Contacts of the helix formed by residues 1842 - 1846 (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 ASN1842 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C GLU* 4.0 19.0 + - - +
1830D TRP* 4.2 0.4 - - - -
1841D GLN* 1.3 72.0 + - - +
1843D TYR* 1.3 63.3 + - - +
1844D ARG* 2.7 59.8 + - - +
1845D ASN* 3.1 32.5 + - - +
1846D TYR* 3.3 11.3 - - - -
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Residues in contact with TYR1843 (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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1732D TYR* 4.4 18.2 - + - -
1801D GLN* 4.0 19.3 + - + -
1803D LEU* 3.6 30.3 - - + -
1824D PRO* 4.1 19.5 - - + +
1826D VAL* 4.0 24.3 - - + +
1830D TRP* 3.5 31.0 - + + +
1841D GLN 3.2 5.8 + - - -
1842D ASN* 1.3 69.0 + - - +
1844D ARG* 1.3 103.2 + - + +
1845D ASN 2.9 5.8 - - - -
1846D TYR* 2.7 22.7 + - - -
1847D LEU* 3.3 14.0 + - + +
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Residues in contact with ARG1844 (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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168C HIS* 5.4 1.2 + - - -
171C GLU* 6.0 4.5 - - + -
247C ASN* 4.8 1.2 - - - +
249C ARG* 3.7 18.4 + - - +
1842D ASN* 2.7 31.8 + - - +
1843D TYR* 1.3 125.3 + - + +
1845D ASN* 1.3 59.7 + - - +
1846D TYR 3.3 1.5 + - - -
1847D LEU* 4.0 28.2 + - + +
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Residues in contact with ASN1845 (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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171C GLU* 3.5 19.7 + - - +
174C ARG* 6.1 4.2 - - - +
244C GLY* 2.9 47.4 + - - +
245C GLY 4.6 0.7 - - - -
247C ASN* 3.1 18.5 - - - +
249C ARG* 2.7 33.6 + - - +
1842D ASN* 3.1 39.8 + - - +
1843D TYR 2.9 1.2 + - - -
1844D ARG* 1.3 78.9 - - - +
1846D TYR* 1.3 60.7 + - + +
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Residues in contact with TYR1846 (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* 3.4 19.3 - - + +
243C MET* 3.6 24.4 - - + +
244C GLY* 3.3 22.0 - - - -
247C ASN* 3.4 3.1 - - - -
1826D VAL* 3.8 14.6 - - + -
1827D SER* 3.0 27.0 + - - +
1829D VAL* 3.9 6.3 - - + -
1830D TRP* 3.6 36.3 - + + -
1833D ASP* 2.9 36.8 + - + +
1841D GLN* 3.6 20.5 - - + +
1842D ASN 3.3 22.4 - - - -
1843D TYR* 2.7 9.0 + - - +
1845D ASN* 1.3 83.5 - - + +
1847D LEU* 1.3 64.7 + - - +
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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