Contacts of the strand formed by residues 1899 - 1904 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1872D LEU 3.4 3.0 + - - +
1873D LYS* 3.3 24.1 - - - +
1874D VAL* 3.0 25.2 + - - +
1893D MET* 3.7 10.3 - - - -
1897D ALA 3.2 1.4 - - - -
1898D ALA* 1.3 83.5 - - - +
1900D VAL* 1.3 69.2 + - - +
1901D LYS 5.5 0.2 - - - -
1917D PHE* 6.1 1.0 - - - -
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Residues in contact with VAL1900 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1874D VAL* 3.3 17.7 - - + -
1876D LEU* 3.5 35.0 - - + -
1889D SER* 4.0 15.7 - - - +
1892D LEU* 4.0 20.9 - - + -
1893D MET* 3.6 28.6 - - + -
1897D ALA* 4.2 3.8 - - + -
1899D SER* 1.3 83.8 - - - +
1901D LYS* 1.3 64.9 + - - +
1902D GLN* 3.5 10.8 + - + +
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Residues in contact with LYS1901 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1874D VAL 2.8 10.1 + - - -
1875D LEU* 3.1 22.9 - - + +
1876D LEU 2.8 26.1 + - - -
1899D SER 4.3 0.2 - - - -
1900D VAL* 1.3 69.5 - - - +
1902D GLN* 1.3 72.2 + - - +
1909D ASN* 5.6 1.6 - - - +
1911D ASP* 3.3 29.2 + - - -
1912D ILE* 3.8 21.0 - - + +
1913D ALA 5.7 0.4 - - - +
1917D PHE* 3.6 31.1 - - + -
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Residues in contact with GLN1902 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1876D LEU* 3.8 11.7 - - + -
1881D GLN* 4.5 9.3 + - - +
1885D LEU* 3.4 41.8 - - + +
1886D GLU* 4.1 5.4 + - - +
1889D SER* 3.0 26.4 + - - -
1900D VAL* 3.5 9.5 + - + +
1901D LYS* 1.3 85.0 - - - +
1903D HIS* 1.3 61.3 + - - +
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Residues in contact with HIS1903 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1875D LEU* 4.1 16.6 - - + -
1876D LEU 2.8 18.8 + - - +
1877D VAL* 3.3 18.7 - - + -
1878D SER 3.1 23.7 + - - +
1885D LEU* 3.7 5.5 - - - +
1902D GLN* 1.3 75.6 + - - +
1904D HIS* 1.3 77.5 + - - +
1905D SER* 4.7 3.1 + - - -
1907D ALA* 2.8 33.5 + - + +
1909D ASN* 3.3 34.8 + - + +
1912D ILE* 4.2 16.8 - - + +
1927D PRO* 5.5 3.9 - - + +
1930D VAL* 5.5 9.4 - - + +
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Residues in contact with HIS1904 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1878D SER 3.2 7.7 + - - -
1879D ASP* 3.4 35.6 - - - +
1881D GLN* 4.6 22.0 + - + +
1885D LEU* 4.1 6.5 - - + +
1902D GLN 4.4 0.2 - - - -
1903D HIS* 1.3 89.8 + - - +
1905D SER* 1.3 71.2 + - - +
1906D SER* 2.8 46.1 + - - -
1907D ALA* 2.9 29.9 + - + +
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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
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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