Contacts of the helix formed by residues 866 - 871 (chain A) 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 GLY 866 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862A LEU 4.3 3.2 + - - -
863A GLU* 3.0 22.4 + - - -
864A ARG 4.2 0.9 - - - -
865A GLY* 1.3 75.3 - - - +
867A ARG* 1.3 64.5 + - - -
868A ALA 3.3 0.9 + - - -
869A VAL* 3.3 13.3 + - - +
870A VAL* 3.6 10.0 + - - +
895A GLY 4.4 11.2 - - - -
897A VAL* 4.0 13.6 - - - +
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Residues in contact with ARG 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A GLY 3.4 1.8 + - - -
866A GLY* 1.3 72.9 - - - -
868A ALA* 1.3 51.9 + - - +
870A VAL* 3.2 9.5 + - - -
871A LYS* 2.6 15.6 + - - -
872A MET* 2.5 61.8 + - + +
895A GLY* 4.7 4.9 + - - +
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Residues in contact with ALA 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A GLY 3.8 9.1 + - - +
866A GLY 3.3 1.0 + - - -
867A ARG* 1.3 79.2 - - - +
869A VAL* 1.3 65.0 + - + +
871A LYS* 3.2 16.4 + - - +
939A HIS* 5.7 3.9 - - - -
796C HIS* 5.6 2.3 + - - -
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Residues in contact with VAL 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A GLY* 4.3 11.4 - - - +
866A GLY 3.3 8.7 + - - +
867A ARG 3.3 0.4 - - - -
868A ALA* 1.3 79.5 - - + +
870A VAL* 1.3 60.0 + - + +
871A LYS* 3.5 3.5 + - - +
897A VAL* 4.4 7.0 - - + -
937A PHE* 3.7 20.4 - - - +
938A PRO* 5.7 0.3 - - - +
939A HIS* 3.9 17.5 + - + +
940A LEU* 3.7 46.9 - - + +
943A HIS* 3.7 37.0 - - + +
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Residues in contact with VAL 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A GLY 3.8 1.1 - - - +
867A ARG* 3.5 14.8 - - - +
869A VAL* 1.3 77.5 - - + +
871A LYS* 1.3 66.7 + - - +
872A MET* 3.2 15.8 + - - +
873A ASP 3.1 16.6 - - - +
874A TRP* 3.5 14.9 + - + -
877A ASN* 3.6 2.3 + - - -
894A GLY 3.8 16.6 - - - +
895A GLY* 4.1 8.3 - - - +
896A SER 4.3 4.7 - - - +
897A VAL* 3.7 40.2 - - + +
900A LEU* 4.3 14.6 - - + -
937A PHE* 3.8 10.0 - - - -
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Residues in contact with LYS 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A GLU* 4.5 11.8 + - - +
867A ARG 2.6 12.0 + - - -
868A ALA* 3.2 13.4 + - - +
869A VAL 4.3 4.5 - - - +
870A VAL* 1.3 76.8 - - - +
872A MET* 1.3 58.3 + - - +
873A ASP* 2.9 13.1 + - - +
877A ASN* 3.3 32.3 + - - +
935A SER 5.8 0.4 + - - -
936A ARG* 3.7 20.7 + - - +
937A PHE* 4.7 2.7 - - + +
938A PRO* 4.5 8.8 - - - +
796C HIS* 4.1 46.3 + - + +
798C GLU* 4.4 12.9 + - - +
799C LYS* 4.7 7.8 - - + +
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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