Contacts of the helix formed by residues 1878 - 1891 (chain B) in PDB entry 3RYT
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 ARG1878 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1874B ALA 3.5 0.2 - - - -
1875B ARG* 2.9 17.2 + - - +
1876B ARG 3.2 2.1 - - - +
1877B GLN* 1.3 81.4 - - - +
1879B LEU* 1.3 59.6 + - - +
1880B ARG* 3.1 6.3 - - - +
1881B SER* 3.8 20.2 - - - +
1882B LYS* 2.9 28.9 + - + +
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Residues in contact with LEU1879 (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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1359B LEU* 4.9 6.4 - - + +
1365B PHE* 5.5 9.0 - - + -
1868B LEU* 4.2 22.5 - - + +
1874B ALA* 2.8 40.8 + - + +
1877B GLN* 3.3 4.6 + - + -
1878B ARG* 1.3 72.5 - - - +
1880B ARG* 1.3 57.7 + - - +
1882B LYS* 4.9 2.5 - - - -
1883B LEU* 3.3 25.6 + - - +
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Residues in contact with ARG1880 (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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1865B LEU* 3.8 32.1 - - + +
1868B LEU* 4.2 11.6 + - - +
1869B GLU* 3.0 48.0 + - + +
1878B ARG* 3.1 2.8 - - - -
1879B LEU* 1.3 79.9 - - - +
1881B SER* 1.3 71.5 - - - +
1883B LEU* 4.4 0.4 - - - +
1884B GLU* 3.1 30.8 + - - +
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Residues in contact with SER1881 (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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1878B ARG* 3.4 18.5 + - - -
1880B ARG* 1.3 92.2 - - - +
1882B LYS* 1.3 65.6 + - - +
1884B GLU* 3.2 13.6 + - - +
1885B GLN* 3.4 27.8 + - - +
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Residues in contact with LYS1882 (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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1359B LEU* 4.9 11.4 - - + -
1877B GLN 4.7 4.9 - - - +
1878B ARG* 2.9 21.7 + - + +
1879B LEU* 4.9 1.8 - - - -
1881B SER* 1.3 77.5 - - - +
1883B LEU* 1.3 61.6 + - - +
1885B GLN* 4.7 1.8 - - - +
1886B VAL* 3.1 28.4 + - + +
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Residues in contact with LEU1883 (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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1359B LEU* 3.5 29.5 - - + +
1365B PHE* 5.9 0.2 - - + -
1865B LEU* 5.8 2.9 - - + -
1868B LEU* 5.1 8.5 - - + -
1879B LEU 3.3 21.9 + - - +
1880B ARG* 4.4 2.2 - - - +
1881B SER 3.2 0.6 - - - -
1882B LYS* 1.3 78.1 - - - +
1884B GLU* 1.3 60.5 + - - +
1886B VAL* 3.3 5.8 - - - +
1887B VAL* 2.9 39.1 + - + +
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Residues in contact with GLU1884 (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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1865B LEU* 5.6 7.6 - - + +
1880B ARG* 3.1 26.9 + - - +
1881B SER* 3.2 8.9 + - - +
1883B LEU* 1.3 72.2 - - - +
1885B GLN* 1.3 78.9 + - - +
1886B VAL 2.9 1.2 + - - -
1887B VAL* 3.0 14.8 + - - +
1888B ASP* 3.0 15.0 + - - +
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Residues in contact with GLN1885 (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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1881B SER* 3.4 22.4 + - - +
1882B LYS* 4.7 2.0 - - - +
1884B GLU* 1.3 87.4 - - - +
1886B VAL* 1.3 61.5 + - - +
1888B ASP* 4.1 8.1 - - - +
1889B THR* 3.2 26.0 + - - -
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Residues in contact with VAL1886 (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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1352B SER* 5.8 0.2 - - - -
1355B LEU* 3.2 44.3 - - + +
1356B PHE 4.9 0.4 - - - +
1359B LEU* 4.8 9.2 - - + -
1882B LYS* 3.1 23.8 + - + +
1883B LEU* 3.3 11.0 - - - +
1884B GLU 2.9 0.8 + - - -
1885B GLN* 1.3 80.8 - - - +
1887B VAL* 1.3 72.8 + - + +
1889B THR* 3.5 5.3 + - - -
1890B MET* 3.3 18.2 + - + +
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Residues in contact with VAL1887 (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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1359B LEU* 5.7 2.7 - - + -
1857B ILE* 6.0 10.1 - - + -
1883B LEU* 2.9 26.5 + - + +
1884B GLU* 3.8 2.9 - - - +
1886B VAL* 1.3 81.7 - - + +
1888B ASP* 1.3 70.1 + - - +
1890B MET* 2.9 24.0 + - + +
1891B ALA* 3.5 7.4 + - + +
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Residues in contact with ASP1888 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1884B GLU 3.0 15.1 + - - +
1885B GLN* 4.1 9.9 - - - +
1887B VAL* 1.3 78.9 - - - +
1889B THR* 1.3 60.2 + - - +
1890B MET 3.5 0.2 + - - -
1891B ALA* 4.0 14.7 - - - +
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Residues in contact with THR1889 (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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1351B LYS* 5.6 7.9 - - - +
1885B GLN 3.2 20.2 + - - -
1886B VAL* 3.7 5.8 - - - -
1887B VAL 3.1 0.6 - - - -
1888B ASP* 1.3 74.9 - - - +
1890B MET* 1.3 68.3 + - - +
1891B ALA 4.4 1.7 - - - -
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Residues in contact with MET1890 (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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1348B ASN* 3.6 28.8 - - - +
1351B LYS* 5.8 3.6 - - - -
1352B SER* 3.9 31.6 - - - +
1355B LEU* 6.2 0.2 - - + -
1886B VAL 3.3 9.3 + - - +
1887B VAL* 2.9 17.3 + - + +
1889B THR* 1.3 83.2 - - - +
1891B ALA* 1.3 61.5 + - + +
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Residues in contact with ALA1891 (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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1348B ASN* 5.9 1.8 - - - -
1887B VAL* 3.5 8.9 + - + +
1888B ASP 4.0 13.2 - - - +
1889B THR 4.4 1.6 - - - -
1890B MET* 1.3 83.3 - - + +
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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