Contacts of the strand formed by residues 474 - 480 (chain B) in PDB entry 4PO2
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 ILE 474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427B ILE* 3.4 4.8 - - - +
428B PHE* 2.8 49.1 + - + +
429B THR* 5.1 2.2 - - - -
430B THR* 5.6 0.2 - - + -
438B VAL* 4.1 22.7 - - + -
461B LEU* 3.6 23.1 - - + -
464B ILE* 3.8 29.6 - - + -
472B PRO* 4.8 6.5 - - + -
473B GLN* 1.3 86.0 - - - +
475B GLU* 1.3 63.6 + - - +
476B VAL* 3.5 11.1 + - + +
490B ALA* 4.3 7.6 - - + -
491B THR 3.5 8.1 - - - +
492B ASP* 3.8 23.1 - - - +
5D LEU* 5.2 0.4 - - + -
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Residues in contact with GLU 475 (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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425B THR* 3.6 25.4 - - + +
426B GLN 4.1 2.0 - - - -
427B ILE* 4.6 15.8 - - + +
473B GLN 4.2 1.0 + - - -
474B ILE* 1.3 69.5 - - - +
476B VAL* 1.3 60.0 + - - +
477B THR* 4.3 9.8 + - - +
489B THR 3.5 2.1 - - - +
490B ALA* 3.3 3.6 - - - -
491B THR* 2.9 55.0 + - - +
493B LYS* 4.1 29.4 + - + +
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Residues in contact with VAL 476 (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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403B LEU* 4.2 12.6 - - + -
413B LEU* 3.7 3.6 - - + +
425B THR* 3.3 3.7 - - - +
426B GLN 2.9 39.8 + - - +
428B PHE* 3.6 26.0 - - + -
440B ILE* 4.2 24.0 - - + -
474B ILE* 4.1 13.0 - - + +
475B GLU* 1.3 76.0 - - - +
477B THR* 1.3 64.1 + - - +
478B PHE* 3.9 26.9 - - + -
488B VAL* 4.4 6.5 - - + -
489B THR 3.3 6.5 - - - +
490B ALA* 4.3 3.4 - - + -
5D LEU* 4.5 2.0 - - + -
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Residues in contact with THR 477 (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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423B LYS* 3.6 39.7 - - + +
424B GLN 3.4 4.3 - - - +
425B THR* 2.8 21.9 + - - +
475B GLU* 4.3 10.0 + - - +
476B VAL* 1.3 75.2 - - - +
478B PHE* 1.3 68.4 + - - +
479B ASP* 4.4 4.7 - - + +
487B ASN 3.5 1.6 - - - +
488B VAL* 3.2 6.9 - - - +
489B THR* 2.9 45.4 + - - +
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Residues in contact with PHE 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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401B LEU* 3.9 17.0 - - + -
402B GLY* 3.4 46.7 - - - -
403B LEU* 4.0 8.5 - - + -
413B LEU* 3.6 26.9 - - + -
414B ILE* 3.7 23.0 - - + +
423B LYS* 3.4 3.3 - - - +
424B GLN 2.9 36.1 + - - +
442B VAL* 4.1 11.2 - - + -
476B VAL* 3.9 13.2 - - + -
477B THR* 1.3 77.6 - - - +
479B ASP* 1.3 60.7 + - - +
486B LEU* 4.1 11.2 - - + -
487B ASN 3.8 2.7 - - - -
488B VAL* 3.6 35.7 - - + -
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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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422B THR 3.6 4.8 - - - +
423B LYS* 3.2 37.1 - - + +
477B THR* 4.5 4.3 - - + -
478B PHE* 1.3 74.0 - - - +
480B ILE* 1.3 72.0 + - - +
481B ASP* 4.1 8.9 + - - +
485B ILE 3.4 2.4 - - - +
486B LEU* 3.4 3.8 - - - +
487B ASN* 2.9 54.3 + - + +
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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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397B ALA* 4.2 6.7 - - + -
401B LEU* 3.6 21.3 - - + -
414B ILE* 3.6 34.3 - - + -
420B ILE* 3.9 31.9 - - + -
421B PRO* 3.2 5.5 - - - +
422B THR* 2.9 36.1 + - + +
479B ASP* 1.3 78.0 - - - +
481B ASP* 1.3 64.8 + - - +
484B GLY* 3.7 32.3 - - - +
485B ILE 3.4 2.2 - - - -
486B LEU* 3.8 13.7 - - + -
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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