Contacts of the helix formed by residues 413 - 424 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A TYR* 3.1 28.0 - - - -
411A ALA* 3.7 1.9 - - - +
412A GLY* 1.3 77.5 - - - +
414A LEU* 1.3 63.4 + - - +
415A GLU* 3.8 7.8 + - - +
416A GLU* 3.3 25.6 + - - +
417A ALA 3.5 11.3 + - - -
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ALA* 5.1 2.0 - - - -
313A ASN 3.6 24.7 - - - +
314A PRO* 3.8 25.1 - - + +
316A THR* 4.0 19.3 - - + +
319A TYR* 3.4 19.0 - - + +
413A SER* 1.3 73.1 - - - +
415A GLU* 1.3 56.5 + - - +
416A GLU 3.1 1.8 - - - -
417A ALA* 3.1 4.9 + - + +
418A LEU* 2.8 54.0 + - + +
446A ARG* 4.2 11.9 - - + +
449A GLU* 5.4 0.2 - - - +
450A ASP* 3.8 32.0 + - + +
465G TYR* 4.5 3.6 - - - +
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A SER* 4.2 7.8 + - - +
414A LEU* 1.3 77.1 - - - +
416A GLU* 1.3 56.4 + - - +
418A LEU* 3.3 8.2 + - - +
419A ASN* 2.8 34.7 + - + +
447A ARG* 3.7 19.6 + - - +
450A ASP* 4.3 18.4 + - - +
454A ARG* 4.2 19.0 + - - -
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LYS* 3.3 33.6 + - + +
411A ALA* 4.0 8.1 - - + -
412A GLY* 3.2 25.7 + - - -
413A SER* 3.3 20.9 + - - +
415A GLU* 1.3 77.2 - - - +
417A ALA* 1.3 65.7 + - - +
418A LEU 2.8 1.7 + - - -
419A ASN* 2.9 11.1 + - - +
420A ALA* 2.8 23.3 + - + +
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Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LYS 3.2 18.5 - - - +
309A ASN* 3.6 0.9 - - + -
310A ALA* 3.3 28.9 - - - +
319A TYR* 3.0 28.7 - - - +
411A ALA* 3.6 14.1 - - + +
413A SER 3.5 2.4 + - - +
414A LEU* 3.1 7.3 + - + +
416A GLU* 1.3 79.0 - - - +
418A LEU* 1.3 60.7 + - - +
420A ALA* 3.6 1.5 - - - +
421A LEU 3.1 15.9 + - - -
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ALA* 4.0 18.2 - - + +
414A LEU* 2.8 35.8 + - + +
415A GLU* 3.5 5.2 - - - +
416A GLU 2.8 0.6 + - - -
417A ALA* 1.3 73.3 - - - +
419A ASN* 1.3 67.2 + - - +
420A ALA 3.0 1.3 - - - -
421A LEU* 2.8 17.0 + - - +
422A ASP* 2.8 11.2 + - - +
442A TYR* 4.5 4.9 - - + -
443A ILE* 4.0 24.3 - - + +
446A ARG* 3.9 34.3 - - + +
447A ARG* 3.7 44.0 - - + +
450A ASP* 5.4 1.3 - - + -
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Residues in contact with ASN 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A GLU* 2.8 23.2 + - + +
416A GLU* 3.6 7.9 - - - +
418A LEU* 1.3 73.1 - - - +
420A ALA* 1.3 62.0 + - - +
422A ASP* 2.9 31.2 + - - +
423A LEU* 3.1 30.7 + - - +
447A ARG* 3.5 15.8 - - - +
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LYS* 3.6 37.9 - - + -
307A ALA* 3.9 3.8 - - + +
416A GLU* 2.8 16.2 + - + +
417A ALA 3.6 6.3 - - - +
419A ASN* 1.3 77.8 + - - +
421A LEU* 1.3 61.2 + - - +
422A ASP 3.2 0.2 + - - -
423A LEU* 3.3 5.8 + - - +
424A ASP* 2.8 35.6 + - + +
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ALA* 3.7 21.7 - - + +
310A ALA* 3.9 20.0 - - + -
311A LEU* 4.5 11.2 - - + -
417A ALA 3.1 9.9 + - - +
418A LEU* 2.8 10.4 + - + +
420A ALA* 1.3 76.5 - - - +
422A ASP* 1.3 65.1 + - - +
425A ARG* 3.2 19.7 + - - +
428A LEU* 3.5 31.9 - - + -
434A PHE* 6.4 0.7 - - + -
439A ILE* 4.1 21.5 - - + +
442A TYR* 4.4 14.8 - - + -
443A ILE* 3.8 24.7 - - + -
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Residues in contact with ASP 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A LEU 2.8 8.3 + - - +
419A ASN* 2.9 26.6 + - - +
421A LEU* 1.3 79.2 - - - +
423A LEU* 1.3 72.0 + - - +
425A ARG* 2.7 61.1 + - - +
443A ILE* 4.0 14.1 - - + -
447A ARG* 5.7 4.3 + - - +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ASN* 3.1 32.0 + - - +
420A ALA* 3.9 5.6 - - - +
422A ASP* 1.3 86.4 - - - +
424A ASP* 1.3 55.4 + - - +
425A ARG* 2.5 23.3 + - - +
426A GLU* 4.1 6.4 + - - +
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Residues in contact with ASP 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LYS* 4.2 4.5 - - - +
304A HIS* 2.8 49.9 + - - +
307A ALA* 4.0 7.6 + - + +
420A ALA* 2.8 19.2 + - + +
421A LEU* 4.0 4.7 - - - -
423A LEU* 1.3 70.3 - - + +
425A ARG* 1.3 55.3 + - - +
426A GLU* 3.1 7.8 + - - +
427A PHE* 3.0 26.7 + - - -
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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