Contacts of the helix formed by residues 804 - 809 (chain B) in PDB entry 4AY6
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 ASN 804 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B THR* 2.7 17.9 + - - +
803B ILE* 1.3 79.5 - - + +
805B ASN* 1.3 67.3 + - - +
806B LYS* 3.1 15.2 + - - +
807B ALA* 3.1 29.2 + - + +
808B ALA 3.3 8.1 + - - -
812B GLU* 3.2 23.4 + - - +
813B VAL 5.1 0.6 + - - -
815B ARG* 3.2 28.0 - - - +
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Residues in contact with ASN 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B THR* 3.5 26.2 + - - +
802B GLN 5.1 0.2 - - - -
804B ASN* 1.3 73.2 - - - +
806B LYS* 1.3 90.9 + - + +
808B ALA* 3.3 12.0 + - - +
809B THR* 3.3 20.9 + - + +
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Residues in contact with LYS 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B GLY 4.6 5.3 + - - -
589B THR* 4.6 6.3 - - - +
590B ASN* 4.2 11.4 + - - +
804B ASN* 3.1 2.8 + - - +
805B ASN* 1.3 95.2 + - - +
807B ALA* 1.3 61.0 + - - +
809B THR* 3.2 9.7 + - + -
811B GLU* 2.9 66.4 + - + +
812B GLU* 3.2 37.0 + - + +
597C ALA 5.8 1.8 - - - +
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Residues in contact with ALA 807 (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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800B THR* 5.7 2.7 - - - -
804B ASN* 3.1 31.8 + - + +
806B LYS* 1.3 78.3 - - - +
808B ALA* 1.3 61.3 + - - +
810B GLY* 3.5 5.9 + - - -
812B GLU* 3.5 19.5 - - + +
813B VAL 4.4 1.3 - - - -
814B PRO* 3.8 31.4 - - + +
899B GLU* 3.3 21.7 - - - +
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Residues in contact with ALA 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B THR* 3.8 19.6 - - - +
801B THR* 3.6 37.0 - - + +
804B ASN 3.3 4.2 + - - +
805B ASN 3.3 11.2 + - - +
807B ALA* 1.3 79.7 - - - +
809B THR* 1.3 57.6 + - + +
897B PRO* 3.6 16.6 - - + +
898B LYS 3.7 0.2 + - - -
899B GLU* 3.1 30.3 + - - +
900B GLU 4.5 0.4 + - - +
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Residues in contact with THR 809 (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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557B ASN* 4.7 17.1 - - - +
562B HIS* 4.9 0.7 + - - -
591B PHE* 3.9 11.8 - - - -
701B MET* 4.6 0.2 - - - +
801B THR* 6.4 0.4 - - + -
805B ASN* 3.3 16.9 + - + +
806B LYS* 3.2 11.6 + - + -
807B ALA 3.3 0.4 - - - -
808B ALA* 1.3 77.8 - - + +
810B GLY* 1.3 54.2 + - - +
811B GLU* 3.0 31.2 + - - +
897B PRO* 5.1 4.7 - - + -
898B LYS* 3.6 22.1 - - - +
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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