Contacts of the strand formed by residues 1832 - 1834 (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 VAL1832 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1808X VAL* 3.2 9.2 - - + +
1810X VAL* 3.9 27.8 - - + -
1821X PHE 5.3 0.4 - - - +
1824X ILE* 3.7 35.7 - - + -
1825X GLY 4.8 1.1 - - - +
1830X ALA 3.5 10.3 + - - +
1831X PRO* 1.3 74.9 - - - +
1833X VAL* 1.3 64.5 + - - +
1854X LEU* 3.4 6.8 - - - +
1855X ILE* 2.8 38.2 + - + +
1857X GLN* 3.9 32.6 - - + +
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Residues in contact with VAL1833 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1807X ILE* 3.9 9.4 - - + -
1808X VAL 2.6 18.7 + - - +
1809X VAL* 3.3 18.5 - - + -
1810X VAL* 2.8 27.9 + - - +
1831X PRO* 4.0 1.5 - - + -
1832X VAL* 1.3 79.9 - - - +
1834X THR* 1.3 62.9 + - - +
1837X TRP* 3.8 24.7 - - + -
1850X LEU* 4.1 27.4 - - + +
1853X TYR* 3.4 14.8 - - + +
1854X LEU* 3.9 20.9 - - + -
1855X ILE* 4.6 3.6 - - - -
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Residues in contact with THR1834 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809X VAL* 4.4 0.6 - - - +
1810X VAL 3.3 6.5 - - - -
1811X GLN* 5.9 0.2 - - - +
1812X PRO* 3.6 22.9 - - - +
1833X VAL* 1.3 78.7 - - - +
1835X ARG* 1.3 59.2 + - - +
1836X GLU* 3.1 23.2 + - + -
1837X TRP* 3.0 25.5 + - - +
1853X TYR* 3.1 38.7 + - + +
1855X ILE* 4.3 11.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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