Contacts of the helix formed by residues 1730 - 1735 (chain X) in PDB entry 1N5O
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 ASN1730 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1718X TRP* 4.2 1.1 - - - -
1729X LEU* 1.3 77.1 - - - +
1731X GLU* 1.3 66.8 + - - +
1732X HIS* 3.0 20.4 + - + +
1733X ASP* 3.1 35.0 + - - +
1734X PHE* 3.4 14.4 - - - -
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Residues in contact with GLU1731 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650X MET* 3.6 11.5 - - - +
1686X HIS* 2.6 44.0 + - + +
1712X TRP* 3.5 40.5 + - + -
1714X VAL* 3.4 15.5 - - + +
1718X TRP* 3.9 24.2 - - + +
1728X MET* 5.6 1.0 - - - +
1729X LEU 3.5 8.6 + - - +
1730X ASN* 1.3 73.6 - - - +
1732X HIS* 1.3 63.7 + - - +
1734X PHE 3.0 2.5 + - - -
1735X GLU 3.0 21.0 + - - -
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Residues in contact with HIS1732 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1712X TRP* 3.6 28.3 - + - -
1730X ASN* 3.7 20.1 - - + +
1731X GLU* 1.3 82.2 + - - +
1733X ASP* 1.3 60.6 + - - +
1734X PHE 3.3 0.3 + - - -
1735X GLU* 3.7 11.3 + - - +
1753X ARG* 3.4 22.9 + - - -
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Residues in contact with ASP1733 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695X PHE* 4.1 10.9 - - - -
1730X ASN* 3.1 24.7 + - - +
1732X HIS* 1.3 77.9 - - - +
1734X PHE* 1.3 73.9 + - + +
1735X GLU 3.7 0.2 - - - -
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Residues in contact with PHE1734 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695X PHE* 3.6 24.5 - + + -
1714X VAL* 3.9 2.0 - - + -
1715X SER* 2.9 27.9 + - - -
1717X PHE* 3.6 19.1 - - + -
1718X TRP* 3.6 43.3 - + + +
1721X GLN* 3.9 15.3 - - + -
1729X LEU* 3.7 41.1 - - + -
1730X ASN* 3.4 16.4 - - - -
1731X GLU 3.0 6.9 + - - +
1733X ASP* 1.3 91.0 - - + +
1735X GLU* 1.3 61.7 + - - +
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Residues in contact with GLU1735 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1695X PHE* 4.1 8.8 - - - +
1712X TRP* 3.8 19.5 - - + -
1713X VAL 3.6 9.4 - - - +
1714X VAL* 3.9 2.2 - - - -
1731X GLU 3.0 13.4 + - - +
1732X HIS 3.7 8.4 + - - +
1733X ASP 3.7 1.6 - - - -
1734X PHE* 1.3 79.7 - - - +
1736X VAL* 1.3 66.1 + - - +
1737X ARG* 3.6 3.8 + - - +
1749X PRO* 5.7 3.8 - - + -
1750X LYS* 6.3 3.6 - - + +
1753X ARG* 5.5 3.6 - - - +
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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