Contacts of the helix formed by residues 823 - 830 (chain A) in PDB entry 3DPK
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 ALA 823 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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821A TRP 3.9 0.2 + - - -
822A MET* 1.3 76.2 - - - +
824A PRO* 1.3 74.4 - - + +
825A GLU* 3.5 28.3 - - - +
826A SER* 3.0 18.8 + - - +
827A ILE* 3.0 11.1 + - - +
836A SER* 4.0 10.9 + - - +
839A TRP* 3.6 29.2 - - + -
840A SER* 4.7 1.8 + - - -
900A ARG* 3.9 2.2 - - - +
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Residues in contact with PRO 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822A MET 4.2 0.9 - - - +
823A ALA* 1.3 84.9 - - + +
825A GLU* 1.3 58.5 + - - +
827A ILE* 3.0 7.7 + - + +
828A PHE* 2.7 63.2 + - + +
839A TRP* 3.5 37.2 - - + -
869A VAL* 4.6 10.1 - - + +
870A LYS* 5.2 2.0 - - - -
895A LEU* 4.1 22.7 - - + +
900A ARG* 4.5 3.6 - - - +
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Residues in contact with GLU 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823A ALA* 3.5 12.3 - - - +
824A PRO* 1.3 76.0 - - - +
826A SER* 1.3 59.4 + - - +
828A PHE* 5.1 0.9 - - - -
829A ASP* 2.9 36.7 + - - +
830A CYS 3.2 5.0 + - - -
831A VAL* 3.2 34.2 + - + +
833A THR* 4.5 2.1 + - - -
836A SER* 3.6 14.8 + - - -
895A LEU 4.6 1.0 - - - +
897A PRO* 3.7 19.8 - - + +
900A ARG* 2.9 40.0 + - - -
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Residues in contact with SER 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A LEU* 5.7 0.9 - - - +
822A MET* 3.9 17.7 - - - +
823A ALA* 3.0 16.0 + - - +
825A GLU* 1.3 79.8 - - - +
827A ILE* 1.3 58.5 + - - +
830A CYS* 3.2 23.4 + - - -
831A VAL 2.6 24.3 + - - +
832A TYR* 3.9 23.2 + - - -
836A SER* 3.4 22.7 + - - -
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Residues in contact with ILE 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819A VAL* 4.0 27.8 - - + +
822A MET* 3.8 37.9 - - + +
823A ALA 3.0 8.2 + - - +
824A PRO* 3.0 11.0 + - + +
826A SER* 1.3 77.6 - - - +
828A PHE* 1.3 77.7 + - + +
829A ASP 3.5 0.4 + - - -
830A CYS* 4.5 6.1 + - - -
865A PHE* 4.9 2.7 - - + -
866A TYR* 3.5 30.3 - - + -
869A VAL* 4.7 13.5 - - + -
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Residues in contact with PHE 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A PRO* 2.7 39.1 + - + +
825A GLU* 5.1 0.2 - - - -
827A ILE* 1.3 91.9 - - + +
829A ASP* 1.3 72.9 + - - +
830A CYS* 5.8 0.7 - - - -
866A TYR* 3.6 43.3 - + + -
869A VAL* 4.0 14.8 - - + -
870A LYS* 3.9 38.4 - - + +
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Residues in contact with ASP 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A GLU* 2.9 22.7 + - - +
828A PHE* 1.3 94.6 - - - +
830A CYS* 1.3 72.6 + - - +
831A VAL* 2.9 22.4 + - + +
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Residues in contact with CYS 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A LEU* 6.1 5.6 - - - -
826A SER 3.2 21.6 + - - -
827A ILE 5.0 5.4 - - - -
828A PHE 3.8 0.6 - - - -
829A ASP* 1.3 79.4 - - - +
831A VAL* 1.3 60.1 + - - +
832A TYR* 3.6 20.5 + - + -
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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