Contacts of the strand formed by residues 863 - 870 (chain A) 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 TYR 863 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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774A LEU* 4.9 14.3 - - + +
776A LEU* 3.8 29.5 - - + +
811A PRO 4.1 17.3 - - - -
812A LEU* 3.4 24.0 - - + +
814A LEU* 3.9 21.1 - - + -
832A VAL* 4.7 15.5 - - + -
833A LYS 3.3 16.7 + - - +
834A VAL* 3.3 16.7 - - + -
835A ILE* 2.9 25.2 + - - +
862A THR* 1.3 81.7 - - + +
864A PHE* 1.3 60.1 + - - +
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Residues in contact with PHE 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810A ASP* 3.7 21.1 - - + -
812A LEU* 2.9 34.6 + - + +
813A GLU* 3.5 37.9 - - + -
814A LEU* 2.8 25.8 + - - +
834A VAL* 4.5 2.5 - - - -
835A ILE* 3.2 28.5 - - + +
837A LYS* 4.2 41.5 - - + -
862A THR 3.7 11.2 - - - +
863A TYR* 1.3 75.2 - - - +
865A TYR* 1.3 68.9 + - - +
866A GLN* 4.8 3.4 - - - -
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Residues in contact with TYR 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778A ARG* 4.6 23.7 + - - -
797A PHE* 4.6 4.0 - + + -
813A GLU* 5.1 0.7 - - - -
814A LEU* 3.2 28.5 - - + +
815A PHE* 4.7 0.7 - - - +
816A LEU* 3.5 47.4 - - + +
834A VAL* 3.8 16.8 - - + -
835A ILE 2.9 26.1 + - - -
836A TYR* 3.3 50.3 - + + +
837A LYS 2.9 23.9 + - - -
864A PHE* 1.3 77.8 - - - +
866A GLN* 1.3 67.1 + - - +
867A LEU 4.6 0.7 - - - +
879A PRO* 4.8 1.8 - - + -
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Residues in contact with GLN 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A GLU* 3.0 27.4 + - - +
814A LEU 4.3 1.8 + - - -
836A TYR* 4.0 10.5 + - - -
837A LYS* 3.4 37.9 - - + +
839A PRO* 5.8 6.1 - - + +
864A PHE* 4.8 5.5 - - + -
865A TYR* 1.3 76.2 - - - +
867A LEU* 1.3 81.2 + - + +
879A PRO* 3.4 23.0 - - - +
1288A VAL* 3.1 28.4 + - - +
1289A ARG* 4.7 5.9 + - - +
1291A GLY* 3.8 17.5 - - - -
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Residues in contact with LEU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814A LEU 4.4 0.2 - - - +
815A PHE* 3.3 26.4 - - + -
816A LEU* 3.2 24.8 + - - +
865A TYR* 4.6 1.0 - - - -
866A GLN* 1.3 100.9 - - + +
868A TRP* 1.3 62.5 + - - +
876A PHE* 4.0 18.2 - - + -
877A GLU* 3.3 24.9 - - - +
878A SER* 4.1 5.6 - - - +
879A PRO* 4.6 0.9 - - + -
1288A VAL* 4.0 27.6 - - + +
1291A GLY 4.6 9.0 - - - +
1292A TYR 3.3 26.7 - - - +
1293A GLN* 4.6 5.8 - - + -
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Residues in contact with TRP 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A LEU* 3.3 38.7 - - + +
817A VAL* 3.8 9.0 - - - +
818A ASP* 3.3 39.4 + - - -
867A LEU* 1.3 73.8 - - - +
869A TYR* 1.3 65.1 + - - +
870A ASP* 3.6 42.0 - - + -
875A ARG 3.5 0.5 - - - +
876A PHE* 3.4 4.5 - - - -
877A GLU* 2.9 68.1 + - + +
878A SER 4.3 2.5 - - - +
879A PRO* 4.4 4.1 - - + -
880A PRO* 3.9 32.5 - - + -
898A ARG* 3.5 21.9 - - - +
902A MET* 5.6 3.6 - - + -
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Residues in contact with TYR 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798A CYS* 4.5 2.7 - - - -
802A ASP 4.8 1.6 + - - -
803A THR* 3.6 29.1 - - + -
804A VAL* 3.2 29.4 + - + +
815A PHE* 3.8 21.3 - - + -
816A LEU 2.7 11.8 + - - +
817A VAL* 3.8 23.1 - - + +
868A TRP* 1.3 82.6 - - - +
870A ASP* 1.3 75.0 + - - +
871A GLN* 3.6 35.5 + - + +
874A ALA* 4.2 2.7 - - - -
875A ARG 3.4 2.7 - - - -
876A PHE* 3.5 42.8 - + + -
1348A LYS* 5.9 0.2 - - - +
1350A PHE* 3.5 15.8 - - - -
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Residues in contact with ASP 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A TRP* 3.6 31.8 - - + -
869A TYR* 1.3 74.8 - - - +
871A GLN* 1.3 61.5 + - - +
872A ASP* 3.2 19.4 + - - +
873A TYR* 3.4 28.1 + - - -
874A ALA* 3.0 9.7 + - - -
875A ARG* 2.9 47.9 + - + +
877A GLU* 5.2 0.2 - - - +
902A MET* 6.0 1.7 - - - +
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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