Contacts of the helix formed by residues 856 - 864 (chain C) in PDB entry 4YZ9
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 GLY 856 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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852C GLU* 5.0 5.6 - - - -
853C SER* 2.9 23.3 + - - +
855C ASP* 1.3 82.2 - - - +
857C PRO* 1.3 75.5 - - - +
858C ILE 3.2 3.4 + - - -
859C VAL 3.8 1.5 + - - -
860C LYS* 3.3 21.2 + - - +
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Residues in contact with PRO 857 (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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852C GLU* 5.4 3.6 - - - +
855C ASP 4.6 0.7 - - - +
856C GLY* 1.3 84.4 - - - +
858C ILE* 1.3 67.1 + - + +
860C LYS* 3.8 6.8 - - + +
861C GLN* 3.4 24.3 + - - +
950C LEU* 5.5 8.5 - - + +
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Residues in contact with ILE 858 (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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848C ARG* 3.7 19.5 - - + +
849C ILE* 3.8 28.0 - - + -
852C GLU* 3.9 24.5 - - + +
856C GLY 3.2 1.0 - - - -
857C PRO* 1.3 77.1 - - + +
859C VAL* 1.3 68.0 + - - +
860C LYS 3.0 1.3 - - - -
861C GLN* 3.0 16.9 + - - +
862C LEU* 3.1 11.6 + - + +
947C ALA* 5.6 1.8 - - - +
948C MET* 4.4 15.7 - - + -
950C LEU* 4.7 17.0 - - + -
951C CYS* 3.4 27.6 - - - -
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Residues in contact with VAL 859 (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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849C ILE* 4.4 8.3 - - + -
852C GLU* 3.9 22.0 - - + +
853C SER 3.6 24.9 - - - +
854C LEU* 4.1 24.5 - - + +
856C GLY 3.8 1.8 + - - -
858C ILE* 1.3 75.4 - - - +
860C LYS* 1.3 62.2 + - - +
862C LEU* 3.3 7.9 + - - +
863C GLU* 3.1 36.7 + - + +
898C ARG* 4.0 33.7 - - + +
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Residues in contact with LYS 860 (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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854C LEU 4.7 5.7 + - - +
855C ASP 5.1 2.7 - - - +
856C GLY 3.3 19.7 + - - +
857C PRO* 3.8 8.3 - - + +
858C ILE 3.0 0.8 - - - -
859C VAL* 1.3 76.9 - - - +
861C GLN* 1.3 63.5 + - + +
863C GLU* 3.2 7.1 + - - +
864C ARG* 3.1 20.1 + - - +
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Residues in contact with GLN 861 (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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857C PRO 3.4 10.9 + - - +
858C ILE* 3.0 10.3 + - - +
860C LYS* 1.3 78.2 - - + +
862C LEU* 1.3 63.6 + - - +
864C ARG* 3.2 21.4 + - - +
943C HIS* 4.0 6.4 + - - -
946C ARG 4.9 0.5 - - - +
947C ALA* 3.3 26.8 - - + +
950C LEU* 3.1 34.3 - - + +
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Residues in contact with LEU 862 (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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845C VAL* 5.0 1.8 - - + -
849C ILE* 3.7 34.5 - - + -
858C ILE* 3.1 11.3 + - + +
859C VAL* 3.7 11.4 - - - +
860C LYS 3.3 0.4 - - - -
861C GLN* 1.3 78.3 - - - +
863C GLU* 1.3 57.6 + - + +
897C VAL* 3.8 19.3 - - + +
898C ARG* 4.0 21.8 - - + +
901C LEU* 4.1 8.5 - - + -
943C HIS* 2.6 24.5 + - + -
944C THR* 4.0 40.4 - - + +
947C ALA* 3.9 15.2 - - + +
948C MET* 4.9 8.5 - - - -
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Residues in contact with GLU 863 (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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859C VAL* 3.1 28.5 + - + +
860C LYS* 3.6 6.1 - - - +
861C GLN 3.2 0.2 - - - -
862C LEU* 1.3 77.4 - - + +
864C ARG* 1.3 67.0 + - - +
866C GLY* 2.9 17.7 + - - +
867C ARG 4.7 0.3 + - - -
895C GLY 3.9 4.5 - - - +
896C SER* 2.7 34.2 + - - -
897C VAL* 2.9 26.8 + - - +
898C ARG* 3.0 13.9 + - - +
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Residues in contact with ARG 864 (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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860C LYS 3.1 10.5 + - - +
861C GLN* 3.2 20.8 + - + +
862C LEU 3.4 0.4 - - - -
863C GLU* 1.3 78.1 - - - +
865C GLY* 1.3 59.6 + - - +
866C GLY 3.5 0.7 + - - -
943C HIS* 5.0 1.6 - - + -
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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