Contacts of the helix formed by residues 473 - 484 (chain B) in PDB entry 4OE4
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469B TYR* 4.2 3.5 - - + -
470B PRO* 2.8 43.7 + - + +
472B THR* 1.3 86.2 + - - +
474B PHE* 1.3 57.5 + - - -
475B ASN 3.3 3.1 - - - -
476B GLU* 3.3 17.8 + - + +
477B ILE* 2.9 28.9 + - + +
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Residues in contact with PHE 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B LEU* 3.6 26.9 - - + -
327B HIS* 3.7 38.4 - + + +
328B PRO* 5.1 1.1 - - + -
469B TYR* 3.4 30.9 - + + +
471B ASP 3.3 13.7 + - - +
472B THR 3.3 3.8 - - - +
473B GLU* 1.3 77.0 - - - +
475B ASN* 1.3 79.2 + - - +
477B ILE* 3.1 10.3 - - + +
478B CYS* 3.0 40.0 + - - -
493B ILE* 3.7 22.9 - - + -
500B ALA* 3.7 21.3 - - + -
503B TYR* 4.6 2.0 - + - -
504B ALA* 4.2 0.2 - - + -
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Residues in contact with ASN 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B THR 4.7 3.4 + - - +
473B GLU* 3.3 0.8 - - - +
474B PHE* 1.3 93.3 - - - +
476B GLU* 1.3 62.3 + - - +
478B CYS* 3.1 5.4 + - - +
479B ASP* 3.1 28.6 + - - +
500B ALA* 5.9 0.3 - - - -
503B TYR* 3.6 43.2 - - + +
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Residues in contact with GLU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B GLU* 3.3 26.0 + - + +
475B ASN* 1.3 78.0 - - - +
477B ILE* 1.3 58.5 + - - +
479B ASP* 3.0 15.3 + - - +
480B ILE* 2.8 38.0 + - + +
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Residues in contact with ILE 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.8 27.8 - - + -
358B TYR* 3.9 22.2 - - + -
450B PRO* 4.8 1.3 - - + -
467B TYR* 3.7 30.5 - - + -
469B TYR* 4.0 22.0 - - + -
473B GLU* 2.9 13.8 + - + +
474B PHE* 3.1 24.9 + - + +
476B GLU* 1.3 77.1 - - - +
478B CYS* 1.3 63.2 + - - +
480B ILE* 3.3 24.8 + - + +
481B ILE* 3.1 28.9 + - + +
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Residues in contact with CYS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B LEU* 3.9 15.0 - - - -
474B PHE* 3.0 46.7 + - - -
475B ASN 3.1 8.5 + - - +
477B ILE* 1.3 79.1 - - - +
479B ASP* 1.3 56.2 + - - +
481B ILE* 3.4 3.8 + - - -
482B ASP* 3.0 25.7 + - - +
503B TYR* 4.0 17.5 - - + -
504B ALA* 3.9 14.1 - - - -
507B LYS* 4.3 11.4 - - + -
508B LEU* 3.4 17.7 - - + +
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Residues in contact with ASP 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B ASN* 3.2 16.9 - - - +
476B GLU* 3.0 15.5 + - - +
478B CYS* 1.3 74.9 - - - +
480B ILE* 1.3 61.3 + - + +
482B ASP* 3.3 6.7 + - - +
483B ASN* 2.8 34.5 + - - +
503B TYR* 3.3 18.1 + - - -
507B LYS* 4.8 6.2 - - - +
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Residues in contact with ILE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B TYR* 5.6 3.6 - - + +
450B PRO* 4.3 33.7 - - + +
451B ASP* 6.1 2.7 - - + -
467B TYR* 6.1 0.2 - - - +
476B GLU* 2.8 21.2 + - + +
477B ILE* 3.7 30.5 - - + +
479B ASP* 1.3 76.5 - - + +
481B ILE* 1.3 57.2 + - + +
483B ASN* 4.7 3.4 - - - -
484B THR* 2.6 44.6 + - - -
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Residues in contact with ILE 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B PHE* 4.1 28.7 - - + -
325B LEU* 4.5 20.2 - - + -
356B ARG* 4.0 21.0 + - - +
358B TYR* 3.5 48.0 - - + -
477B ILE 3.1 17.8 + - - +
478B CYS* 3.7 7.4 - - - +
480B ILE* 1.3 78.5 - - + +
482B ASP* 1.3 64.6 + - - +
484B THR* 3.5 16.8 + - - -
508B LEU* 3.8 14.8 - - + -
511B SER* 4.2 5.7 + - - +
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Residues in contact with ASP 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU* 4.5 12.5 - - - +
478B CYS 3.0 15.1 + - - +
479B ASP* 3.6 9.8 - - - +
481B ILE* 1.3 80.2 - - - +
483B ASN* 1.3 65.3 + - - +
484B THR 3.4 3.5 + - - -
507B LYS* 3.6 23.4 - - + +
508B LEU* 3.9 0.8 - - + +
510B PHE* 4.6 12.4 + - - +
511B SER* 3.5 17.4 + - - +
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Residues in contact with ASN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B ASP* 2.8 21.4 + - + +
480B ILE* 4.0 3.6 - - - +
482B ASP* 1.3 74.4 + - - +
484B THR* 1.3 65.3 + - - +
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Residues in contact with THR 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ARG* 4.9 9.9 - - - -
358B TYR* 5.9 0.2 - - - -
450B PRO 6.1 0.9 - - - -
451B ASP* 6.5 0.7 - - - -
456B SER* 6.0 1.6 - - - -
480B ILE* 2.6 29.9 + - - -
481B ILE* 3.7 12.1 - - - -
482B ASP 3.3 6.8 - - - -
483B ASN* 1.3 78.3 - - - +
487B TYR* 4.6 15.9 + - - +
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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