Contacts of the helix formed by residues 471 - 482 (chain F) in PDB entry 4R8A
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 GLY 471 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454F TYR* 4.0 2.2 - - - -
467F TRP 5.3 0.4 - - - -
468F GLU 5.8 0.7 - - - -
469F LEU 2.8 13.1 + - - -
470F LEU* 1.3 78.5 - - - +
472F GLU* 1.3 67.0 + - - -
473F GLU 3.3 2.9 - - - -
474F LEU* 3.4 7.8 + - - +
475F LEU* 3.1 20.1 + - - +
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Residues in contact with GLU 472 (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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454F TYR* 3.7 25.0 + - + +
455F ARG* 3.3 26.6 + - - +
471F GLY* 1.3 71.4 - - - -
473F GLU* 1.3 62.5 + - - +
475F LEU* 3.5 7.5 + - + +
476F GLU* 3.4 44.0 + - - +
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Residues in contact with GLU 473 (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 ALA* 5.8 1.3 - - - +
383F HIS* 4.2 14.4 - - + -
471F GLY 3.3 0.6 - - - -
472F GLU* 1.3 77.1 - - - +
474F LEU* 1.3 64.9 + - - +
475F LEU 3.2 0.3 + - - -
476F GLU* 3.4 4.2 + - - +
477F GLN* 2.9 53.7 + - + +
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Residues in contact with LEU 474 (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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383F HIS* 3.5 45.9 - - + +
385F VAL* 3.6 24.2 - - + -
389F LEU* 4.1 21.1 - - + -
469F LEU* 3.5 23.6 - - + +
470F LEU* 4.1 13.9 - - + -
471F GLY* 3.4 11.5 + - - +
473F GLU* 1.3 78.6 - - - +
475F LEU* 1.3 61.7 + - - +
477F GLN* 4.0 3.3 - - - +
478F ALA* 3.2 23.4 + - - +
511F PHE* 3.9 16.8 - - + -
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Residues in contact with LEU 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393F LEU* 4.1 16.6 - - + -
450F ILE* 3.8 25.6 - - + -
451F ARG* 4.9 12.6 - - + -
454F TYR* 3.7 39.9 - - + -
455F ARG* 5.3 1.8 - - - +
470F LEU* 4.0 19.9 - - + +
471F GLY 3.1 13.8 + - - +
472F GLU* 3.5 9.9 - - - +
473F GLU 3.1 0.4 - - - -
474F LEU* 1.3 77.8 - - - +
476F GLU* 1.3 70.8 + - + +
478F ALA* 3.1 7.7 + - - +
479F LEU* 3.0 36.8 + - + +
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Residues in contact with GLU 476 (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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451F ARG* 3.4 37.8 + - - +
455F ARG* 4.5 13.5 + - - -
472F GLU* 3.4 38.1 + - - +
473F GLU* 4.4 3.4 - - - +
475F LEU* 1.3 88.3 - - + +
477F GLN* 1.3 60.8 + - - +
479F LEU* 3.8 7.6 - - + -
480F ASP* 3.1 34.4 + - - +
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Residues in contact with GLN 477 (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 ALA* 4.0 18.9 - - - +
383F HIS* 3.0 26.9 + - - -
473F GLU* 2.9 46.6 + - + +
474F LEU 4.0 3.4 - - - +
476F GLU* 1.3 76.7 - - - +
478F ALA* 1.3 63.5 + - - +
480F ASP* 3.6 4.0 + - - +
481F CYS* 3.3 32.0 + - - +
511F PHE* 3.8 19.0 - - + -
513F PRO* 4.8 22.7 - - + +
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Residues in contact with ALA 478 (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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389F LEU* 4.2 13.9 - - + -
393F LEU* 4.3 8.3 - - + -
474F LEU 3.2 18.8 + - - +
475F LEU* 3.1 6.1 + - - +
477F GLN* 1.3 76.4 - - - +
479F LEU* 1.3 60.2 + - - +
482F LEU* 3.0 54.6 + - + +
487F LEU* 5.8 0.3 - - - +
511F PHE* 3.9 19.2 - - + -
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Residues in contact with LEU 479 (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 LEU* 5.4 7.6 - - + -
446F TYR* 3.9 23.8 + - + -
447F ARG* 3.5 64.4 + - + +
450F ILE* 4.4 17.3 - - + -
451F ARG* 3.9 31.0 - - + +
475F LEU* 3.0 35.9 + - + +
476F GLU* 4.0 8.1 - - - +
477F GLN 3.4 0.4 - - - -
478F ALA* 1.3 76.5 - - + +
480F ASP* 1.3 64.0 + - - +
482F LEU 4.4 2.4 - - - +
487F LEU* 5.6 4.7 - - + -
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Residues in contact with ASP 480 (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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447F ARG* 3.7 19.0 + - - +
451F ARG* 4.2 13.0 + - - -
476F GLU* 3.1 21.8 + - - +
477F GLN* 4.0 6.0 - - - +
478F ALA 3.2 0.6 - - - -
479F LEU* 1.3 81.8 - - - +
481F CYS* 1.3 67.6 + - - +
482F LEU 4.5 1.4 - - - +
513F PRO* 5.6 6.1 - - + +
516F ARG* 3.2 33.9 + - + +
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Residues in contact with CYS 481 (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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477F GLN 3.3 18.9 + - - +
480F ASP* 1.3 84.1 - - - +
482F LEU* 1.3 66.2 + - - +
483F PRO* 3.2 11.5 - - - +
511F PHE* 3.6 36.1 - - + -
513F PRO* 3.8 25.8 - - - -
516F ARG* 4.0 22.4 - - - +
517F ARG* 4.3 14.1 + - - -
518F TYR* 4.3 11.2 - - + -
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Residues in contact with LEU 482 (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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389F LEU* 4.5 11.2 - - + -
390F ILE* 5.8 2.9 - - + -
393F LEU* 3.7 21.5 - - + -
446F TYR* 4.0 11.3 + - - -
447F ARG* 5.5 0.7 + - - -
478F ALA* 3.0 39.9 + - + +
479F LEU 4.4 4.0 - - - +
480F ASP 4.5 1.6 - - - +
481F CYS* 1.3 75.7 - - - +
483F PRO* 1.3 70.0 - - + +
484F ALA 3.7 1.2 + - - -
487F LEU* 4.2 23.1 - - + +
490F TRP* 3.6 27.6 - - + -
509F ILE* 5.2 2.0 - - + -
511F PHE* 4.2 11.4 - - + -
518F TYR* 3.8 25.8 - - + -
520F MET* 4.9 3.4 - - + -
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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