Contacts of the helix formed by residues 896 - 907 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766B LEU* 3.7 20.4 - - + -
770B LEU* 4.8 1.8 - - + -
863B PHE* 3.6 16.4 - - + -
894B HIS 3.4 10.1 - - - +
895B ALA* 1.3 83.5 - - + +
897B ALA* 1.3 57.1 + - - +
898B GLU* 3.2 5.4 - - - +
899B MET* 2.7 36.4 + - + +
900B TYR* 3.0 10.4 + - - -
927B GLN* 4.2 20.6 - - - +
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Residues in contact with ALA 897 (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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895B ALA 3.6 2.9 + - - -
896B PRO* 1.3 70.3 - - - +
898B GLU* 1.3 67.6 + - - +
900B TYR* 3.4 7.1 + - - +
901B ASP* 2.9 37.0 + - - +
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Residues in contact with GLU 898 (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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896B PRO* 4.7 2.9 - - + +
897B ALA* 1.3 86.9 + - - +
899B MET* 1.3 60.0 + - - +
901B ASP* 3.4 17.3 - - + +
902B ILE* 3.1 30.4 + - + +
927B GLN* 3.4 38.7 + - + +
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Residues in contact with MET 899 (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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770B LEU* 3.4 26.0 - - + -
773B SER* 3.5 27.8 - - - +
859B LEU* 4.5 9.3 - - - +
863B PHE* 4.0 24.5 - - + -
895B ALA* 4.8 2.0 - - + -
896B PRO* 2.7 23.6 + - + +
898B GLU* 1.3 77.4 - - - +
900B TYR* 1.3 63.2 + - - +
901B ASP 3.2 0.2 - - - -
902B ILE* 3.1 25.8 + - - +
903B MET* 3.2 19.4 + - + +
924B ILE* 3.9 21.5 - - + -
927B GLN* 2.9 28.4 + - - +
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Residues in contact with TYR 900 (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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888B ARG* 5.4 0.9 - - - +
889B MET 2.8 26.1 + - - -
890B LEU* 3.6 6.6 - - - -
891B SER* 3.4 51.1 - - - +
892B PRO* 4.7 0.2 - - + -
895B ALA* 4.8 1.8 - - + +
896B PRO 3.0 10.4 + - - +
897B ALA* 3.9 9.0 - - - +
899B MET* 1.3 72.5 - - - +
901B ASP* 1.3 68.3 + - - +
903B MET* 3.2 25.2 + - + +
904B LYS* 3.0 59.1 + - + +
907B TRP* 4.2 9.6 - + - -
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Residues in contact with ASP 901 (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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897B ALA* 2.9 30.9 + - - +
898B GLU* 3.4 19.0 - - + +
900B TYR* 1.3 80.6 - - - +
902B ILE* 1.3 62.0 + - + +
904B LYS* 3.5 21.3 + - - +
905B THR* 3.0 25.3 + - - +
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Residues in contact with ILE 902 (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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859B LEU* 3.8 19.1 - - + -
898B GLU* 3.1 22.8 + - + +
899B MET* 3.1 28.2 + - - +
901B ASP* 1.3 76.0 - - - +
903B MET* 1.3 60.3 + - - +
905B THR* 2.6 22.5 + - - +
906B CYS* 3.0 25.4 + - - -
915B PRO* 5.4 1.8 - - + -
920B ILE* 4.1 20.4 - - + +
923B LEU* 3.8 42.4 - - + +
924B ILE* 4.3 11.9 - - + -
927B GLN* 4.2 6.5 - - - +
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Residues in contact with MET 903 (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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856B GLY* 3.8 5.6 - - - +
859B LEU* 3.7 39.9 - - + +
860B TRP* 4.3 9.9 - - - -
863B PHE* 4.7 3.6 - - + -
892B PRO* 3.8 24.0 - - + -
895B ALA* 4.0 10.5 - - + -
899B MET 3.2 10.6 + - - +
900B TYR* 3.2 36.2 + - + +
902B ILE* 1.3 75.9 - - - +
904B LYS* 1.3 57.7 + - - +
906B CYS* 3.0 12.1 + - - +
907B TRP* 2.9 62.9 + - + -
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Residues in contact with LYS 904 (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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888B ARG* 5.5 5.4 - - + +
900B TYR* 3.0 60.1 + - + +
901B ASP* 3.7 19.4 + - - +
903B MET* 1.3 79.8 - - - +
905B THR* 1.3 59.7 + - + +
907B TRP* 3.5 31.0 + - + +
908B ASP* 3.7 1.9 + - - +
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Residues in contact with THR 905 (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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901B ASP 3.0 14.6 + - - +
902B ILE* 2.6 24.8 + - - -
904B LYS* 1.3 76.5 - - + +
906B CYS* 1.3 63.3 + - - +
907B TRP 3.2 1.1 - - - -
908B ASP* 3.4 17.2 + - - +
913B LYS 5.2 2.9 - - - +
914B ARG* 3.2 26.5 - - - +
915B PRO* 3.8 17.5 - - - +
923B LEU* 6.0 0.5 - - - +
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Residues in contact with CYS 906 (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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852B VAL* 3.7 33.0 - - + +
853B TRP* 3.5 11.4 - - - -
855B TYR* 4.4 1.3 - - - -
856B GLY* 3.7 30.3 - - - -
902B ILE* 3.0 33.6 + - - -
903B MET 3.0 6.8 + - - +
905B THR* 1.3 76.5 - - - +
907B TRP* 1.3 60.4 + - - +
908B ASP 3.2 0.6 + - - -
914B ARG* 3.1 23.9 + - - -
915B PRO* 4.4 2.5 - - - -
920B ILE* 3.8 19.5 - - - -
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Residues in contact with TRP 907 (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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853B TRP* 3.4 37.2 - + + -
856B GLY 3.4 20.2 - - - -
857B ILE* 3.2 40.8 - - + +
860B TRP* 4.1 18.2 - + + -
870B TYR* 5.6 0.9 - - - -
888B ARG* 2.8 53.8 + - + +
889B MET* 3.7 35.2 - - + -
900B TYR* 4.2 8.1 - + - -
903B MET* 2.9 44.7 + - + +
904B LYS* 3.5 16.2 + - + +
905B THR 3.2 0.2 - - - -
906B CYS* 1.3 77.7 - - + +
908B ASP* 1.3 60.4 + - - -
909B ALA 3.4 0.2 + - - -
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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