Contacts of the helix formed by residues 473 - 480 (chain E) in PDB entry 4P0S
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 GLU 473 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472E ARG* 1.3 80.7 - - - +
474E VAL* 1.3 69.1 + - + +
476E ALA* 3.6 11.3 + - - +
477E ARG* 4.1 7.7 + - - +
457F PHE* 6.5 0.2 - - - -
459F PHE* 3.3 66.1 - - + +
462F GLU* 5.7 0.7 - - - +
488F GLN 5.6 1.4 - - - +
566F LEU* 5.6 5.4 - - - +
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Residues in contact with VAL 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472E ARG 2.8 9.4 + - - +
473E GLU* 1.3 84.0 - - + +
475E PHE* 1.3 59.0 + - - +
476E ALA 3.2 2.2 - - - -
477E ARG* 3.2 15.4 + - + +
478E GLN* 3.1 45.8 + - + +
485F GLN 5.6 1.6 - - - +
488F GLN* 4.8 19.3 - - + +
489F LEU* 5.2 8.3 - - + -
556F GLN* 3.7 29.2 - - + +
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Residues in contact with PHE 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472E ARG* 2.8 18.7 + - - +
474E VAL* 1.3 72.5 - - - +
476E ALA* 1.3 64.1 + - - +
478E GLN* 3.4 21.2 + - - -
479E LEU* 3.3 47.7 + - + +
493E LEU 4.7 1.6 - - - -
494E VAL* 3.6 27.6 - - + -
497E TYR* 3.1 27.4 - - + -
499E THR* 4.1 15.9 - - - -
500E PRO* 3.8 36.6 - - + -
503E LEU* 4.4 17.5 - - + -
544E TYR* 3.7 12.6 - + - -
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Residues in contact with ALA 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472E ARG* 3.5 5.4 + - + +
473E GLU 3.8 11.2 - - - +
474E VAL 3.2 0.8 - - - -
475E PHE* 1.3 78.3 - - - +
477E ARG* 1.3 64.1 + - + +
479E LEU* 3.4 13.3 + - - +
480E MET* 3.3 30.7 + - + +
490E ALA* 3.9 7.0 - - + +
491E ALA* 5.8 0.4 - - - +
494E VAL* 3.6 23.9 - - + +
457F PHE* 5.5 10.3 - - + -
459F PHE* 5.2 6.1 - - + -
460F CYS* 6.0 2.9 - - - -
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Residues in contact with ARG 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E GLU* 4.1 17.7 + - - +
474E VAL* 3.2 14.3 + - + +
476E ALA* 1.3 78.9 - - + +
478E GLN* 1.3 61.7 + - + +
480E MET* 3.1 20.1 + - + +
481E GLN* 3.2 21.8 + - - +
459F PHE* 3.4 45.6 + - + +
460F CYS* 6.2 3.4 - - - -
462F GLU* 5.3 2.2 + - - -
464F ASP 5.7 0.6 + - - -
465F TRP* 3.0 42.3 - - + -
488F GLN* 2.0 53.2 + - + +
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Residues in contact with GLN 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474E VAL* 3.1 34.0 + - + +
475E PHE* 3.4 30.9 - - + +
476E ALA 3.3 0.4 - - - -
477E ARG* 1.3 76.1 - - + +
479E LEU* 1.3 62.5 + - - +
480E MET 3.4 0.2 + - - -
481E GLN* 3.6 19.4 + - - +
482E VAL* 5.1 1.2 + - - +
500E PRO* 4.0 12.6 - - - +
544E TYR* 4.7 9.4 + - - +
481F VAL* 5.3 0.2 - - - +
485F GLN* 3.6 40.0 + - + +
556F GLN* 5.9 0.8 - - - +
557F MET* 5.7 9.9 - - - +
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Residues in contact with LEU 479 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475E PHE* 3.3 37.3 + - + +
476E ALA* 3.6 7.4 - - - +
477E ARG 3.2 0.4 - - - -
478E GLN* 1.3 78.9 - - - +
480E MET* 1.3 58.1 + - - +
481E GLN 3.2 0.4 - - - -
482E VAL* 2.9 29.0 - - - +
485E VAL* 3.0 18.9 - - + +
490E ALA* 4.5 4.0 - - + +
493E LEU* 3.7 38.8 - - + -
494E VAL* 3.8 17.3 - - + -
503E LEU* 5.5 1.1 - - + -
540E LEU* 4.7 8.5 - - + -
544E TYR* 3.3 33.2 - - + +
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Residues in contact with MET 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E ALA* 3.3 29.8 + - + +
477E ARG* 3.1 13.9 + - + +
479E LEU* 1.3 77.3 - - - +
481E GLN* 1.3 74.8 + - - +
482E VAL 3.4 2.0 - - - -
485E VAL* 3.4 25.1 - - + +
486E SER* 3.3 7.2 - - - +
487E GLY* 3.1 33.4 - - - -
490E ALA* 3.6 13.9 - - + -
460F CYS* 4.2 22.2 - - + -
465F TRP* 5.6 12.3 - - + -
468F GLY* 3.3 13.1 - - - -
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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