Contacts of the helix formed by residues 413 - 424 (chain F) in PDB entry 5I4V
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 VAL 413 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336F VAL* 5.1 10.5 - - + -
339F ILE* 5.4 13.0 - - + -
408F ALA* 3.0 19.7 + - + +
411F ALA* 4.3 11.2 - - + +
412F GLY* 1.3 77.2 - - - +
414F GLY* 1.3 63.8 + - - +
415F ALA 3.4 2.5 - - - -
416F ILE* 3.3 17.2 - - + +
417F PHE* 3.3 20.9 + - + +
506F HIS* 3.4 39.0 - - + +
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Residues in contact with GLY 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408F ALA 3.3 6.9 + - - -
409F HIS* 3.6 39.7 - - - +
412F GLY* 3.6 2.4 - - - -
413F VAL* 1.3 77.2 - - - +
415F ALA* 1.3 66.0 + - - +
417F PHE* 3.1 6.3 + - - +
418F ASP* 2.9 26.9 + - - -
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Residues in contact with ALA 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409F HIS* 4.5 2.3 + - - -
413F VAL 3.4 0.4 - - - -
414F GLY* 1.3 76.3 - - - +
416F ILE* 1.3 62.7 + - - +
418F ASP* 3.2 10.2 + - - +
419F ARG* 3.1 28.5 + - - +
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Residues in contact with ILE 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413F VAL* 3.3 27.4 - - + +
415F ALA* 1.3 79.4 - - - +
417F PHE* 1.3 65.6 + - - +
419F ARG* 3.3 19.4 + - - +
420F VAL* 3.1 23.3 + - + +
499F ILE* 4.0 25.6 - - + +
502F LYS* 3.8 36.6 - - + -
503F CYS* 3.7 23.3 - - - +
506F HIS* 3.9 20.6 - - + +
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Residues in contact with PHE 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F GLY* 3.8 12.8 - - - -
395F ILE* 4.1 31.0 - - + -
403F VAL* 3.8 32.5 - - + -
404F HIS 4.2 1.6 - - - -
405F ARG* 3.7 31.0 - - + -
408F ALA* 3.7 18.6 - - + -
409F HIS* 5.5 0.9 - + - -
413F VAL* 3.4 16.4 - - + +
414F GLY 3.1 9.6 + - - +
416F ILE* 1.3 83.6 - - - +
418F ASP* 1.3 63.7 + - - +
420F VAL* 3.2 17.8 + - + +
421F LEU* 3.2 39.0 + - + +
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Residues in contact with ASP 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F ARG* 2.6 43.3 + - - +
409F HIS* 3.2 21.2 + - - -
414F GLY 2.9 12.7 + - - +
415F ALA* 3.7 9.2 - - - +
417F PHE* 1.3 77.2 - - - +
419F ARG* 1.3 58.7 + - + +
421F LEU* 3.4 8.6 + - - +
422F THR* 2.9 36.8 + - - +
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Residues in contact with ARG 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E ASP* 4.8 17.9 + - - +
384E PRO* 6.1 7.5 - - - +
415F ALA* 3.1 20.5 + - - +
416F ILE* 3.6 15.6 - - + +
417F PHE 3.3 0.2 - - - -
418F ASP* 1.3 73.2 - - - +
420F VAL* 1.3 61.5 + - - +
422F THR* 4.6 4.0 - - - -
423F GLU* 2.9 41.6 + - + +
495F ALA 4.9 0.4 + - - -
498F SER* 3.7 29.1 + - - -
499F ILE* 3.7 28.6 - - + +
502F LYS* 4.0 29.7 - - - +
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Residues in contact with VAL 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F ILE* 4.9 4.5 - - + -
384F PHE* 4.2 19.7 - - + -
385F SER* 3.7 21.3 - - - +
395F ILE* 4.7 8.3 - - + -
416F ILE* 3.1 19.5 + - + +
417F PHE* 3.2 12.3 + - + +
419F ARG* 1.3 77.6 - - - +
421F LEU* 1.3 56.9 + - - +
424F LEU* 2.9 27.4 + - + +
425F VAL* 3.1 16.7 + - + -
499F ILE* 3.9 30.3 - - + -
503F CYS* 5.0 4.5 - - - -
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Residues in contact with LEU 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393F ASP* 4.6 7.0 - - - +
394F GLY 3.8 34.1 - - - +
395F ILE* 4.2 12.3 - - + -
405F ARG* 4.2 15.3 - - + -
417F PHE* 3.2 40.2 + - + +
418F ASP* 3.8 11.2 - - - +
420F VAL* 1.3 75.5 - - - +
422F THR* 1.3 62.0 + - - +
425F VAL* 3.9 16.8 - - + +
426F SER* 2.8 35.0 + - - -
429F ARG* 6.3 0.2 - - - +
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Residues in contact with THR 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E PRO* 5.7 10.3 - - + -
418F ASP* 2.9 21.2 + - - +
419F ARG* 4.0 3.4 - - - -
421F LEU* 1.3 80.1 - - - +
423F GLU* 1.3 78.6 + - - +
426F SER* 3.5 12.9 - - - -
427F LYS* 3.0 29.0 + - - +
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Residues in contact with GLU 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E ALA* 4.2 6.8 - - - +
382E ASP* 3.6 40.2 + - + +
389E PRO* 5.3 3.8 - - - +
393E GLU* 4.8 2.4 - - - +
419F ARG* 2.9 26.7 + - + +
422F THR* 1.3 95.5 - - + +
424F LEU* 1.3 63.1 + - - +
427F LYS* 3.2 18.1 + - - +
492F ARG* 2.7 48.1 + - - +
495F ALA* 4.3 6.3 - - + -
499F ILE* 4.1 15.5 - - + -
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Residues in contact with LEU 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381F ILE* 3.7 23.1 - - + -
382F ALA* 5.7 1.6 - - - -
385F SER* 3.5 28.3 - - - +
420F VAL* 2.9 18.0 + - + +
423F GLU* 1.3 88.9 - - + +
425F VAL* 1.3 61.6 + - - +
426F SER 3.3 0.7 - - - -
427F LYS* 3.2 2.4 + - - +
428F MET* 2.8 45.8 + - + +
492F ARG* 4.6 17.5 - - + +
495F ALA* 5.1 0.7 - - + -
496F LEU* 4.0 31.6 - - + +
499F ILE* 4.1 19.7 - - + -
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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