Contacts of the helix formed by residues 865 - 876 (chain B) in PDB entry 6WCZ
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 865 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329B LEU* 5.7 2.0 - - + -
776B LEU* 5.5 1.8 - - + +
780B ALA* 4.3 24.2 - - + -
861B TRP* 3.3 25.4 - - + +
862B ALA* 3.3 34.8 - - - +
863B GLU 4.3 1.6 - - - -
864B ASN* 1.3 75.2 - - - +
866B LYS* 1.3 61.1 + - - +
867B ASP* 3.2 2.9 - - - -
868B THR* 2.8 25.6 + - - -
869B VAL* 2.9 21.2 + - + +
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Residues in contact with LYS 866 (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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865B ILE* 1.3 76.5 - - - +
867B ASP* 1.3 54.2 + - - +
869B VAL* 3.3 8.2 - - + +
870B ASN* 2.5 58.4 + - - +
873B ARG* 3.3 13.5 + - - +
886B LEU* 5.8 8.5 - - + -
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Residues in contact with ASP 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B ASN* 3.0 54.4 + - - +
866B LYS* 1.3 77.6 - - - +
868B THR* 1.3 68.1 + - - -
870B ASN* 3.0 11.3 + - - +
871B MET* 2.9 33.8 + - - +
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Residues in contact with THR 868 (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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328B LEU 4.0 21.4 - - - +
329B LEU* 4.5 19.1 - - + +
331B LYS* 5.7 10.9 - - + -
861B TRP* 4.9 10.3 + - + +
864B ASN* 3.1 21.1 + - - -
865B ILE* 2.8 15.2 + - - -
867B ASP* 1.3 82.0 + - - +
869B VAL* 1.3 60.0 + - - +
871B MET* 3.2 27.4 - - + +
872B VAL* 3.8 4.2 + - - +
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Residues in contact with VAL 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B LEU* 3.8 24.9 - - + -
780B ALA 4.0 20.0 - - - +
783B SER* 4.1 13.5 - - - +
784B ALA* 4.6 8.1 - - + -
865B ILE* 2.9 22.3 + - + +
866B LYS* 3.3 20.2 - - - +
868B THR* 1.3 72.4 - - - +
870B ASN* 1.3 59.2 + - - +
871B MET 3.1 1.8 - - - -
872B VAL* 3.2 12.5 + - + +
873B ARG* 2.8 50.0 + - - +
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Residues in contact with ASN 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866B LYS* 2.5 54.5 + - - +
867B ASP* 3.0 10.7 + - - +
869B VAL* 1.3 74.2 - - - +
871B MET* 1.3 61.8 + - - +
873B ARG* 2.9 33.8 + - - +
874B ARG* 2.9 32.6 + - - +
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Residues in contact with MET 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 5.8 9.0 - - + +
867B ASP 2.9 21.2 + - - +
868B THR* 3.2 19.1 - - + +
869B VAL 3.1 0.2 - - - -
870B ASN* 1.3 76.9 - - - +
872B VAL* 1.3 58.2 + - - +
874B ARG* 3.1 25.4 + - - +
875B ILE* 2.9 40.4 + - + +
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Residues in contact with VAL 872 (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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325B VAL* 4.9 21.5 - - + -
328B LEU* 5.9 5.6 - - + +
329B LEU* 4.7 11.2 - - + -
750B ILE* 6.3 0.7 - - + -
784B ALA* 3.7 30.7 - - + +
868B THR 3.8 2.6 + - - +
869B VAL* 3.2 20.3 + - - +
871B MET* 1.3 79.2 - - - +
873B ARG* 1.3 53.7 + - - +
875B ILE* 2.7 22.1 + - + -
876B ILE* 2.5 54.7 + - + +
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Residues in contact with ARG 873 (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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783B SER* 4.2 13.2 + - - +
784B ALA* 4.4 9.4 - - - +
866B LYS* 3.3 21.8 + - - +
869B VAL* 2.8 33.7 + - - +
870B ASN* 2.9 48.0 + - - +
871B MET 3.3 0.2 - - - -
872B VAL* 1.3 76.4 - - + +
874B ARG* 1.3 59.9 + - - +
876B ILE* 2.9 17.8 - - - +
877B GLY 4.2 8.5 - - - +
878B ASP* 4.2 15.0 - - - +
882B TYR* 3.5 51.0 - - + +
883B MET 5.6 2.0 + - - -
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Residues in contact with ARG 874 (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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870B ASN 2.9 18.4 + - - +
871B MET* 3.1 25.9 + - - +
873B ARG* 1.3 78.8 - - - +
875B ILE* 1.3 64.3 + - + +
876B ILE 2.9 10.2 - - - +
877B GLY* 4.9 0.9 - - - -
878B ASP* 5.5 0.8 + - - -
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Residues in contact with ILE 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 5.2 16.6 - - + -
750B ILE* 4.9 14.0 - - + +
871B MET* 2.9 34.7 + - + +
872B VAL* 2.7 27.3 + - + +
874B ARG* 1.3 74.6 - - + +
876B ILE* 1.3 61.2 + - + +
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Residues in contact with ILE 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 6.5 0.7 - - + -
750B ILE* 3.8 33.4 - - + -
754B ALA* 5.5 4.7 - - + -
784B ALA 3.6 19.7 - - - +
785B VAL* 4.6 1.8 - - + -
786B PRO* 3.7 20.6 - - + -
789B TRP* 4.7 14.6 - - + -
872B VAL* 2.5 38.3 + - + +
873B ARG* 2.9 23.5 - - - +
874B ARG 2.9 7.8 - - - +
875B ILE* 1.3 75.7 - - + +
877B GLY* 1.3 60.6 + - - +
878B ASP 3.7 0.2 + - - -
880B GLU* 5.2 0.2 - - + -
882B TYR* 3.4 23.8 - - - +
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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