Contacts of the helix formed by residues 904 - 911 (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 ALA 904 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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887B MET* 5.3 0.4 - - - -
901B LYS 4.4 9.8 + - - +
902B GLU* 2.6 12.9 + - - +
903B VAL* 1.3 70.7 - - - +
905B LYS* 1.3 62.0 + - + +
906B ILE 2.9 6.3 - - - -
907B VAL* 3.0 35.0 + - + +
908B GLN* 3.4 8.0 + - - +
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Residues in contact with LYS 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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869B TRP 4.8 5.4 - - - +
870B LYS* 3.3 35.7 - - + +
873B VAL* 4.5 18.1 - - + +
902B GLU* 3.3 42.5 + - - +
903B VAL* 4.4 4.7 - - - -
904B ALA 1.3 80.3 - - - +
906B ILE* 1.3 56.9 + - - +
908B GLN* 4.3 9.0 + - - +
909B LYS* 2.9 32.4 + - - +
955B LYS 4.7 4.0 + - - -
956B GLN* 5.1 8.5 - - - +
957B ALA 4.9 1.0 + - - -
958B MET* 3.7 34.7 - - + +
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Residues in contact with ILE 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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873B VAL* 3.3 21.8 - - + -
877B VAL* 3.5 24.7 - - + +
883B PHE* 4.5 15.7 - - - +
886B SER* 4.3 11.2 - - - +
887B MET* 3.1 39.3 - - + +
890B LEU* 3.2 28.7 - - + -
903B VAL* 3.5 13.5 - - + +
905B LYS* 1.3 77.6 - - - +
907B VAL* 1.3 72.0 + - - +
909B LYS* 3.8 0.6 - - - +
910B LEU* 2.8 25.8 + - + +
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Residues in contact with VAL 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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887B MET* 4.7 13.5 - - + -
904B ALA* 3.4 26.9 - - + +
906B ILE* 1.3 83.7 - - + +
908B GLN* 1.3 66.8 + - - +
910B LEU* 2.7 17.9 + - - +
911B ILE* 3.3 12.5 + - + +
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Residues in contact with GLN 908 (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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904B ALA 3.4 9.6 + - - +
905B LYS* 4.3 8.1 + - - +
907B VAL* 1.3 77.1 - - - +
909B LYS* 1.3 60.9 + - - +
910B LEU 2.6 13.3 + - - -
911B ILE* 2.7 33.6 + - + +
912B LYS* 3.2 32.3 - - - +
958B MET* 3.6 44.8 - - - +
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Residues in contact with LYS 909 (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 VAL* 5.5 0.7 - - + -
874B ALA* 4.2 33.9 - - + -
877B VAL* 4.0 19.6 - - + +
905B LYS 2.9 22.9 + - - +
906B ILE* 4.0 3.1 - - - +
908B GLN* 1.3 85.0 - - - +
910B LEU* 1.3 61.4 + - - +
912B LYS* 3.7 12.0 + - + +
913B GLU 2.9 15.4 + - - +
914B ARG* 2.3 44.5 + - - +
915B THR* 3.6 8.7 - - - +
958B MET* 4.9 10.3 - - + -
959B PRO* 6.0 2.2 - - + -
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Residues in contact with LEU 910 (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 VAL* 4.5 13.2 - - + -
881B ARG* 4.0 11.7 - - + +
882B ASP 3.5 42.2 - - - +
883B PHE* 5.0 3.6 - - + -
906B ILE* 2.8 16.3 + - + +
907B VAL* 2.7 18.1 + - - +
908B GLN 2.6 4.8 + - - -
909B LYS* 1.3 67.7 - - - +
911B ILE* 1.3 68.8 + - + +
912B LYS 2.9 12.0 + - - -
913B GLU* 3.3 12.5 + - - -
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Residues in contact with ILE 911 (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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907B VAL* 3.9 16.6 - - + +
908B GLN* 2.7 26.4 + - + +
910B LEU* 1.3 81.7 - - + +
912B LYS* 1.3 73.2 + - + +
913B GLU 3.8 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