Contacts of the strand formed by residues 1897 - 1903 (chain G) in PDB entry 2VKZ
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 GLN1897 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A MET* 3.0 31.6 - - - +
59A ARG* 3.4 38.8 - - - +
1857G ILE 3.6 2.2 - - - -
1892G ASN* 3.2 18.9 + - + +
1893G VAL* 2.9 54.6 + - + +
1896G GLN* 1.3 81.7 - - + +
1898G TYR* 1.3 67.1 + - - +
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Residues in contact with TYR1898 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.8 5.8 - - + -
1856G ALA* 3.4 2.4 - - - +
1857G ILE* 2.7 37.3 + - + +
1859G PRO* 3.4 33.2 - - + -
1868G GLN* 2.8 52.2 + - + +
1871G LEU* 4.1 15.9 - - + -
1888G ILE* 4.4 12.8 - - + -
1890G ASN 3.3 11.4 - - - +
1891G TYR* 3.6 25.8 - + - -
1892G ASN 4.7 0.2 - - - +
1893G VAL 3.6 8.3 - - - -
1894G GLU* 3.4 2.8 - - - -
1895G ASN 2.9 32.8 + - - -
1896G GLN 3.7 2.0 - - - -
1897G GLN* 1.3 76.7 - - - +
1899G VAL* 1.3 68.4 + - - +
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Residues in contact with VAL1899 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1854G MET* 3.7 19.1 - - + -
1855G ILE 3.2 17.0 - - - +
1856G ALA* 4.3 11.0 - - + -
1857G ILE* 4.5 0.9 - - - +
1888G ILE* 3.6 3.5 - - - +
1889G VAL* 2.6 32.1 + - + -
1890G ASN* 2.9 42.1 + - + +
1892G ASN* 3.9 9.4 - - - +
1897G GLN* 6.4 0.2 - - + -
1898G TYR* 1.3 82.0 - - - +
1900G ALA* 1.3 57.9 + - - +
1969G LEU* 3.6 27.8 - - + -
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Residues in contact with ALA1900 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1854G MET* 3.4 4.6 - - - +
1855G ILE* 2.7 37.9 + - + +
1857G ILE* 4.2 20.8 - - + +
1875G VAL* 5.1 7.0 - - + -
1886G VAL* 5.1 2.5 - - + -
1887G GLU 3.3 19.5 - - - +
1888G ILE* 4.3 7.4 - - + -
1889G VAL* 4.4 0.2 - - - -
1899G VAL* 1.3 75.0 - - - +
1901G ALA* 1.3 61.9 + - - +
1907G LEU* 3.7 14.9 - - + +
1910G VAL* 6.2 0.7 - - + -
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Residues in contact with ALA1901 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1853G GLY 3.4 7.6 - - - +
1854G MET* 3.2 23.8 - - + -
1885G LEU* 5.4 0.2 - - - -
1886G VAL* 3.5 26.5 - - - +
1887G GLU 3.2 10.3 + - - -
1889G VAL* 3.4 20.1 - - + +
1900G ALA* 1.3 74.0 - - - +
1902G GLY* 1.3 60.4 + - - +
1907G LEU* 3.6 5.6 - - - -
1975G PRO* 3.9 20.2 - - + +
1978G SER* 5.1 3.6 - - - -
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Residues in contact with GLY1902 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1852G TYR* 3.3 21.7 - - - +
1853G GLY 3.3 6.5 + - - -
1885G LEU* 3.3 24.5 - - - -
1901G ALA* 1.3 79.8 - - - +
1903G ASP* 1.3 67.3 + - - -
1904G LEU 3.2 2.9 + - - -
1907G LEU* 3.1 9.4 - - - +
1975G PRO* 4.0 9.9 - - - +
1978G SER* 6.0 0.2 - - - -
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Residues in contact with ASP1903 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1851G ASN* 4.0 6.7 - - - +
1852G TYR* 3.6 17.7 - - + -
1884G TRP* 3.8 11.7 - - - +
1885G LEU* 2.8 32.9 + - + +
1902G GLY* 1.3 67.5 - - - -
1904G LEU* 1.3 66.3 + - - +
1905G ARG* 2.9 52.9 + - - +
1906G ALA* 2.9 17.6 + - + -
1907G LEU* 2.9 12.8 + - - +
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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