Contacts of the strand formed by residues 1897 - 1903 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C GLY 4.9 0.8 + - - -
56C MET* 3.0 31.8 - - - +
59C ARG* 3.4 39.0 - - - +
1857I ILE 3.6 2.5 - - - -
1892I ASN* 3.1 19.4 + - + +
1893I VAL* 2.9 54.2 + - + +
1896I GLN* 1.3 80.9 - - + +
1898I TYR* 1.3 64.3 + - - +
1899I VAL* 6.4 0.2 - - + -
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Residues in contact with TYR1898 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ILE* 4.0 6.3 - - + -
1856I ALA* 3.4 1.9 - - - +
1857I ILE* 2.7 37.5 + - + +
1859I PRO* 3.4 35.0 - - + -
1868I GLN* 2.8 51.8 + - + +
1871I LEU* 4.0 15.3 - - + -
1888I ILE* 4.4 12.8 - - + -
1890I ASN 3.2 10.3 - - - +
1891I TYR* 3.5 26.5 - + - -
1892I ASN* 5.1 0.2 - - - +
1893I VAL 3.6 8.3 - - - -
1894I GLU* 3.4 3.1 - - - +
1895I ASN* 2.9 32.3 + - - -
1896I GLN 3.8 1.3 - - - -
1897I GLN* 1.3 77.8 - - - +
1899I VAL* 1.3 68.9 + - - +
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Residues in contact with VAL1899 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1854I MET* 3.7 18.4 - - + -
1855I ILE 3.2 17.3 - - - +
1856I ALA* 4.3 11.0 - - + -
1857I ILE* 5.2 0.4 - - - -
1888I ILE* 3.6 3.9 - - - +
1889I VAL* 2.6 31.9 + - + -
1890I ASN* 2.8 42.3 + - + +
1892I ASN* 3.9 11.4 - - - +
1897I GLN* 6.4 0.2 - - + -
1898I TYR* 1.3 82.9 - - - +
1900I ALA* 1.3 56.1 + - - +
1969I LEU* 3.7 27.8 - - + -
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Residues in contact with ALA1900 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1854I MET* 3.4 4.9 - - - +
1855I ILE* 2.8 34.5 + - - +
1857I ILE* 4.2 19.9 - - + +
1875I VAL* 5.1 7.2 - - + -
1886I VAL* 5.1 2.2 - - + -
1887I GLU 3.3 19.1 - - - +
1888I ILE* 4.4 7.6 - - + -
1889I VAL* 4.3 0.4 - - - -
1899I VAL* 1.3 75.0 - - - +
1901I ALA* 1.3 62.6 + - - +
1907I LEU* 3.8 14.2 - - + +
1910I VAL* 6.2 1.1 - - + -
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Residues in contact with ALA1901 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1853I GLY 3.4 7.2 - - - +
1854I MET* 3.2 24.2 - - + -
1886I VAL* 3.5 26.2 - - - +
1887I GLU 3.2 11.3 + - - -
1889I VAL* 3.4 21.2 - - + +
1900I ALA* 1.3 73.4 - - - +
1902I GLY* 1.3 61.6 + - - +
1907I LEU* 3.6 5.8 - - - -
1975I PRO* 3.9 19.7 - - + +
1978I SER* 5.1 2.5 - - - -
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Residues in contact with GLY1902 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1852I TYR* 3.3 21.0 - - - +
1853I GLY 3.3 6.9 + - - -
1885I LEU* 3.3 24.2 - - - -
1901I ALA* 1.3 79.6 - - - +
1903I ASP* 1.3 67.0 + - - -
1904I LEU 3.2 2.6 + - - -
1907I LEU* 3.1 9.6 - - - +
1975I PRO* 4.0 9.3 - - - +
1978I SER* 6.0 0.4 - - - -
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Residues in contact with ASP1903 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1851I ASN* 4.0 6.3 - - - +
1852I TYR* 3.6 17.0 - - + -
1884I TRP* 3.8 9.8 - - - +
1885I LEU* 2.8 33.4 + - + +
1902I GLY* 1.3 68.7 - - - -
1904I LEU* 1.3 66.6 + - - +
1905I ARG* 2.9 53.8 + - - +
1906I ALA* 2.8 17.2 + - + +
1907I 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