Contacts of the helix formed by residues 896 - 907 (chain A) in PDB entry 1PKG
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 PRO 896 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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766A LEU* 4.2 25.4 - - + -
770A LEU* 4.8 7.2 - - + -
863A PHE* 3.7 17.7 - - + -
891A SER* 5.3 0.4 - - - -
894A HIS 3.7 4.0 - - - +
895A ALA* 1.3 90.3 - - + +
897A ALA* 1.3 66.7 + - - +
898A GLU* 4.6 6.5 - - + +
899A MET* 3.3 20.6 + - + -
900A TYR* 3.3 17.0 + - - +
927A GLN* 4.8 5.2 - - - +
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Residues in contact with ALA 897 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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891A SER* 5.8 0.4 - - - -
895A ALA 4.0 0.4 + - - -
896A PRO* 1.3 71.1 - - - +
898A GLU* 1.3 65.3 + - + +
900A TYR* 3.2 7.6 + - - +
901A ASP* 2.9 40.0 + - - +
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Residues in contact with GLU 898 (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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896A PRO* 5.1 4.0 - - + -
897A ALA* 1.3 80.9 - - + +
899A MET* 1.3 61.2 + - - +
901A ASP* 3.7 11.0 - - - +
902A ILE* 3.1 32.2 + - + +
923A LEU* 6.5 0.9 - - + -
926A LYS 4.6 7.4 - - - +
927A GLN* 3.5 35.7 + - + +
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Residues in contact with MET 899 (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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770A LEU* 4.1 8.7 - - + -
773A SER* 4.2 13.5 - - - -
859A LEU* 4.0 9.4 - - + +
863A PHE* 3.7 39.0 - - + -
896A PRO* 3.3 24.0 + - + +
898A GLU* 1.3 74.4 - - - +
900A TYR* 1.3 66.8 + - - +
902A ILE* 3.2 32.4 + - + +
903A MET* 3.0 31.4 + - + +
924A ILE* 4.1 10.5 - - + -
927A GLN* 3.0 44.4 - - - +
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Residues in contact with TYR 900 (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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888A ARG* 5.1 1.4 + - - +
889A MET 2.5 29.2 + - - -
890A LEU* 3.4 7.5 - - - -
891A SER* 3.4 49.1 - - - +
895A ALA* 5.0 0.2 - - + -
896A PRO 3.3 6.3 + - - +
897A ALA* 3.2 11.7 + - - +
899A MET* 1.3 78.6 - - - +
901A ASP* 1.3 69.3 + - - +
903A MET* 3.2 21.1 + - + +
904A LYS* 2.9 61.8 + - + +
907A TRP* 4.1 8.1 - + - -
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Residues in contact with ASP 901 (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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897A ALA* 2.9 29.5 + - - +
898A GLU* 3.7 11.1 - - - +
899A MET 3.2 0.4 - - - -
900A TYR* 1.3 83.1 - - - +
902A ILE* 1.3 63.0 + - + +
904A LYS* 3.3 15.5 + - - +
905A THR* 3.0 29.2 + - + +
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Residues in contact with ILE 902 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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859A LEU* 4.1 12.6 - - + -
898A GLU* 3.1 11.4 + - + +
899A MET* 3.2 37.5 - - + +
900A TYR 3.3 0.4 - - - -
901A ASP* 1.3 72.0 - - + +
903A MET* 1.3 68.4 + - - +
905A THR* 2.9 13.4 + - - +
906A CYS* 2.7 36.9 + - - -
915A PRO* 4.9 2.5 - - + -
920A ILE* 4.1 21.3 - - + -
923A LEU* 3.8 42.2 - - + +
924A ILE* 4.4 8.7 - - + -
927A GLN* 4.5 1.8 - - - +
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Residues in contact with MET 903 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856A GLY* 3.8 9.2 - - - +
859A LEU* 3.4 39.6 - - + +
860A TRP* 3.8 22.9 - - - -
863A PHE* 4.4 3.4 - - + -
892A PRO* 4.2 6.5 - - + -
895A ALA* 4.1 19.5 - - + -
899A MET 3.0 26.3 + - - +
900A TYR* 3.3 29.8 - - + +
902A ILE* 1.3 73.1 - - - +
904A LYS* 1.3 64.6 + - - +
906A CYS* 2.8 13.2 + - - +
907A TRP* 2.8 45.8 + - + -
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Residues in contact with LYS 904 (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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888A ARG* 5.6 4.7 - - + -
900A TYR* 2.9 64.1 + - + +
901A ASP* 3.7 16.2 + - - +
903A MET* 1.3 72.0 - - - +
905A THR* 1.3 57.0 + - + +
907A TRP* 2.6 41.4 + - + +
908A ASP* 3.2 5.5 + - - -
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Residues in contact with THR 905 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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901A ASP* 3.0 14.5 + - + +
902A ILE* 2.9 18.5 + - - +
904A LYS* 1.3 72.1 - - + +
906A CYS* 1.3 61.1 + - - +
907A TRP 3.2 0.3 + - - -
908A ASP* 3.3 16.2 + - - +
913A LYS 5.0 5.6 - - - -
914A ARG* 3.3 17.0 - - - +
915A PRO* 3.6 23.0 - - - +
923A LEU* 5.5 2.9 - - - +
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Residues in contact with CYS 906 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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852A VAL* 3.6 37.2 - - - +
853A TRP* 3.5 12.6 - - - -
855A TYR* 4.1 9.0 - - - -
856A GLY* 4.0 9.9 - - - -
902A ILE* 2.7 30.7 + - - -
903A MET* 2.8 12.5 + - - +
905A THR* 1.3 73.3 + - - +
907A TRP* 1.3 56.7 + - + +
914A ARG* 3.2 27.8 + - - +
915A PRO* 3.9 3.1 - - - +
920A ILE* 3.8 18.8 - - - -
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Residues in contact with TRP 907 (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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853A TRP* 3.1 33.5 - + + -
856A GLY* 3.4 20.0 - - - -
857A ILE* 3.3 39.7 - - + +
860A TRP* 4.0 16.8 - + + -
870A TYR* 5.8 1.1 - - - -
888A ARG* 2.9 59.4 + - + +
889A MET* 3.5 41.5 - - + -
900A TYR* 4.1 10.1 - + - -
903A MET* 2.8 24.2 + - + -
904A LYS* 2.6 28.2 + - + +
906A CYS* 1.3 75.5 - - - +
908A ASP* 1.3 65.5 + - - -
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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