Contacts of the helix formed by residues 930 - 939 (chain A) 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 930 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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770A ARG* 4.4 5.4 - - - +
839A ILE* 4.3 17.0 - - + -
925A LYS* 2.8 28.5 - - + +
926A ALA* 4.1 0.2 - - - -
928A ARG 2.2 17.7 + - - +
929A GLU* 1.3 69.4 - - - +
931A LYS* 1.3 67.3 - - - +
932A GLU 3.3 2.0 - - - -
933A PHE* 3.0 5.0 + - - -
934A MET* 2.7 48.3 + - + +
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Residues in contact with LYS 931 (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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926A ALA 3.3 6.3 + - - +
927A LEU* 2.9 22.3 + - + +
929A GLU 3.8 0.2 - - - -
930A ALA* 1.3 77.7 - - - +
932A GLU* 1.3 68.8 + - - +
934A MET* 3.8 4.3 - - - +
935A GLU* 2.4 62.8 + - - +
941A GLU* 5.5 0.6 - - - +
942A ILE* 2.9 49.1 + - + +
943A ILE* 4.7 2.0 - - - +
944A ILE* 4.1 15.7 - - + +
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Residues in contact with GLU 932 (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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927A LEU 4.4 2.6 - - - +
929A GLU* 4.7 17.9 + - - +
931A LYS* 1.3 86.8 + - - +
933A PHE* 1.3 72.4 + - + +
935A GLU* 3.1 10.9 + - - +
936A LYS* 2.7 25.1 + - + +
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Residues in contact with PHE 933 (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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766A TRP* 4.2 9.9 - + - -
769A ARG* 4.6 18.4 - - + -
770A ARG* 2.6 74.3 - - + +
843A MET* 4.2 15.9 - - + -
929A GLU 3.9 7.9 - - - +
930A ALA 3.0 7.5 + - - +
932A GLU* 1.3 80.8 - - - +
934A MET* 1.3 68.6 + - + +
936A LYS* 2.7 27.8 + - + +
937A GLU* 2.8 54.9 + - + -
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Residues in contact with MET 934 (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 ARG* 5.9 0.9 - - - +
839A ILE* 4.5 13.9 - - + +
842A VAL* 5.2 5.2 - - - -
843A MET* 4.3 27.1 - - + -
846A ILE* 6.0 2.0 - - - -
862A TYR* 4.5 10.8 - - - +
926A ALA* 2.8 42.2 - - + +
930A ALA* 2.7 37.7 + - + +
931A LYS* 3.8 5.4 - - - +
933A PHE* 1.3 77.1 - - + +
935A GLU* 1.3 52.7 + - - +
938A LEU* 2.7 51.1 + - + +
942A ILE* 4.6 23.1 - - + -
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Residues in contact with GLU 935 (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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931A LYS* 2.4 58.0 + - - +
932A GLU* 3.1 9.3 + - - +
934A MET* 1.3 74.4 - - - +
936A LYS* 1.3 55.8 + - - +
939A GLY* 2.7 32.9 + - - -
940A ILE 3.1 19.5 + - - +
941A GLU* 3.2 13.7 - - - +
942A ILE* 2.9 32.7 + - + +
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Residues in contact with LYS 936 (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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769A ARG 6.1 0.4 - - - -
772A GLU* 3.0 31.4 + - + -
932A GLU 2.7 13.5 + - - +
933A PHE* 2.7 26.0 + - + +
935A GLU* 1.3 73.8 - - - +
937A GLU* 1.3 68.7 + - - +
939A GLY* 3.9 5.7 + - - -
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Residues in contact with GLU 937 (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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769A ARG* 3.3 36.4 + - - +
843A MET* 4.7 6.1 - - + -
847A LYS* 6.1 5.6 - - - +
933A PHE* 2.8 52.1 + - + +
934A MET 3.8 2.7 - - - +
936A LYS* 1.3 89.3 + - - +
938A LEU* 1.3 70.1 + - + +
939A GLY 3.5 0.2 + - - -
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Residues in contact with LEU 938 (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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843A MET* 3.5 44.2 - - + +
846A ILE* 3.8 45.5 - - + -
847A LYS* 5.1 12.1 - - + +
934A MET* 2.7 36.2 + - + +
937A GLU* 1.3 77.7 - - + +
939A GLY* 1.3 62.6 + - - +
940A ILE* 3.4 25.5 + - + +
942A ILE* 4.7 4.0 - - + -
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Residues in contact with GLY 939 (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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858A ALA* 5.7 0.3 - - - -
935A GLU 2.7 19.4 + - - -
936A LYS 3.9 5.6 + - - -
937A GLU 3.2 3.6 - - - -
938A LEU* 1.3 74.4 - - - +
940A ILE* 1.3 66.5 + - - +
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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