Contacts of the helix formed by residues 860 - 866 (chain C) in PDB entry 4YOC
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 THR 860 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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815C ASN 3.7 9.8 + - - -
816C ARG* 3.5 20.9 - - - +
817C MET 3.3 10.5 - - - +
818C ASN* 4.6 4.5 - - + +
857C TYR* 4.9 0.4 - - - -
858C GLU 5.2 1.8 - - - +
859C GLY* 1.3 77.5 - - - +
861C LEU* 1.3 65.5 + - - +
862C ARG* 3.8 5.9 + - - +
863C ASP* 3.2 28.6 + - - +
864C LEU* 3.2 25.8 + - - +
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Residues in contact with LEU 861 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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794C VAL* 3.9 9.0 - - + -
796C VAL* 3.7 29.2 - - + -
798C PHE* 5.5 0.4 - - + -
813C LEU* 3.8 22.2 - - + -
814C SER 3.5 27.1 - - - +
815C ASN 3.7 1.1 + - - +
817C MET* 3.0 11.3 + - + +
822C VAL* 4.5 20.8 - - + +
860C THR* 1.3 72.5 - - - +
862C ARG* 1.3 60.3 + - - +
864C LEU* 3.0 19.5 + - + +
865C LEU* 2.9 57.2 + - + +
876C LEU* 5.0 5.6 - - + -
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Residues in contact with ARG 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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1065A GLY 5.9 0.4 + - - -
1066A GLU* 2.5 42.1 + - - -
1072A VAL* 5.7 4.4 - - - +
1086A LEU* 4.1 21.4 - - - +
791C TYR* 4.4 10.3 + - - -
792C HIS* 4.5 7.4 - - - -
815C ASN* 3.3 53.4 + - - +
860C THR* 3.2 5.6 - - - +
861C LEU* 1.3 79.3 - - - +
863C ASP* 1.3 58.4 - - - +
865C LEU* 3.1 4.5 + - - +
866C GLN* 2.8 39.1 + - + +
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Residues in contact with ASP 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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1036A HIS* 4.2 10.7 + - + -
841C LYS* 3.9 11.1 + - - -
857C TYR* 3.6 12.3 - - - +
859C GLY* 3.7 8.0 - - - -
860C THR* 3.2 32.8 + - - +
861C LEU 3.2 0.2 - - - -
862C ARG* 1.3 79.5 - - - +
864C LEU* 1.3 62.1 + - - +
866C GLN* 3.4 33.0 + - - +
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Residues in contact with LEU 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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1391A GLU* 5.3 0.9 - - - +
819C TYR* 5.9 2.7 - - + -
822C VAL* 5.9 7.2 - - + -
841C LYS* 3.9 26.6 - - + +
842C SER 5.1 0.3 + - - -
853C LEU* 3.9 36.6 - - + -
857C TYR* 3.2 31.0 - - + +
860C THR 3.5 13.9 - - - +
861C LEU* 3.0 20.3 + - + +
863C ASP* 1.3 77.8 - - - +
865C LEU* 1.3 65.0 + - + +
866C GLN 3.6 0.4 - - - -
867C PHE* 3.4 21.1 - - - -
868C PHE* 4.4 2.4 - - - -
876C LEU* 4.1 25.6 - - + +
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Residues in contact with LEU 865 (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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794C VAL* 4.0 20.4 - - + -
796C VAL* 3.6 30.3 - - + -
815C ASN* 5.3 1.8 - - - +
861C LEU* 2.9 31.8 + - + +
862C ARG* 3.1 4.0 + - - +
864C LEU* 1.3 85.0 - - - +
866C GLN* 1.3 61.7 + - - +
867C PHE 3.3 2.7 - - - -
868C PHE* 3.2 43.4 + - + +
874C LYS* 4.1 22.3 - - + +
875C LYS 4.0 12.3 - - - +
876C LEU* 4.3 13.0 - - + -
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Residues in contact with GLN 866 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1398A ARG* 6.2 2.2 - - - +
1403A ALA* 5.6 7.9 - - - +
841C LYS* 5.3 6.6 - - - +
862C ARG* 2.8 19.8 + - + +
863C ASP* 3.4 28.8 + - - +
864C LEU 3.6 1.2 - - - -
865C LEU* 1.3 77.2 - - - +
867C PHE* 1.3 66.4 + - + +
868C PHE 3.3 8.4 + - - +
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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