Contacts of the helix formed by residues 823 - 831 (chain B) in PDB entry 4X52
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 ASP 823 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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750B SER* 3.9 21.6 - - - +
786B PHE* 3.8 3.8 - - - -
821B ALA* 3.4 15.6 - - - +
822B LYS* 1.4 109.9 + - - +
824B ALA* 1.3 65.0 + - - +
825B ILE* 4.2 10.7 - - + +
826B TYR* 3.1 15.9 + - + +
875B SER 4.7 1.0 + - - -
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Residues in contact with ALA 824 (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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746B HIS 5.5 0.2 + - - -
747B PHE* 3.9 13.0 - - + +
750B SER* 3.2 6.7 + - - +
751B MET* 3.5 24.7 - - + -
786B PHE* 3.3 46.6 - - + -
823B ASP* 1.3 70.5 - - - +
825B ILE* 1.4 56.6 + - - +
827B SER* 3.2 3.3 + - - -
828B HIS* 3.0 24.3 + - - +
840B MET* 3.3 12.1 - - + +
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Residues in contact with ILE 825 (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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750B SER* 3.1 41.8 + - - +
751B MET* 3.4 20.1 - - - -
754B PHE* 3.7 21.5 - - + -
823B ASP* 4.2 9.4 - - + +
824B ALA* 1.4 73.7 - - - +
826B TYR* 1.3 59.6 + - + +
828B HIS* 3.5 8.7 + - + +
829B LYS* 2.9 47.8 + - + +
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Residues in contact with TYR 826 (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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808B GLU* 4.8 2.0 - - - -
810B ASN* 3.1 28.4 + - - -
814B TYR* 4.2 6.6 + - - -
821B ALA* 3.8 14.8 - - + -
823B ASP* 3.1 17.7 + - + +
825B ILE* 1.3 79.5 - - + +
827B SER* 1.4 69.6 + - - +
829B LYS* 3.2 19.9 + - - +
830B TYR* 3.1 63.6 + + + -
869B ASP* 5.1 3.0 + - - -
875B SER* 3.8 29.6 - - - +
876B VAL* 3.9 33.6 - - + +
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Residues in contact with SER 827 (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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786B PHE* 3.8 7.4 + - - -
787B TYR* 3.4 6.9 - - - -
788B ALA* 2.7 34.7 + - - +
819B TYR 5.1 2.8 + - - -
821B ALA* 3.7 18.2 + - - +
823B ASP 3.6 2.2 + - - -
824B ALA 3.2 7.7 + - - -
826B TYR* 1.4 80.8 - - - +
828B HIS* 1.3 62.6 + - - +
830B TYR* 3.5 3.7 + - - +
831B CYS* 3.2 24.1 + - - +
840B MET* 4.1 6.7 - - - -
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Residues in contact with HIS 828 (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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751B MET* 3.8 15.0 - - + -
754B PHE* 3.4 37.3 - + - -
788B ALA* 3.9 10.4 - - - +
824B ALA 3.0 16.8 + - - +
825B ILE* 3.6 11.9 - - + +
827B SER* 1.3 75.9 - - - +
829B LYS* 1.3 68.5 + - + +
831B CYS* 3.3 17.6 + - - +
835B ALA* 5.2 10.1 - - + -
838B VAL* 4.5 9.0 - - + +
840B MET* 4.0 2.9 - - + -
893B TYR* 2.7 28.4 + + - -
895B GLU* 4.0 13.8 + - + -
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Residues in contact with LYS 829 (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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809B THR* 4.6 2.4 + - - +
825B ILE* 2.9 34.3 + - + +
826B TYR* 3.3 38.3 - - - +
828B HIS* 1.3 81.5 - - + +
830B TYR* 1.4 88.9 + - + +
831B CYS 3.3 5.3 + - - +
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Residues in contact with TYR 830 (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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808B GLU* 3.4 21.7 - - + +
809B THR* 3.0 47.2 + - - +
810B ASN* 3.4 29.8 - - - +
813B LYS* 5.3 3.8 + - - -
826B TYR* 3.1 63.2 + + + +
827B SER* 3.8 4.0 - - - +
829B LYS* 1.4 100.6 - - + +
831B CYS* 1.3 60.0 + - - +
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Residues in contact with CYS 831 (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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788B ALA* 3.9 12.8 - - + +
789B THR* 4.0 12.6 - - - -
808B GLU* 4.9 2.7 - - - -
809B THR* 4.5 1.3 - - - +
827B SER 3.2 15.6 + - - +
828B HIS* 3.3 14.6 + - - +
829B LYS 4.2 4.2 - - - +
830B TYR* 1.3 75.2 - - - +
832B PRO* 1.4 66.8 - - - +
833B TYR* 3.5 35.2 + - - +
838B VAL* 3.6 31.2 - - + -
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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