Contacts of the strand formed by residues 475 - 480 (chain B) in PDB entry 4PE5
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 THR 475 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B GLY* 6.5 0.7 - - - -
404B ASP* 2.9 10.3 + - + +
405B HIS* 2.5 42.4 + - - +
406B LEU 3.0 23.9 + - - -
474B PHE* 1.3 76.6 - - - +
476B TYR* 1.3 60.6 + - - +
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Residues in contact with TYR 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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405B HIS* 3.9 0.6 - - - -
406B LEU 3.3 6.1 - - - +
408B ILE* 3.7 25.1 - - + -
434B VAL* 3.4 34.3 - - + +
435B PRO* 5.8 0.9 - - + -
462B ILE 5.4 0.3 + - - -
465B LEU* 3.7 31.7 - - + +
466B LYS* 4.3 11.4 + - - +
469B SER* 3.5 34.1 - - - -
474B PHE* 3.9 10.8 - + + -
475B THR* 1.3 77.9 - - - +
477B ASP* 1.3 67.3 + - - +
478B LEU* 3.8 19.5 + - + -
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Residues in contact with ASP 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B VAL* 4.8 17.1 - - - +
405B HIS* 2.6 33.7 + - - +
406B LEU 3.0 12.0 + - - +
407B SER* 3.8 13.2 + - - +
408B ILE 3.2 20.3 + - - +
476B TYR* 1.3 73.6 - - - +
478B LEU* 1.3 65.5 + - - +
479B TYR* 4.1 2.4 - - - +
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ILE* 3.2 26.9 - - + +
410B THR* 3.8 26.5 - - + -
434B VAL* 4.0 13.5 - - + -
435B PRO 3.8 13.8 + - - +
436B CYS* 3.2 29.3 - - + -
437B GLN* 3.4 3.1 + - - +
457B CYS* 4.3 2.2 - - + -
462B ILE* 3.7 30.3 - - + -
465B LEU* 3.8 23.1 - - + -
476B TYR* 3.8 14.5 + - + -
477B ASP* 1.3 73.2 - - - +
479B TYR* 1.3 66.0 + - - +
510B VAL* 4.0 4.0 - - + -
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Residues in contact with TYR 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B SER* 3.7 16.8 - - - -
408B ILE 3.1 15.3 + - - -
409B VAL* 3.3 30.7 - - + +
410B THR* 3.1 23.1 + - - -
436B CYS* 4.1 1.8 - - - -
437B GLN* 3.4 22.7 - - + +
438B LYS* 6.2 0.2 - - - -
477B ASP 4.1 2.9 - - - +
478B LEU* 1.3 78.4 - - - +
480B LEU* 1.3 76.5 + - - +
481B VAL* 4.6 2.9 - - - -
482B THR 5.7 0.2 - - - -
500B GLU* 3.0 28.3 + - - -
505B ARG* 3.5 9.9 + - - +
506B ALA* 3.2 26.9 - - + +
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Residues in contact with LEU 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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410B THR* 3.4 32.1 - - + +
411B LEU 4.8 0.2 - - - -
412B GLU* 4.5 14.6 - - + +
417B VAL* 5.0 0.2 - - + -
419B VAL* 3.9 43.3 - - + -
436B CYS* 4.2 13.7 - - - -
437B GLN 2.7 18.5 + - - +
438B LYS* 4.0 22.5 - - + -
439B ARG 4.9 0.2 + - - -
455B LYS* 5.0 2.9 - - + -
479B TYR* 1.3 85.0 - - - +
481B VAL* 1.3 66.8 + - - +
482B THR* 3.6 12.4 + - + +
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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
------------------------------------------------------------
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