Contacts of the helix formed by residues 884 - 892 (chain B) in PDB entry 1WZ2
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 LYS 884 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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882B ASP* 2.8 3.4 + - - -
883B PHE* 1.3 111.8 + - + +
885B SER* 1.3 52.9 + - - +
886B SER 2.4 6.8 + - - -
887B MET* 2.4 44.0 + - - +
888B GLU* 2.7 41.8 + - + +
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Residues in contact with SER 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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880B LYS* 3.2 38.3 - - - +
882B ASP* 2.5 25.1 + - - +
883B PHE* 5.0 1.2 - - - -
884B LYS* 1.3 73.5 - - - +
886B SER* 1.3 53.8 + - - -
888B GLU* 3.6 20.2 - - - +
889B GLU* 3.1 24.8 + - - +
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Residues in contact with SER 886 (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 VAL* 4.5 5.8 - - - -
877B VAL* 4.1 27.6 - - - +
880B LYS* 3.3 20.3 - - - +
882B ASP* 2.8 16.3 + - - -
883B PHE* 3.9 10.7 + - - -
884B LYS 2.4 9.8 + - - -
885B SER* 1.3 69.6 - - - +
887B MET* 1.3 52.7 + - - -
888B GLU 3.0 4.5 - - - -
889B GLU* 2.8 9.9 + - - +
890B LEU* 2.8 39.5 + - - +
906B ILE* 4.3 7.3 - - - +
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Residues in contact with MET 887 (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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883B PHE 3.9 19.5 - - - +
884B LYS* 2.4 32.9 + - - +
886B SER* 1.3 73.7 + - - +
888B GLU* 1.3 54.6 + - - -
890B LEU* 3.8 3.1 - - - -
891B MET* 3.2 46.8 + - + +
903B VAL* 3.5 26.5 - - - +
904B ALA* 5.3 0.2 - - - -
906B ILE* 3.1 39.4 - - + +
907B VAL* 4.7 12.8 - - + -
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Residues in contact with GLU 888 (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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884B LYS* 2.7 46.2 + - + +
885B SER* 3.6 18.7 + - - +
887B MET* 1.3 76.1 - - - +
889B GLU* 1.3 62.2 + - - +
890B LEU 3.0 5.3 + - - -
891B MET* 4.7 2.2 - - - +
892B LYS* 3.2 27.6 + - - +
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Residues in contact with GLU 889 (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 VAL* 3.7 31.5 - - + +
880B LYS* 4.9 14.3 - - - +
885B SER 3.1 12.4 + - - +
886B SER* 2.8 12.1 + - - +
888B GLU* 1.3 79.5 - - - +
890B LEU* 1.3 57.8 + - + +
892B LYS* 2.9 34.4 + - - +
893B ASP* 4.9 2.4 - - - +
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Residues in contact with LEU 890 (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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872B LYS* 4.4 7.6 - - + +
873B VAL* 4.2 22.4 - - + +
876B VAL* 4.2 30.5 - - + -
877B VAL* 5.1 0.2 - - + -
886B SER* 2.8 16.0 + - - +
887B MET* 4.0 4.0 - - - +
888B GLU 3.0 1.6 - - - -
889B GLU* 1.3 79.1 - - + +
891B MET* 1.3 52.4 + - + +
892B LYS 2.5 18.4 + - - -
893B ASP* 2.6 27.9 + - + +
896B ILE* 4.2 33.1 - - + +
903B VAL* 4.4 5.4 - - + -
906B ILE* 3.2 35.9 - - + -
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Residues in contact with MET 891 (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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887B MET* 3.2 31.4 + - + +
888B GLU* 4.7 1.8 - - - +
890B LEU* 1.3 77.2 - - + +
892B LYS* 1.3 54.3 + - - +
893B ASP 2.9 7.4 + - - -
897B ARG* 3.5 58.9 - - + +
900B GLY* 4.3 22.9 - - - -
903B VAL* 4.7 9.9 - - - -
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Residues in contact with LYS 892 (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 GLU* 3.2 19.1 + - - +
889B GLU* 2.9 41.6 + - - +
890B LEU 2.5 4.9 + - - -
891B MET* 1.3 73.3 - - - +
893B ASP* 1.3 55.7 - - + +
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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