Contacts of the strand formed by residues 292 - 294 (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 VAL 292 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1635 SER* 3.1 28.8 - - - +
1645 GLY 3.8 2.2 + - - +
1655 ILE* 4.3 4.0 - - - -
1665 ILE* 3.8 30.3 - - + +
2585 LEU* 5.8 1.1 - - + -
2865 VAL* 3.4 39.7 - - + -
2905 THR* 3.6 15.5 - - - +
2915 ARG* 1.3 81.1 - - - +
2935 THR* 1.3 60.7 + - - +
2945 ILE* 5.1 7.4 - - + -
3335 ILE* 5.1 3.1 - - + -
3345 GLN 4.7 1.1 - - - +
3355 SER* 4.6 10.8 - - - +
3365 ASP* 2.9 21.0 + - - +
3395 THR* 4.7 0.4 - - - +
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Residues in contact with THR 293 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455 GLN* 4.5 9.6 - - - +
1615 ARG* 5.1 18.6 + - + +
1625 LEU* 3.5 18.2 - - - +
1635 SER* 3.6 15.7 - - - -
2925 VAL* 1.3 71.1 - - - +
2945 ILE* 1.3 63.5 + - - +
2955 VAL* 5.4 1.6 - - - +
3335 ILE* 3.3 4.2 - - - +
3345 GLN* 2.6 55.5 + - - +
3355 SER 3.8 1.7 + - - -
3365 ASP* 2.3 34.8 + - - +
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Residues in contact with ILE 294 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1605 VAL 3.6 1.7 - - - +
1615 ARG* 3.9 0.9 - - - +
1625 LEU* 2.8 37.5 + - + +
1635 SER 4.6 6.0 + - - +
1665 ILE* 5.3 1.3 - - + -
2565 LEU* 3.5 32.1 - - + -
2585 LEU* 3.5 20.2 - - + -
2765 MET* 4.3 13.2 - - - -
2925 VAL* 4.4 5.6 + - + -
2935 THR* 1.3 79.4 - - - +
2955 VAL* 1.3 74.5 + - - +
2965 GLY* 4.2 2.0 - - - +
3285 ILE* 5.3 0.2 - - + -
3305 ILE* 3.8 34.1 - - + -
3325 GLY 4.4 0.7 - - - -
3335 ILE* 3.7 20.9 - - + -
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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
------------------------------------------------------------
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