Contacts of the strand formed by residues 841 - 843 (chain B) in PDB entry 6CNF
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 ILE 841 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820B GLN* 3.6 24.9 + - + +
821B HIS* 4.4 14.6 - - + +
823B SER* 2.4 32.6 + - - +
824B LEU* 3.9 15.6 - - + +
830B GLY* 5.3 0.3 - - - -
839B GLY 5.0 2.0 - - - +
840B GLN* 1.3 77.7 - - - +
842B TYR* 1.3 55.6 + - - +
843B ILE 3.1 32.1 - - - +
844B ASN* 3.7 11.4 - - + +
870B PRO* 3.6 26.0 - - + -
871B VAL 4.0 1.8 - - - +
872B ILE* 3.5 28.3 - - + -
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Residues in contact with TYR 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791B THR* 3.0 34.9 + - + +
823B SER* 4.0 3.8 - - - +
824B LEU* 6.1 0.2 - - - -
829B LEU* 4.1 1.7 - - - +
830B GLY* 3.7 20.0 + - - -
836B VAL* 5.5 4.0 - - + -
840B GLN 3.9 0.4 + - - -
841B ILE* 1.3 74.5 - - - +
843B ILE* 1.3 65.8 + - + +
871B VAL* 3.6 24.4 + - + +
872B ILE 3.8 6.1 - - - -
873B TYR* 3.3 49.6 - + + -
881B ILE* 3.4 23.9 - - + +
898B VAL* 3.5 35.5 - - + +
900B LEU* 3.6 22.9 - - + -
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Residues in contact with ILE 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793B THR* 3.1 37.5 - - + +
795B LEU* 5.9 1.1 - - + -
806B ILE* 5.6 2.5 - - + -
824B LEU* 6.2 0.4 - - - -
828B GLY 5.6 0.2 - - - +
829B LEU* 3.4 17.9 - - + +
830B GLY 4.8 1.6 - - - +
841B ILE* 3.1 15.2 - - - +
842B TYR* 1.3 85.0 - - + +
844B ASN* 1.3 69.9 + - - +
845B LYS* 4.5 10.1 - - + +
870B PRO* 3.2 10.4 - - - +
871B VAL* 3.3 34.2 + - + +
896B ILE* 3.6 33.4 - - + -
898B VAL* 5.2 4.3 - - + -
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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
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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