Contacts of the helix formed by residues 413 - 424 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319K TYR* 3.1 28.5 - - - -
411K ALA* 3.7 1.4 - - - +
412K GLY* 1.3 77.6 - - - +
414K LEU* 1.3 62.7 + - - +
415K GLU* 3.8 8.1 + - - +
416K GLU* 3.3 26.2 + - - +
417K ALA 3.5 11.8 + - - -
450K ASP* 6.0 0.4 - - - -
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Residues in contact with LEU 414 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465E TYR* 4.5 3.4 - - - +
310K ALA* 5.1 2.0 - - - -
313K ASN 3.6 24.0 - - - +
314K PRO* 3.8 25.6 - - + +
315K THR 4.1 0.2 - - - +
316K THR* 4.0 20.2 - - + +
319K TYR* 3.4 18.3 - - + +
413K SER* 1.3 72.9 - - - +
415K GLU* 1.3 58.6 + - - +
416K GLU 3.1 1.6 - - - -
417K ALA* 3.1 5.5 + - + +
418K LEU* 2.8 52.8 + - + +
446K ARG* 4.2 12.3 - - + +
450K ASP* 3.8 33.3 + - + +
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Residues in contact with GLU 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413K SER* 4.2 7.7 + - - +
414K LEU* 1.3 76.5 - - - +
416K GLU* 1.3 58.2 + - - +
418K LEU* 3.3 8.3 + - - +
419K ASN* 2.8 34.8 + - + +
447K ARG* 3.7 19.5 + - - +
450K ASP* 4.3 17.8 + - - +
454K ARG* 4.2 19.1 - - - -
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Residues in contact with GLU 416 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306K LYS* 3.3 34.6 + - + -
411K ALA* 4.0 7.4 - - + -
412K GLY* 3.2 26.2 + - - -
413K SER* 3.3 20.6 + - - +
415K GLU* 1.3 78.3 - - - +
417K ALA* 1.3 66.7 + - - +
418K LEU 2.8 1.9 + - - -
419K ASN* 2.9 11.3 + - - +
420K ALA* 2.8 23.6 + - + +
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Residues in contact with ALA 417 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306K LYS 3.2 18.6 - - - +
309K ASN* 3.6 0.4 - - + -
310K ALA* 3.3 28.5 - - - +
319K TYR* 3.0 29.2 - - - +
411K ALA* 3.6 15.0 - - + +
413K SER 3.5 2.7 + - - +
414K LEU* 3.1 7.9 + - + +
416K GLU* 1.3 79.2 - - - +
418K LEU* 1.3 61.3 + - - +
420K ALA* 3.6 1.5 - - - +
421K LEU 3.1 16.3 + - - -
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Residues in contact with LEU 418 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310K ALA* 4.0 18.6 - - + +
414K LEU* 2.8 36.1 + - + +
415K GLU* 3.5 4.3 - - - +
416K GLU 2.8 0.8 + - - -
417K ALA* 1.3 73.0 - - - +
419K ASN* 1.3 67.5 + - - +
420K ALA 3.0 1.1 - - - -
421K LEU* 2.8 17.4 + - - +
422K ASP* 2.8 11.4 + - - +
442K TYR* 4.5 4.5 - - + -
443K ILE* 4.0 24.6 - - + +
446K ARG* 3.9 35.4 - - + -
447K ARG* 3.6 44.2 - - + +
450K ASP* 5.4 1.6 - - + -
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Residues in contact with ASN 419 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415K GLU* 2.8 23.1 + - + +
416K GLU* 3.6 8.8 - - - +
418K LEU* 1.3 72.7 - - - +
420K ALA* 1.3 62.3 + - - +
422K ASP* 2.9 31.1 + - - +
423K LEU* 3.1 31.4 + - - +
447K ARG* 3.5 15.4 - - - +
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Residues in contact with ALA 420 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306K LYS* 3.6 38.1 - - + -
307K ALA* 3.9 3.1 - - + +
416K GLU* 2.8 16.2 + - + +
417K ALA 3.6 5.6 - - - +
419K ASN* 1.3 78.9 + - - +
421K LEU* 1.3 61.1 + - - +
422K ASP 3.2 0.2 + - - -
423K LEU* 3.3 5.5 + - - +
424K ASP* 2.8 35.4 + - + +
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Residues in contact with LEU 421 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307K ALA* 3.7 20.3 - - + +
310K ALA* 3.9 20.4 - - + -
311K LEU* 4.5 11.2 - - + -
417K ALA 3.1 10.1 + - - +
418K LEU 2.8 10.6 + - - +
420K ALA* 1.3 76.7 - - - +
422K ASP* 1.3 64.6 + - - +
424K ASP 4.8 0.2 - - - +
425K ARG* 3.2 20.0 + - - +
428K LEU* 3.5 32.8 - - + -
434K PHE* 6.4 0.7 - - + -
439K ILE* 4.1 20.7 - - + +
442K TYR* 4.4 14.1 - - + -
443K ILE* 3.8 25.4 - - + -
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Residues in contact with ASP 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418K LEU 2.8 8.5 + - - +
419K ASN* 2.9 28.0 + - - +
421K LEU* 1.3 78.4 - - - +
423K LEU* 1.3 71.9 + - - +
425K ARG* 2.7 61.0 + - - +
443K ILE* 4.0 15.2 - - + +
447K ARG* 5.7 3.5 + - - +
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Residues in contact with LEU 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419K ASN* 3.1 32.9 + - - +
420K ALA* 3.9 5.4 - - - +
422K ASP* 1.3 86.9 - - - +
424K ASP* 1.3 53.6 + - + +
425K ARG* 2.5 24.7 + - - +
426K GLU* 4.1 6.6 + - - +
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Residues in contact with ASP 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303K LYS* 4.2 4.1 - - - +
304K HIS* 2.8 50.9 + - - +
307K ALA* 4.0 8.4 + - + +
420K ALA* 2.8 19.9 + - + +
421K LEU* 4.0 4.7 - - - -
423K LEU* 1.3 70.1 - - + +
425K ARG* 1.3 55.1 + - - +
426K GLU* 3.1 7.6 + - - +
427K PHE* 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
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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