Contacts of the helix formed by residues 822 - 828 (chain C) in PDB entry 4YZ9
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 822 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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680C HIS* 6.2 0.2 - - - -
753C TYR* 4.0 27.6 + - - -
757C ILE* 4.2 0.4 - - - -
820C ARG 3.9 0.6 + - - -
821C PRO* 1.3 76.5 - - - +
823C ALA* 1.3 67.4 + - - +
824C LYS* 3.7 5.6 + - - +
825C HIS* 2.9 22.7 + - - +
826C VAL* 2.9 20.8 + - - +
962C PHE* 4.0 11.1 - - - -
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Residues in contact with ALA 823 (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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673C THR* 3.5 15.6 - - + +
676C LEU* 4.5 3.8 - - + -
677C ALA* 3.6 34.3 - - + +
680C HIS* 4.0 17.6 + - + +
757C ILE* 3.8 15.4 - - + +
822C SER* 1.3 73.8 - - - +
824C LYS* 1.3 62.7 + - - +
826C VAL* 3.2 6.8 + - - +
827C LEU* 3.2 26.5 + - - +
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Residues in contact with LYS 824 (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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677C ALA* 4.3 22.2 - - + -
681C SER* 5.4 9.8 - - - -
822C SER* 3.2 5.6 + - - +
823C ALA* 1.3 77.3 - - + +
825C HIS* 1.3 63.3 + - - +
827C LEU* 3.1 23.6 + - + +
828C LYS* 3.5 14.6 + - - +
962C PHE* 3.9 27.8 - - + -
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Residues in contact with HIS 825 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808C LEU* 6.6 0.2 - - + -
811C LYS* 5.9 8.1 + - + -
821C PRO* 3.5 23.6 - - + +
822C SER* 2.9 25.1 + - - +
824C LYS* 1.3 78.9 - - - +
826C VAL* 1.3 62.6 + - - +
828C LYS* 3.0 13.8 + - + +
829C HIS* 3.6 12.7 + + + +
945C TYR* 4.8 11.4 + - - -
962C PHE* 3.6 45.6 + + + +
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Residues in contact with VAL 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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673C THR* 3.8 18.2 - - + -
757C ILE* 4.8 4.5 - - + -
764C PHE* 4.0 14.1 - - + -
808C LEU* 4.0 19.1 - - + -
812C MET* 3.9 18.2 - - + -
821C PRO* 3.8 26.5 - - + +
822C SER 2.9 19.6 + - - +
823C ALA* 3.2 11.2 + - - +
825C HIS* 1.3 75.8 - - - +
827C LEU* 1.3 62.1 + - - +
829C HIS* 3.2 14.6 + - - +
832C PHE* 3.1 28.1 - - + -
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Residues in contact with LEU 827 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670C GLN* 3.7 43.8 - - + +
673C THR* 3.8 15.5 - - + +
674C SER* 4.1 23.3 - - - +
677C ALA* 4.5 6.3 - - + -
823C ALA 3.2 16.0 + - - +
824C LYS* 3.1 17.5 + - + +
826C VAL* 1.3 76.0 - - - +
828C LYS* 1.3 64.8 + - + +
829C HIS 3.6 0.5 + - - +
832C PHE* 3.6 23.6 - - + +
833C TRP* 5.3 1.2 - - - -
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Residues in contact with LYS 828 (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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824C LYS 3.9 11.4 - - - +
825C HIS* 3.0 11.2 + - + +
827C LEU* 1.3 80.5 - - - +
829C HIS* 1.3 61.4 + - - +
830C PRO* 4.1 0.3 - - - +
833C TRP* 2.8 28.6 + - - +
837C LYS* 4.9 10.0 + - - +
945C TYR* 4.9 1.6 + - - -
959C PRO* 4.0 24.7 + - + +
960C TYR 4.3 5.2 - - - +
961C TYR 5.2 1.8 - - - +
962C PHE* 4.0 36.3 - - + +
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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
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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