Contacts of the helix formed by residues 1828 - 1838 (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 HIS1828 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1771D PHE* 3.2 67.9 - + + +
1772D ASN 4.8 0.2 + - - -
1776D THR* 4.3 8.6 + - - +
1805D ILE* 3.7 14.4 - - + -
1806D ALA 3.1 14.1 + - - +
1807D ASP* 4.4 9.0 + - - +
1826D VAL 3.7 0.8 + - - -
1827D SER* 1.3 76.8 + - - +
1829D VAL* 1.3 85.9 + - + +
1830D TRP 2.9 0.7 - - - -
1831D VAL* 2.7 33.3 + - + +
1832D HIS* 3.1 6.5 + - + +
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Residues in contact with VAL1829 (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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243C MET* 3.6 34.1 - - + +
1827D SER* 2.9 14.7 + - - +
1828D HIS* 1.3 93.6 - - + +
1830D TRP* 1.3 57.4 + - - +
1832D HIS* 3.6 16.2 - - + -
1833D ASP* 2.8 50.4 + - - +
1846D TYR* 3.9 1.6 - - + -
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Residues in contact with TRP1830 (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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1729D PHE* 3.8 26.2 - + - -
1732D TYR* 4.7 7.4 - + - -
1734D PHE* 3.4 29.8 - + - -
1803D LEU* 3.7 21.3 - - + -
1805D ILE* 4.3 8.3 - - + -
1826D VAL* 3.5 13.5 - - + -
1827D SER 2.9 14.3 + - - +
1829D VAL* 1.3 79.1 - - - +
1831D VAL* 1.3 75.8 + - + +
1833D ASP* 4.5 0.5 - - - +
1834D SER* 2.7 41.5 + - - -
1840D LEU* 3.6 23.3 - - + -
1841D GLN* 2.9 28.5 + - + -
1843D TYR* 3.5 34.5 - + + +
1846D TYR* 3.6 27.8 - + + -
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Residues in contact with VAL1831 (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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1729D PHE* 4.1 14.1 - - + -
1776D THR* 4.1 22.0 - - + +
1779D GLN* 3.8 36.3 - - + +
1780D LEU* 4.3 7.4 - - + -
1805D ILE* 3.9 19.7 - - + -
1828D HIS* 2.7 14.6 + - + +
1830D TRP* 1.3 97.3 - - + +
1832D HIS* 1.3 65.7 + - - +
1834D SER* 3.2 5.1 + - - -
1835D CYS* 2.9 23.8 + - - -
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Residues in contact with HIS1832 (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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181C ARG* 4.8 10.7 + - - -
1779D GLN* 4.8 14.3 + - - +
1828D HIS* 3.1 6.1 + - + +
1829D VAL* 3.5 21.5 - - + +
1831D VAL* 1.3 81.3 - - - +
1833D ASP* 1.3 80.3 + - - +
1835D CYS* 3.1 1.6 + - - +
1836D HIS* 2.9 38.5 + - + +
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Residues in contact with ASP1833 (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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177C PRO* 4.1 18.8 - - + +
178C HIS* 4.5 8.8 + - - +
181C ARG* 3.5 20.7 + - - +
243C MET 4.4 3.5 - - - +
1829D VAL* 2.8 26.1 + - - +
1830D TRP 4.5 0.4 - - - +
1832D HIS* 1.3 84.3 - - - +
1834D SER* 1.3 57.2 + - - +
1836D HIS* 4.0 4.9 - - - +
1837D ALA* 3.1 31.5 + - - +
1841D GLN* 4.1 9.0 - - + +
1846D TYR* 2.9 39.2 + - + +
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Residues in contact with SER1834 (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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1728D LEU* 3.5 5.5 - - - +
1729D PHE* 4.0 20.6 - - - -
1830D TRP* 2.7 32.0 + - - -
1831D VAL 3.5 4.3 - - - -
1832D HIS 3.1 0.6 - - - -
1833D ASP* 1.3 74.9 - - - +
1835D CYS* 1.3 55.5 + - - +
1838D ASN* 2.7 28.1 + - - -
1839D GLN 3.0 22.5 + - - -
1840D LEU* 3.9 2.3 - - - -
1841D GLN* 3.3 24.5 + - - +
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Residues in contact with CYS1835 (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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1728D LEU* 3.9 9.2 - - - -
1729D PHE* 3.9 25.1 - - - -
1779D GLN* 3.4 38.8 - - - +
1831D VAL* 2.9 19.3 + - - +
1832D HIS 3.8 2.0 - - - +
1834D SER* 1.3 73.1 - - - +
1836D HIS* 1.3 60.6 + - - +
1838D ASN* 2.6 29.3 + - - +
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Residues in contact with HIS1836 (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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181C ARG* 3.1 52.7 + - - +
1832D HIS* 2.9 32.3 + - + +
1833D ASP* 4.0 6.7 - - - +
1835D CYS* 1.3 78.5 - - - +
1837D ALA* 1.3 63.6 + - + +
1838D ASN* 4.7 1.4 - - - +
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Residues in contact with ALA1837 (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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177C PRO* 6.1 3.4 - - + -
181C ARG* 6.0 3.8 - - - +
1833D ASP 3.1 19.7 + - - +
1836D HIS* 1.3 81.3 - - + +
1838D ASN* 1.3 72.5 + - - +
1839D GLN* 3.2 9.9 + - + +
1841D GLN* 4.2 17.9 - - - +
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Residues in contact with ASN1838 (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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1725D ASN* 2.7 47.5 + - - +
1728D LEU* 4.1 12.0 - - - +
1834D SER 2.7 10.0 + - - -
1835D CYS* 2.6 22.8 + - - +
1836D HIS 4.7 1.3 - - - +
1837D ALA* 1.3 75.5 - - - +
1839D GLN* 1.3 60.6 + - - +
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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