Contacts of the strand formed by residues 1899 - 1904 (chain B) in PDB entry 1GZH
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 SER1899 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1872B LEU 3.4 2.8 + - - +
1873B LYS* 3.6 20.8 - - - +
1874B VAL 3.0 24.7 + - - -
1893B MET* 3.7 10.8 - - - -
1897B ALA 3.2 1.8 - - - -
1898B ALA* 1.3 84.6 - - - +
1900B VAL* 1.3 68.8 + - - +
1901B LYS 4.3 0.4 - - - -
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Residues in contact with VAL1900 (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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1874B VAL* 3.3 11.9 - - + +
1876B LEU* 3.5 39.5 - - + -
1889B SER* 3.8 20.4 + - - +
1892B LEU* 3.8 29.2 - - + -
1893B MET* 3.6 24.2 - - + -
1897B ALA* 4.2 3.8 - - + -
1899B SER* 1.3 82.8 - - - +
1901B LYS* 1.3 62.1 + - - +
1902B GLN* 3.6 6.2 + - - +
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Residues in contact with LYS1901 (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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1874B VAL 2.9 8.5 + - - -
1875B LEU* 3.4 19.1 - - + +
1876B LEU 2.8 27.5 + - - -
1899B SER 4.3 0.4 - - - -
1900B VAL* 1.3 70.7 - - - +
1902B GLN* 1.3 71.4 + - - +
1903B HIS* 5.9 1.1 - - - -
1911B ASP* 5.2 14.3 - - - +
1912B ILE* 4.7 16.4 - - + +
1917B PHE* 3.8 29.8 - - + -
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Residues in contact with GLN1902 (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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1876B LEU* 3.8 9.0 - - + -
1881B GLN* 3.8 17.0 - - - +
1885B LEU* 3.7 37.6 + - + +
1886B GLU* 4.5 6.9 + - - +
1889B SER* 3.0 31.2 + - - +
1900B VAL 3.6 6.0 + - - +
1901B LYS* 1.3 83.2 - - - +
1903B HIS* 1.3 59.7 - - - +
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Residues in contact with HIS1903 (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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1875B LEU* 4.1 12.3 - - + -
1876B LEU 2.8 16.9 + - - +
1877B VAL* 3.2 26.4 - - + -
1878B SER 3.1 23.6 + - - +
1885B LEU* 3.6 5.5 - - - +
1901B LYS* 5.3 1.9 - - + -
1902B GLN* 1.3 76.2 + - - +
1904B HIS* 1.3 76.8 + - - +
1905B SER* 5.2 2.3 + - - -
1907B ALA* 4.0 10.9 + - + +
1908B HIS 3.8 25.2 - - - -
1909B ASN 4.6 0.8 + - - -
1912B ILE* 3.5 41.4 - - + +
1927B PRO* 5.4 2.9 - - + +
1930B VAL* 5.0 8.1 - - + +
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Residues in contact with HIS1904 (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 SER 3.3 11.2 - - - -
1879B ASP* 3.5 29.9 + - + -
1881B GLN* 3.6 34.4 - - + +
1885B LEU* 4.3 3.2 - - + +
1903B HIS* 1.3 83.3 + - - +
1905B SER* 1.3 58.3 + - - +
1906B SER* 3.1 45.9 + - - -
1907B ALA* 2.8 41.7 + - + +
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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