Contacts of the helix formed by residues 876 - 885 (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 ASP 876 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873B MET* 5.7 0.9 - - - +
874B PRO* 3.2 31.6 + - + +
875B VAL* 1.3 75.7 - - - +
877B SER* 1.3 69.2 + - - +
878B LYS* 3.0 19.8 - - - +
879B PHE* 2.9 25.9 + - - +
880B TYR* 3.0 23.3 + - - -
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Residues in contact with SER 877 (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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876B ASP* 1.3 73.9 - - - +
878B LYS* 1.3 71.3 + - - +
880B TYR* 3.7 9.6 + - - +
881B LYS* 3.2 23.4 + - - +
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Residues in contact with LYS 878 (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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876B ASP* 3.5 16.8 + - - +
877B SER* 1.3 83.6 - - - +
879B PHE* 1.3 55.9 + - - +
881B LYS* 3.1 13.0 + - - +
882B MET* 2.7 60.5 + - + +
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Residues in contact with PHE 879 (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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833B VAL* 3.8 25.8 - - + -
834B LYS* 4.1 13.9 - - + -
841B ILE* 4.9 3.8 - - + -
870B TYR* 3.5 48.9 - + + -
873B MET* 4.1 26.6 - - + +
874B PRO 3.5 21.1 - - - +
875B VAL* 4.3 6.1 - - + -
876B ASP* 2.9 17.0 + - - +
878B LYS* 1.3 73.6 - - - +
880B TYR* 1.3 74.6 + + - +
882B MET* 3.5 7.0 + - - +
883B ILE* 3.0 53.7 + - + +
887B PHE* 5.2 1.1 - + - -
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Residues in contact with TYR 880 (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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833B VAL* 3.1 44.4 - - + +
841B ILE* 3.7 31.9 - - + +
842B PHE* 3.9 20.4 - + + -
875B VAL* 3.4 16.5 - - + +
876B ASP* 3.0 21.4 + - - -
877B SER* 3.9 9.0 - - - +
879B PHE* 1.3 81.7 - + - +
881B LYS* 1.3 62.1 + - - +
883B ILE* 2.9 7.5 + - + +
884B LYS* 2.8 27.7 + - - +
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Residues in contact with LYS 881 (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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877B SER 3.2 14.1 + - - +
878B LYS* 3.1 11.5 + - - +
880B TYR* 1.3 78.1 - - - +
882B MET* 1.3 62.9 + - + +
884B LYS* 3.9 8.8 - - + +
885B GLU* 3.1 63.0 + - + +
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Residues in contact with MET 882 (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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873B MET* 3.8 27.8 - - + -
878B LYS* 2.7 45.4 + - + +
879B PHE* 3.6 7.4 - - - +
881B LYS* 1.3 73.9 - - + +
883B ILE* 1.3 68.8 + - - +
885B GLU* 3.4 7.1 + - - +
886B GLY 3.6 0.5 + - - -
887B PHE* 3.0 45.7 + - + +
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Residues in contact with ILE 883 (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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836B MET 5.7 1.1 - - - +
838B PRO* 4.2 24.2 - - + -
841B ILE* 5.6 5.2 - - + -
842B PHE* 5.0 2.9 - - + -
853B TRP* 4.3 15.5 - - + -
870B TYR* 3.7 37.5 - - + +
879B PHE* 3.0 38.6 + - + +
880B TYR* 2.9 9.7 + - + +
882B MET* 1.3 72.9 - - - +
884B LYS* 1.3 66.0 + - - +
885B GLU 2.9 1.7 + - - -
886B GLY 3.0 5.4 + - - -
887B PHE* 3.7 22.0 - - + +
888B ARG* 3.0 29.8 + - - +
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Residues in contact with LYS 884 (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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838B PRO* 5.2 3.8 - - + -
842B PHE* 3.5 36.3 - - + -
880B TYR 2.8 15.6 + - - +
881B LYS* 3.9 10.5 - - + +
883B ILE* 1.3 75.2 - - - +
885B GLU* 1.3 67.4 + - + +
886B GLY 3.2 5.2 + - - -
888B ARG* 5.4 0.2 + - - -
909B ALA* 5.2 9.7 - - - +
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Residues in contact with GLU 885 (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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881B LYS* 3.1 53.5 + - + +
882B MET* 4.1 3.8 - - - +
883B ILE 2.9 0.8 + - - -
884B LYS* 1.3 81.7 - - + +
886B GLY* 1.3 55.8 + - - +
887B PHE 3.7 2.2 + - - -
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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