Contacts of the helix formed by residues 868 - 876 (chain C) in PDB entry 4OQB
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 ASN 868 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766C ASP* 4.5 1.0 - - - +
767C ASN* 3.2 30.4 + - - +
770C ASP* 3.0 32.6 - - - +
864C SER* 2.7 29.7 + - - +
865C ARG* 2.9 13.0 + - - +
867C THR* 1.3 81.6 + - - +
869C PHE* 1.3 59.8 + - - +
870C ALA 3.1 3.1 - - - -
871C GLY* 2.8 21.1 + - - -
872C ILE* 2.9 21.7 + - + +
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Residues in contact with PHE 869 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C ILE* 4.0 18.2 - - + +
864C SER* 3.3 36.3 - - - -
865C ARG 3.3 13.2 + - - -
866C THR* 3.9 9.6 - - - +
867C THR 3.4 1.0 - - - -
868C ASN* 1.3 75.3 - - - +
870C ALA* 1.3 61.0 + - - +
872C ILE* 3.8 15.5 - - + -
873C LEU* 3.3 35.6 + - + +
918C LEU* 3.5 47.6 - - + -
919C ILE* 4.0 2.7 - - - -
920C LEU* 3.7 30.7 - - + -
1002C LEU* 3.6 26.5 - - + -
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Residues in contact with ALA 870 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C ILE* 3.4 30.0 - - - +
677C PHE* 4.8 10.2 - - + -
773C VAL* 5.6 1.1 - - - -
774C ALA* 3.9 28.5 - - + -
777C LEU* 5.0 5.8 - - - +
797C LEU* 3.9 21.4 - - - +
867C THR 3.8 10.8 + - - +
868C ASN 3.1 0.2 - - - -
869C PHE* 1.3 79.6 - - - +
871C GLY* 1.3 59.6 + - - +
874C SER* 3.5 12.3 + - - -
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Residues in contact with GLY 871 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770C ASP* 5.2 6.4 + - - +
773C VAL* 4.4 17.9 - - - +
867C THR 4.7 0.8 + - - -
868C ASN 2.8 7.5 + - - -
870C ALA* 1.3 77.6 - - - +
872C ILE* 1.3 58.3 + - - +
873C LEU 3.3 2.0 - - - -
874C SER* 3.0 9.2 + - - -
875C GLN* 2.9 28.2 + - - +
878C ARG* 3.3 20.3 + - - -
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Residues in contact with ILE 872 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841C ARG* 4.1 2.9 - - - -
864C SER* 3.9 14.4 - - - +
868C ASN* 2.9 41.3 + - + +
869C PHE* 3.8 23.3 - - + -
870C ALA 3.6 0.2 - - - -
871C GLY* 1.3 76.2 - - - +
873C LEU* 1.3 63.1 + - + +
876C GLY* 2.9 35.4 + - - +
877C LEU* 3.6 35.7 - - + -
878C ARG* 3.8 10.8 - - - +
920C LEU* 3.8 17.5 - - + -
999C LEU* 4.3 7.2 - - + +
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Residues in contact with LEU 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676C ILE* 5.2 4.7 - - + -
797C LEU* 3.5 24.2 - - + +
799C THR* 3.2 47.8 - - + +
801C ILE* 4.4 15.3 - - + -
839C ILE* 4.6 19.1 - - + -
841C ARG* 2.8 26.2 + - + +
869C PHE* 3.3 31.2 + - + +
871C GLY 3.3 0.4 - - - -
872C ILE* 1.3 84.6 - - + +
874C SER* 1.3 57.0 + - - +
920C LEU* 5.3 4.7 - - + -
999C LEU* 5.7 2.5 - - + -
1002C LEU* 4.3 21.1 - - + -
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Residues in contact with SER 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777C LEU* 4.2 30.7 - - - +
796C LYS 4.5 2.0 - - - -
797C LEU* 3.4 17.3 - - - +
798C LYS* 4.8 13.9 + - - +
841C ARG* 3.1 10.1 + - - -
870C ALA 3.5 14.2 + - - -
871C GLY* 3.0 16.9 + - - -
873C LEU* 1.3 80.1 - - - +
875C GLN* 1.3 67.4 + - - +
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Residues in contact with GLN 875 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773C VAL* 3.7 32.9 - - - +
777C LEU* 5.6 1.4 - - - +
841C ARG* 3.6 11.9 + - - +
847C ARG* 4.6 8.1 + - - -
871C GLY* 2.9 11.9 + - - +
874C SER* 1.3 85.7 + - - +
876C GLY* 1.3 63.0 + - - +
877C LEU 4.9 0.9 - - - +
878C ARG* 3.4 37.3 - - - +
994C ILE* 5.7 1.9 - - - +
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Residues in contact with GLY 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841C ARG* 3.2 28.0 - - - +
844C GLU* 4.7 2.5 - - - -
847C ARG* 5.0 3.8 - - - -
872C ILE* 2.9 23.4 + - - +
875C GLN* 1.3 77.2 - - - +
877C LEU* 1.3 63.7 + - - -
878C ARG* 2.9 25.6 + - - +
999C LEU* 5.0 0.4 - - - -
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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