Contacts of the helix formed by residues 413 - 424 (chain I) in PDB entry 1F1H
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415C GLU* 6.0 2.2 - - - -
454C ARG* 6.6 0.4 - - - -
319I TYR* 3.6 20.5 - - - -
411I ALA* 3.3 3.8 - - - +
412I GLY* 1.3 80.3 - - - +
414I LEU* 1.3 65.7 + - - +
415I GLU* 3.8 9.4 + - - +
416I GLU* 3.3 24.3 + - - +
417I ALA 3.2 15.8 + - - -
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Residues in contact with LEU 414 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C TYR* 4.5 3.8 - - - +
310I ALA* 5.0 2.0 - - - -
313I ASN 4.0 10.1 - - - +
314I PRO* 3.8 36.1 - - + +
315I THR* 4.4 0.4 - - - -
316I THR* 4.0 28.4 - - + +
319I TYR* 3.3 20.2 - - + +
413I SER* 1.3 71.0 - - - +
415I GLU* 1.3 57.2 + - - +
417I ALA* 2.9 5.7 + - + +
418I LEU* 2.7 60.6 + - + +
446I ARG* 4.0 23.1 - - + +
449I GLU* 5.6 0.2 - - + -
450I ASP* 4.0 14.5 + - + +
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Residues in contact with GLU 415 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C GLY 5.7 0.3 - - - +
413C SER* 6.0 1.6 - - - -
413I SER* 4.0 9.6 + - - +
414I LEU* 1.3 77.0 - - - +
416I GLU* 1.3 57.6 + - - +
418I LEU* 3.6 7.8 + - - -
419I ASN* 3.0 31.1 + - - +
447I ARG* 3.5 18.5 + - - +
450I ASP* 3.8 18.5 + - - +
454I ARG* 3.9 22.4 - - - -
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Residues in contact with GLU 416 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306I LYS* 3.1 33.9 + - + +
411I ALA* 3.8 7.4 - - + -
412I GLY* 2.8 30.8 + - - -
413I SER* 3.3 17.5 + - - +
414I LEU 3.1 0.6 - - - -
415I GLU* 1.3 79.9 - - - +
417I ALA* 1.3 59.3 + - - +
419I ASN* 3.3 7.5 - - + +
420I ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 417 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306I LYS 3.5 13.6 - - - +
309I ASN* 3.8 3.8 - - + -
310I ALA* 3.4 32.9 - - - +
319I TYR* 3.3 26.0 - - - +
411I ALA* 3.8 5.1 - - + +
413I SER 3.2 7.5 + - - +
414I LEU* 2.9 8.2 + - + +
416I GLU* 1.3 73.1 - - - +
418I LEU* 1.3 67.7 + - - +
420I ALA* 3.3 2.6 + - - +
421I LEU 2.9 18.7 + - - -
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Residues in contact with LEU 418 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310I ALA* 4.1 17.7 - - + -
414I LEU* 2.7 36.6 + - + +
415I GLU* 3.8 7.9 - - - +
417I ALA* 1.3 77.1 - - - +
419I ASN* 1.3 63.2 + - - +
421I LEU* 3.3 4.7 + - - +
422I ASP* 2.9 23.1 + - - +
442I TYR* 4.6 4.0 - - + -
443I ILE* 3.9 23.1 - - + +
446I ARG* 4.0 23.6 - - + -
447I ARG* 3.8 54.7 - - + +
450I ASP* 5.2 2.2 - - + -
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Residues in contact with ASN 419 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415I GLU* 3.0 21.2 + - - +
416I GLU* 3.3 13.4 - - + +
418I LEU* 1.3 75.9 - - - +
420I ALA* 1.3 63.3 + - - +
422I ASP* 2.9 27.8 + - - +
423I LEU* 3.1 34.4 + - + +
447I ARG* 3.9 12.1 + - - +
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Residues in contact with ALA 420 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306I LYS* 3.5 41.5 - - + -
307I ALA* 3.6 4.5 - - + +
416I GLU 3.0 11.2 + - - +
417I ALA 3.5 5.2 - - - +
419I ASN* 1.3 78.1 - - - +
421I LEU* 1.3 55.2 + - - +
423I LEU* 5.0 5.2 - - - -
424I ASP* 2.7 41.1 + - + +
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Residues in contact with LEU 421 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307I ALA* 3.8 20.1 - - + +
310I ALA* 3.8 21.5 - - + -
311I LEU* 4.3 10.1 - - + -
417I ALA 2.9 13.8 + - - +
418I LEU 3.5 7.2 - - - +
420I ALA* 1.3 75.9 - - - +
422I ASP* 1.3 64.8 + - - +
425I ARG* 3.3 21.8 + - - +
428I LEU* 3.5 31.4 - - + -
434I PHE* 6.5 0.4 - - + -
439I ILE* 4.1 19.6 - - + +
442I TYR* 4.1 17.7 - - + -
443I ILE* 3.7 23.3 - - + -
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Residues in contact with ASP 422 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418I LEU 2.9 12.1 + - - +
419I ASN* 3.0 18.3 + - - +
421I LEU* 1.3 77.9 - - - +
423I LEU* 1.3 75.0 + - + +
425I ARG* 2.7 58.7 + - - +
443I ILE* 3.9 11.4 - - + -
447I ARG* 5.0 9.2 + - - +
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Residues in contact with LEU 423 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419I ASN* 3.1 30.3 + - - +
420I ALA* 4.0 3.8 - - - +
422I ASP* 1.3 88.0 - - - +
424I ASP* 1.3 58.1 + - + +
425I ARG* 2.9 15.3 + - - +
426I GLU* 4.7 4.3 + - - +
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Residues in contact with ASP 424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303I LYS* 4.1 3.8 - - - +
304I HIS* 2.7 54.1 + - - +
307I ALA* 3.8 10.9 + - + +
420I ALA* 2.7 23.2 + - + +
421I LEU 3.9 4.3 - - - -
423I LEU* 1.3 70.5 - - + +
425I ARG* 1.3 56.7 + - - +
426I GLU* 3.5 2.9 + - - +
427I PHE* 3.0 21.3 + - - -
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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