Contacts of the strand formed by residues 563 - 567 (chain 4) in PDB entry 5U8T
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 ASN 563 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5614 ASP* 3.5 14.3 - - - +
5624 ILE* 1.3 76.7 - - - +
5644 ILE* 1.3 70.2 + - - +
6454 LEU* 4.4 13.3 - - - +
6494 MET* 2.5 45.2 - - + +
6714 ILE* 3.2 27.6 - - + +
7024 PHE* 5.4 8.3 - - + -
7034 ASP* 3.3 32.9 + - + +
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Residues in contact with ILE 564 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5394 GLY 5.8 3.1 - - - +
5404 ILE* 6.5 0.4 - - + -
5434 GLN* 4.2 21.3 - - + +
5624 ILE* 3.5 34.3 - - + +
5634 ASN* 1.3 85.3 - - - +
5654 LEU* 1.3 63.8 + - - +
6714 ILE 2.9 8.9 + - - +
6724 LEU* 3.4 21.3 - - + +
6734 ALA* 3.3 22.3 + - - +
7034 ASP* 5.4 2.7 - - - +
7044 LEU* 4.1 21.5 - - + +
7064 TYR* 3.4 38.8 - - + -
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Residues in contact with LEU 565 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5644 ILE* 1.3 82.1 - - - +
5664 LEU* 1.3 93.3 + - - +
5674 CYS* 4.2 11.2 - - + -
6344 PHE* 4.3 24.7 - - + -
6354 ASP* 5.3 5.6 - - - +
6734 ALA* 3.8 11.7 - - + +
6754 ALA* 3.6 19.1 - - + -
6924 ILE* 6.1 4.9 - - + +
6994 LEU* 6.2 1.1 - - + -
7024 PHE* 4.6 25.6 - - + +
7044 LEU 3.8 17.0 + - - +
7054 VAL* 3.9 11.5 - - + -
7064 TYR* 3.0 25.3 + - - +
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Residues in contact with LEU 566 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5364 VAL* 4.2 25.8 - - + -
5404 ILE* 5.0 1.1 - - + -
5654 LEU* 1.3 80.9 - - - +
5674 CYS* 1.3 63.0 + - - +
5744 LYS* 3.5 39.0 - - + +
5774 ILE* 5.4 7.6 - - + -
5784 LEU* 5.9 0.4 - - + -
6724 LEU* 3.6 35.4 - - + -
6734 ALA 3.3 3.4 + - - -
6744 SER* 3.8 11.4 - - - -
6754 ALA 2.9 23.9 + - - -
7064 TYR* 3.3 24.7 - - + -
7084 VAL* 5.6 6.7 - - + -
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Residues in contact with CYS 567 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5654 LEU* 4.3 9.9 - - - -
5664 LEU* 1.3 79.8 - - - +
5684 GLY* 1.3 53.6 + - - +
5744 LYS* 3.3 13.5 - - - +
6754 ALA* 3.6 20.2 - - + +
6764 ASN 4.0 0.9 - - - +
6774 PRO* 3.6 17.5 - - + -
6924 ILE* 5.2 16.8 - - - -
7054 VAL* 5.4 2.9 - - - -
7064 TYR 2.6 22.5 + - - +
7074 LEU* 3.2 10.0 - - - -
7084 VAL* 2.3 38.5 + - - +
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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