - - - +
421D LEU 3.1 16.1 + - - -
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Residues in contact with LEU 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D ALA* 4.0 18.6 - - + +
414D LEU* 2.8 35.0 + - + +
415D GLU* 3.5 5.2 - - - +
416D GLU 2.8 0.8 + - - -
417D ALA* 1.3 73.7 - - - +
419D ASN* 1.3 67.1 + - - +
420D ALA 3.0 0.9 - - - -
421D LEU* 2.8 16.5 + - - +
422D ASP* 2.8 11.8 + - - +
442D TYR* 4.5 4.3 - - + -
443D ILE* 4.0 24.3 - - + +
446D ARG* 3.9 35.4 - - + -
447D ARG* 3.6 43.7 - - + +
450D ASP* 5.4 1.6 - - + -
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Residues in contact with ASN 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D GLU* 2.8 23.3 + - + +
416D GLU* 3.6 7.9 - - - +
418D LEU* 1.3 72.4 - - - +
420D ALA* 1.3 62.3 + - - +
422D ASP* 2.9 31.7 + - - +
423D LEU* 3.1 30.6 + - - +
447D ARG* 3.5 15.1 - - - +
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Residues in contact with ALA 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D LYS* 3.6 38.1 - - + +
307D ALA* 3.9 3.6 - - + +
416D GLU* 2.8 15.9 + - + +
417D ALA 3.6 5.4 - - - +
419D ASN* 1.3 78.6 + - - +
421D LEU* 1.3 61.1 + - - +
422D ASP 3.2 0.2 + - - -
423D LEU* 3.3 5.3 + - - +
424D ASP* 2.8 35.6 + - + +
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Residues in contact with LEU 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D ALA* 3.7 21.5 - - + +
310D ALA* 3.9 20.6 - - + -
311D LEU* 4.5 12.1 - - + -
417D ALA 3.1 10.5 + - - +
418D LEU* 2.8 10.9 + - + +
420D ALA* 1.3 76.4 - - - +
422D ASP* 1.3 64.0 + - - +
424D ASP 4.8 0.2 - - - +
425D ARG* 3.2 20.0 + - - +
428D LEU* 3.5 32.5 - - + -
434D PHE* 6.4 0.7 - - + -
439D ILE* 4.1 21.2 - - + +
442D TYR* 4.4 14.1 - - + -
443D ILE* 3.8 24.7 - - + -
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Residues in contact with ASP 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D LEU 2.8 8.7 + - - +
419D ASN* 2.9 27.6 + - - +
421D LEU* 1.3 79.3 - - - +
423D LEU* 1.3 70.7 + - - +
425D ARG* 2.7 61.1 + - - +
443D ILE* 4.0 15.2 - - + +
447D ARG* 5.7 3.5 + - - +
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Residues in contact with LEU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D ASN* 3.1 32.0 + - - +
420D ALA* 3.9 5.6 - - - +
422D ASP* 1.3 86.2 - - - +
424D ASP* 1.3 54.1 + - + +
425D ARG* 2.5 24.4 + - - +
426D GLU* 4.1 6.6 + - - +
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Residues in contact with ASP 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D LYS* 4.2 4.7 - - - +
304D HIS* 2.8 50.8 + - - +
307D ALA* 4.0 8.2 - - + +
420D ALA* 2.8 20.0 + - + +
421D LEU* 4.0 4.9 - - - -
423D LEU* 1.3 70.0 - - + +
425D ARG* 1.3 53.2 + - - +
426D GLU* 3.1 8.2 + - - +
427D 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