Contacts of the helix formed by residues 413 - 424 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B TYR* 3.1 27.6 - - - -
411B ALA* 3.7 1.9 - - - +
412B GLY* 1.3 77.6 - - - +
414B LEU* 1.3 62.5 + - - +
415B GLU* 3.8 7.8 + - - +
416B GLU* 3.3 25.9 + - - +
417B ALA 3.5 11.8 + - - -
450B ASP* 6.0 0.2 - - - -
415H GLU* 6.1 0.7 - - - -
454H ARG* 6.6 0.2 - - - -
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ALA* 5.1 1.6 - - - -
313B ASN 3.6 24.2 - - - +
314B PRO* 3.8 24.7 - - + +
315B THR* 4.1 0.4 - - - +
316B THR* 4.0 19.7 - - + +
319B TYR* 3.4 18.3 - - + +
413B SER* 1.3 74.1 - - - +
415B GLU* 1.3 57.3 + - - +
416B GLU 3.1 1.6 - - - -
417B ALA* 3.1 4.3 + - + +
418B LEU* 2.8 53.9 + - + +
446B ARG* 4.2 11.7 - - + +
449B GLU* 5.4 0.2 - - - +
450B ASP* 3.8 33.1 + - + +
465H TYR* 4.6 3.1 - - - +
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B SER* 4.2 7.3 + - - +
414B LEU* 1.3 77.6 - - - +
416B GLU* 1.3 58.0 + - - +
418B LEU* 3.3 8.0 + - - +
419B ASN* 2.8 35.2 + - + +
447B ARG* 3.7 19.8 + - - +
450B ASP* 4.3 18.3 + - - +
454B ARG* 4.2 19.4 + - - -
413H SER* 6.2 0.7 - - - -
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LYS* 3.3 34.2 + - + +
411B ALA* 4.0 7.6 - - + -
412B GLY* 3.2 27.0 + - - -
413B SER* 3.3 20.2 + - - +
415B GLU* 1.3 77.4 - - - +
417B ALA* 1.3 66.7 + - - +
418B LEU 2.8 1.9 + - - -
419B ASN* 2.9 12.3 + - - +
420B ALA* 2.8 23.2 + - + +
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B LYS 3.2 18.3 - - - +
309B ASN* 3.6 0.4 - - + -
310B ALA* 3.3 28.6 - - - +
319B TYR* 3.0 28.7 - - - +
411B ALA* 3.6 15.7 - - + +
413B SER 3.5 2.2 + - - +
414B LEU* 3.1 8.2 + - + +
416B GLU* 1.3 79.2 - - - +
418B LEU* 1.3 60.8 + - - +
420B ALA* 3.6 1.7 - - - +
421B LEU 3.1 15.9 + - - -
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ALA* 4.0 19.1 - - + -
414B LEU* 2.8 35.4 + - + +
415B GLU* 3.5 4.9 - - - +
416B GLU 2.8 0.8 + - - -
417B ALA* 1.3 73.3 - - - +
419B ASN* 1.3 67.2 + - - +
420B ALA 3.0 0.7 - - - -
421B LEU* 2.8 17.0 + - - +
422B ASP* 2.8 11.2 + - - +
442B TYR* 4.5 4.0 - - + -
443B ILE* 4.0 24.9 - - + +
446B ARG* 3.9 35.2 - - + +
447B ARG* 3.7 43.7 - - + +
450B ASP* 5.4 1.6 - - + -
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Residues in contact with ASN 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B GLU* 2.8 22.5 + - + +
416B GLU* 3.6 8.5 - - - +
418B LEU* 1.3 72.0 - - - +
420B ALA* 1.3 61.6 + - - +
422B ASP* 2.9 31.7 + - - +
423B LEU* 3.1 30.7 + - - +
447B ARG* 3.5 16.0 - - - +
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B LYS* 3.6 37.9 - - + +
307B ALA* 3.9 3.6 - - + +
416B GLU* 2.8 15.5 + - + +
417B ALA 3.6 5.6 - - - +
419B ASN* 1.3 78.6 + - - +
421B LEU* 1.3 60.4 + - - +
422B ASP 3.2 0.2 + - - -
423B LEU* 3.3 4.9 + - - -
424B ASP* 2.8 35.2 + - + +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ALA* 3.7 21.5 - - + +
310B ALA* 3.9 20.0 - - + -
311B LEU* 4.5 12.8 - - + -
417B ALA 3.1 10.5 + - - +
418B LEU* 2.8 10.4 + - + +
420B ALA* 1.3 76.3 - - - +
422B ASP* 1.3 65.2 + - - +
424B ASP 4.8 0.4 - - - +
425B ARG* 3.2 19.3 + - - +
428B LEU* 3.5 32.1 - - + -
434B PHE* 6.4 0.4 - - + -
439B ILE* 4.1 22.2 - - + +
442B TYR* 4.4 13.7 - - + -
443B ILE* 3.8 25.4 - - + -
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Residues in contact with ASP 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B LEU 2.8 8.5 + - - +
419B ASN* 2.9 27.0 + - - +
421B LEU* 1.3 79.4 - - - +
423B LEU* 1.3 71.7 + - - +
425B ARG* 2.7 61.0 + - - +
443B ILE* 4.0 14.1 - - + +
447B ARG* 5.7 4.3 + - - +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ASN* 3.1 33.3 + - - +
420B ALA* 3.9 5.2 - - - +
422B ASP* 1.3 86.4 - - - +
424B ASP* 1.3 54.9 + - + +
425B ARG* 2.5 23.2 + - - +
426B GLU* 4.1 6.6 + - - +
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Residues in contact with ASP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B LYS* 4.2 4.9 - - - +
304B HIS* 2.8 49.9 + - - +
307B ALA* 4.0 8.6 - - + +
420B ALA* 2.8 19.5 + - + +
421B LEU* 4.0 4.7 - - - -
423B LEU* 1.3 70.4 - - + +
425B ARG* 1.3 55.1 + - - +
426B GLU* 3.1 7.5 + - - +
427B PHE* 3.0 27.2 + - - -
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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
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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