Contacts of the helix formed by residues 921 - 928 (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 ILE 921 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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831B THR* 5.6 5.2 - - + -
832B ILE* 5.6 4.3 - - + -
835B GLU* 2.7 32.1 - - - +
920B ARG* 1.3 75.9 - - + +
922B ASN* 1.3 49.9 + - - +
923B GLU* 3.3 9.0 - - - -
924B GLU* 2.6 41.9 + - + +
925B LYS 3.2 2.0 + - - -
928B ARG* 2.9 39.7 - - - +
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Residues in contact with ASN 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B GLU* 4.6 4.9 - - - -
838B PHE* 3.4 32.3 - - - -
864B TYR* 2.9 61.4 + - + +
919B LYS* 2.7 27.4 + - - +
920B ARG* 2.4 22.6 + - - +
921B ILE* 1.3 64.3 - - - +
923B GLU* 1.3 73.4 + - - +
925B LYS* 2.4 33.3 + - - +
926B ALA* 3.0 8.2 + - - +
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Residues in contact with GLU 923 (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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864B TYR* 4.1 17.6 - - + -
865B THR 4.5 6.1 - - - +
920B ARG 3.2 21.8 - - - +
921B ILE* 3.3 14.0 - - - +
922B ASN* 1.3 87.6 - - - +
924B GLU* 1.3 67.2 + - - +
926B ALA* 3.2 10.1 + - - +
927B LEU* 2.8 28.9 + - + +
944B ILE* 4.2 5.2 - - + +
945B ASN* 3.1 31.6 - - - +
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Residues in contact with GLU 924 (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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921B ILE* 2.6 26.5 + - + +
923B GLU* 1.3 83.2 - - - +
925B LYS* 1.3 52.8 + - - +
927B LEU* 2.9 28.1 - - + +
928B ARG* 2.3 67.4 + - + +
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Residues in contact with LYS 925 (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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724B ASP* 3.6 17.6 - - - +
725B ILE* 4.3 4.6 - - - +
728B TRP* 5.5 0.2 - - - -
770B ARG* 5.0 5.4 - - - +
832B ILE* 3.2 30.3 + - - +
835B GLU* 3.5 41.5 - - + +
836B GLU* 4.0 27.6 + - - +
838B PHE* 5.6 2.0 - - + -
839B ILE* 3.7 17.9 - - + -
921B ILE 3.2 3.6 + - - -
922B ASN* 2.4 25.5 + - - +
924B GLU* 1.3 64.1 - - - +
926B ALA* 1.3 50.0 - - - +
927B LEU 2.8 4.9 - - - -
928B ARG* 2.8 30.8 - - + +
929B GLU* 3.9 7.6 + - - -
930B ALA* 2.7 32.4 - - + +
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Residues in contact with ALA 926 (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 PHE* 4.5 16.1 - - + -
839B ILE* 4.3 8.4 - - + +
842B VAL* 6.1 0.7 - - + -
862B TYR* 3.2 28.4 + - + +
922B ASN* 3.0 6.6 + - - +
923B GLU* 3.3 16.4 - - - +
925B LYS* 1.3 76.0 - - - +
927B LEU* 1.3 56.6 + - - +
930B ALA* 3.5 6.0 - - - +
931B LYS* 3.3 18.5 + - - -
934B MET* 4.0 8.5 - - + +
942B ILE* 5.3 0.2 - - - +
944B ILE* 3.1 17.0 - - + +
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Residues in contact with LEU 927 (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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923B GLU* 2.8 9.9 + - + +
924B GLU* 2.9 44.2 - - - +
925B LYS 2.8 0.2 - - - -
926B ALA* 1.3 76.9 - - - +
928B ARG* 1.3 65.5 + - - +
929B GLU 3.5 0.7 + - - -
931B LYS* 2.9 33.1 + - + +
932B GLU* 4.3 0.5 - - - +
944B ILE* 3.1 37.5 - - + -
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Residues in contact with ARG 928 (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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723B LYS* 3.9 15.5 - - - +
724B ASP* 2.6 51.1 + - - -
832B ILE* 5.5 1.0 - - - +
835B GLU* 4.1 7.0 + - - -
921B ILE* 2.9 55.4 + - - +
924B GLU* 2.3 55.6 + - + +
925B LYS* 2.8 39.9 - - + +
927B LEU* 1.3 64.4 - - - +
929B GLU* 1.3 62.6 - - - +
930B ALA* 2.2 22.7 + - - +
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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