Contacts of the helix formed by residues 823 - 826 (chain C) 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 SER 823 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777C ILE* 6.0 2.3 - - - +
780C ILE* 3.9 13.5 - - - +
781C ASN* 4.8 8.2 + - - -
821C THR* 2.6 20.1 + - - -
822C ARG* 1.3 77.4 - - - +
824C GLN* 1.3 60.9 + - - +
826C GLY* 3.2 12.7 + - - +
827C LEU 4.4 2.9 - - - -
829C GLU* 3.2 21.8 + - - -
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Residues in contact with GLN 824 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780C ILE* 3.6 30.0 - - + +
796C ASN* 2.7 30.7 + - - +
797C GLY 3.6 12.8 - - - +
798C LEU* 3.6 32.4 - - + +
819C VAL 3.8 2.2 + - - +
820C THR* 3.5 10.6 - - - +
821C THR* 3.2 38.7 + - - +
822C ARG 3.2 0.4 - - - -
823C SER* 1.3 81.0 + - - +
825C TYR* 1.3 74.4 + - + +
826C GLY 3.5 0.4 + - - -
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Residues in contact with TYR 825 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C GLY 3.9 8.7 + - - -
798C LEU* 4.7 9.6 - - + -
820C THR* 4.4 3.3 - - + +
821C THR 3.5 14.1 - - - -
822C ARG 3.0 6.5 + - - +
824C GLN* 1.3 93.5 + - + +
826C GLY* 1.3 64.0 + - - +
827C LEU* 3.1 13.0 + - + +
864C TRP* 3.9 15.9 - + + -
891C ILE* 4.1 9.4 - - - +
892C PHE 5.5 0.5 - - - +
893C SER* 3.8 25.9 + - - +
894C PRO* 5.3 4.7 - - + -
900C GLU* 2.8 42.9 + - - +
904C ARG* 3.5 32.6 - - + +
907C LEU* 3.7 25.4 - - + -
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Residues in contact with GLY 826 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822C ARG 3.1 3.9 + - - -
823C SER* 3.2 12.2 + - - -
824C GLN 3.5 0.4 + - - -
825C TYR* 1.3 78.4 - - - +
827C LEU* 1.3 64.2 + - - +
828C PRO* 3.7 1.6 - - - +
891C ILE* 3.6 16.1 - - - +
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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