Contacts of the helix formed by residues 279 - 283 (chain 5) 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 ASP 279 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1365 GLN* 2.3 38.7 + - - -
1755 ARG* 6.1 2.0 - - - +
1965 ASN* 5.2 5.4 + - - +
1975 PHE* 5.7 4.5 - - - -
2515 ILE* 4.4 9.6 - - + +
2525 ASP 3.1 14.4 - - - +
2535 GLN* 4.6 4.3 - - + -
2785 CYS* 1.3 78.3 - - - +
2805 ARG* 1.3 92.2 + - + +
2825 LEU* 3.1 13.5 + - - +
2835 THR* 3.7 3.8 - - - -
3295 LYS* 3.6 22.6 + - - +
3305 ILE 4.4 1.0 - - - +
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Residues in contact with ARG 280 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915 GLU* 3.3 16.8 + - - -
1345 THR* 4.9 14.7 + - - +
1355 PHE 3.3 12.6 + - - -
1365 GLN* 3.1 48.4 - - - +
1775 THR* 6.3 0.8 - - - +
1965 ASN* 5.4 6.1 - - - +
1975 PHE* 6.3 0.4 - - - -
2515 ILE* 3.5 42.1 - - + +
2525 ASP* 3.2 16.4 + - - +
2795 ASP* 1.3 93.9 + - - +
2815 TYR* 1.3 74.4 + - + +
2825 LEU 3.0 0.2 - - - -
2835 THR* 2.7 34.3 + - - +
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Residues in contact with TYR 281 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1743 GLN* 5.0 10.4 + - - -
575 LYS* 2.5 25.5 + - - +
585 ASN* 2.9 43.5 - - - +
595 TYR* 3.2 20.1 - - + -
1365 GLN* 2.7 20.7 + - + +
1385 ILE* 4.8 5.8 - - + -
2805 ARG* 1.3 90.6 - - + +
2825 LEU* 1.3 54.6 + - - +
2835 THR 3.3 4.7 - - - +
2855 LYS* 2.7 28.6 + - - +
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Residues in contact with LEU 282 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1365 GLN* 3.3 21.3 - - + +
1375 LEU 5.1 1.6 - - - +
1385 ILE* 3.4 33.2 - - + -
2785 CYS* 3.2 26.6 - - + -
2795 ASP* 3.2 14.8 - - - +
2805 ARG 3.0 0.2 - - - -
2815 TYR* 1.3 78.8 - - - +
2835 THR* 1.3 62.2 + - - +
2855 LYS* 3.2 28.5 + - - +
3305 ILE* 3.3 34.1 - - + +
3315 LEU* 4.8 2.2 - - - -
3335 ILE* 3.5 28.7 - - + +
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Residues in contact with THR 283 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2525 ASP* 3.4 35.8 + - + +
2545 GLN* 4.4 7.0 - - - +
2785 CYS* 4.1 10.3 - - + -
2795 ASP* 3.7 12.6 - - - +
2805 ARG 2.7 36.6 + - - +
2815 TYR 4.3 4.0 - - - +
2825 LEU* 1.3 75.0 - - - +
2845 ASN* 1.3 72.6 + - - +
2855 LYS* 2.9 13.2 + - - +
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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