Contacts of the helix formed by residues 921 - 928 (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 ILE 921 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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724A ASP* 6.0 0.4 - - - -
831A THR* 5.6 3.1 - - + -
832A ILE* 6.0 2.2 - - + -
835A GLU* 3.2 24.9 - - - +
920A ARG* 1.3 74.8 - - + +
922A ASN* 1.3 48.0 + - - +
923A GLU* 2.7 11.1 - - - +
924A GLU* 2.6 34.7 + - + +
928A ARG* 2.6 47.2 + - - +
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Residues in contact with ASN 922 (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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835A GLU* 4.3 6.7 + - - -
838A PHE* 2.8 36.8 - - - -
862A TYR* 6.2 0.4 - - - -
864A TYR* 2.5 51.8 + - + +
919A LYS* 2.7 25.3 + - + +
920A ARG 2.4 21.8 + - - +
921A ILE* 1.3 64.3 - - - +
923A GLU* 1.3 84.7 + - - +
925A LYS* 2.5 31.4 + - - +
926A ALA* 3.1 8.2 + - - +
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Residues in contact with GLU 923 (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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862A TYR* 6.6 0.2 - - - -
864A TYR* 3.9 17.8 - - + -
865A THR 4.7 4.7 - - - +
920A ARG 2.9 13.3 - - - +
921A ILE* 2.7 31.9 - - - +
922A ASN* 1.3 88.9 - - - +
924A GLU* 1.3 60.5 + - + +
926A ALA* 3.2 9.2 + - - +
927A LEU* 2.8 29.4 + - + +
944A ILE* 4.1 9.4 - - + +
945A ASN* 3.3 30.1 - - - +
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Residues in contact with GLU 924 (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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921A ILE* 2.6 19.6 + - + +
923A GLU* 1.3 77.5 - - + +
925A LYS* 1.3 52.6 + - - -
927A LEU* 2.8 48.7 - - - +
928A ARG* 2.3 72.5 + - + +
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Residues in contact with LYS 925 (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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724A ASP* 4.1 12.5 - - - +
725A ILE 5.1 1.4 - - - +
770A ARG* 4.8 4.9 - - - +
832A ILE* 3.2 33.5 + - - +
835A GLU* 3.5 38.0 + - + +
836A GLU* 3.0 30.1 + - - +
838A PHE* 5.4 1.8 - - + -
839A ILE* 3.3 29.8 - - + -
922A ASN* 2.5 17.2 + - - +
924A GLU* 1.3 66.2 - - - +
926A ALA* 1.3 57.2 + - - +
927A LEU 2.8 4.9 - - - -
928A ARG* 2.8 37.2 - - + +
929A GLU* 4.7 4.0 + - + -
930A ALA* 2.8 25.7 - - + +
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Residues in contact with ALA 926 (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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838A PHE* 4.8 1.8 - - + -
839A ILE* 3.8 10.2 - - + +
862A TYR* 2.8 33.2 - - + +
922A ASN* 3.1 11.8 + - - +
923A GLU* 3.4 15.9 - - - +
925A LYS* 1.3 77.6 - - - +
927A LEU* 1.3 56.2 + - - +
931A LYS* 3.3 7.8 + - - -
934A MET* 2.8 30.8 - - + +
944A ILE* 3.2 15.4 - - + +
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Residues in contact with LEU 927 (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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923A GLU* 2.8 13.4 + - + +
924A GLU* 2.8 50.0 - - - +
925A LYS 2.8 0.6 - - - -
926A ALA* 1.3 76.3 - - - +
928A ARG* 1.3 83.3 + - + +
929A GLU 3.6 0.7 + - - -
931A LYS* 2.9 29.5 + - + +
932A GLU* 4.4 1.2 - - - +
944A ILE* 3.3 15.9 - - + -
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Residues in contact with ARG 928 (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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723A LYS* 3.9 16.8 - - - +
724A ASP* 2.9 38.9 + - - -
832A ILE* 6.0 0.6 - - - +
835A GLU* 3.6 9.1 + - - -
921A ILE* 2.6 68.0 + - - +
924A GLU* 2.3 45.9 + - + +
925A LYS* 2.8 45.5 - - + +
927A LEU* 1.3 74.3 - - + +
929A GLU* 1.3 69.4 - - + +
930A ALA* 2.2 24.1 + - - +
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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