Contacts of the strand formed by residues 868 - 872 (chain O) in PDB entry 5Z3U
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 VAL 868 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806O LEU* 4.4 22.4 - - + -
816O ARG 4.5 5.2 - - - +
819O TYR* 3.1 21.3 - - + +
820O LEU* 4.5 1.3 - - - -
821O VAL* 4.8 10.8 - - + +
835O PHE* 6.0 2.0 - - + -
842O LEU* 5.7 7.2 - - + -
843O ARG 3.5 2.7 + - - +
844O THR* 3.2 45.6 - - + -
845O ILE* 3.4 8.8 + - - +
866O PHE* 3.3 10.5 - - - +
867O ASP* 1.3 90.5 - - + +
869O VAL* 1.3 73.5 + - - +
870O LEU* 5.4 0.4 - - + -
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Residues in contact with VAL 869 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819O TYR 3.1 4.6 + - - -
820O LEU* 3.0 25.6 - - + +
821O VAL* 3.0 26.2 + - - +
845O ILE* 4.1 9.4 - - + -
847O PHE* 4.2 22.9 - - + -
866O PHE* 3.5 22.7 - - + -
868O VAL* 1.3 78.2 - - - +
870O LEU* 1.3 64.8 + - - +
871O THR* 4.7 6.3 - - + -
883O LEU* 5.1 10.8 - - + -
888O TRP* 3.4 26.2 - - + -
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Residues in contact with LEU 870 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821O VAL* 3.5 29.8 - - + +
823O VAL* 3.8 16.6 - - + -
828O LEU* 3.8 29.4 - - + +
831O TRP* 4.5 17.7 - - + -
832O SER* 5.1 4.9 - - - +
835O PHE* 4.7 10.5 - - + -
844O THR* 4.5 16.4 - - + +
845O ILE 2.8 30.8 + - - +
846O SER* 3.4 11.1 - - - -
847O PHE* 3.0 17.5 - - - -
868O VAL* 4.0 0.8 + - + -
869O VAL* 1.3 72.8 - - - +
871O THR* 1.3 76.1 + - - +
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Residues in contact with THR 871 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820O LEU* 4.8 9.6 - - + -
821O VAL 3.3 15.4 + - - +
822O ILE* 3.7 11.9 - - + -
823O VAL* 3.5 15.9 + - - +
828O LEU* 5.0 0.4 - - - -
847O PHE* 3.9 20.0 - - - +
869O VAL* 4.7 6.3 - - + -
870O LEU* 1.3 83.5 - - - +
872O THR* 1.3 84.5 + - - +
875O TYR* 3.9 13.3 - - - +
876O ILE* 3.4 27.5 + - + +
879O GLU* 4.6 1.9 + - - -
883O LEU* 5.2 3.9 - - + +
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Residues in contact with THR 872 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822O ILE* 3.6 6.7 - - - -
823O VAL 3.7 12.8 - - - +
825O LEU* 3.4 36.1 - - + +
828O LEU* 4.1 19.5 - - + -
847O PHE 4.5 10.8 - - - +
848O LYS* 5.9 0.2 - - + -
871O THR* 1.3 96.3 + - - +
873O PHE* 1.3 70.2 + - - +
874O GLU* 3.4 4.9 + - - -
875O TYR* 3.0 30.6 + - - +
876O ILE* 3.3 10.2 - - - +
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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