Contacts of the strand formed by residues 887 - 893 (chain A) in PDB entry 6Q0W
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 887 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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882A ALA 4.0 0.2 - - - +
883A SER* 3.3 3.5 - - - -
884A ILE* 2.8 43.3 + - + +
885A ASN* 3.5 1.4 + - + -
886A SER* 1.3 89.5 - - - +
888A VAL* 1.3 63.9 + - - +
889A ARG* 3.9 17.4 + - - +
904A ASN* 3.7 17.0 + - - -
905A HIS 3.3 9.6 - - - -
906A TYR* 3.7 27.6 - - + -
911A ALA* 4.9 0.4 - - - -
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Residues in contact with VAL 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A LEU* 4.7 7.2 - - + -
882A ALA 3.5 7.0 - - - +
883A SER* 4.3 1.6 - - - +
887A THR* 1.3 73.8 + - - +
889A ARG* 1.3 57.9 + - - +
904A ASN* 3.4 4.0 - - - -
905A HIS* 2.8 40.2 + - + +
908A ASN* 3.5 20.9 - - - +
911A ALA* 3.9 16.8 - - + -
914A LEU* 4.5 10.5 - - + -
921A ILE* 5.5 0.7 - - + -
923A VAL* 4.1 18.8 - - + -
933A LEU* 3.5 28.3 - - + -
942A PHE* 3.5 13.9 - - + -
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Residues in contact with ARG 889 (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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865A GLU 5.7 0.4 + - - -
866A VAL* 4.2 10.9 - - - +
867A LYS* 4.2 27.6 - - - +
880A LEU 3.8 1.4 - - - +
881A LEU* 3.5 3.8 - - - +
882A ALA* 2.8 40.3 + - - +
884A ILE* 3.7 25.9 - - + +
887A THR* 3.9 15.9 + - - +
888A VAL* 1.3 75.1 - - - +
890A LEU* 1.3 61.8 + - - +
891A TYR* 3.1 40.7 + - + -
901A THR* 3.7 24.9 + - + +
903A CYS 3.4 9.4 - - - +
904A ASN* 2.7 28.7 + - - +
906A TYR* 5.3 3.6 + - - -
942A PHE* 4.2 4.5 - - - -
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Residues in contact with LEU 890 (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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876A PHE* 3.7 29.8 - - + -
879A LYS* 3.8 29.4 - - + -
880A LEU 3.8 14.6 - - - +
881A LEU* 4.0 10.8 - - + -
889A ARG* 1.3 74.0 - - - +
891A TYR* 1.3 56.0 + - - +
901A THR* 3.7 3.1 - - - -
902A GLU* 2.8 55.4 + - - +
903A CYS* 3.0 18.3 + - - +
935A TYR* 3.7 27.6 - - + -
942A PHE* 3.8 14.1 - - + -
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Residues in contact with TYR 891 (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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848A ILE* 3.5 26.0 - - + -
864A LYS* 3.8 21.7 - - + +
865A GLU 5.1 0.5 + - - -
866A VAL* 3.4 18.4 - - - +
879A LYS* 3.3 8.2 - - - +
880A LEU* 2.9 47.2 + - + +
882A ALA* 4.2 11.2 - - + -
884A ILE* 4.1 1.4 - - + +
889A ARG* 3.1 41.8 + - + -
890A LEU* 1.3 76.0 - - - +
892A GLU* 1.3 61.9 + - - +
899A LEU* 3.9 32.3 - - + +
900A ARG 3.4 4.3 - - - -
901A THR* 3.3 33.6 + - - -
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Residues in contact with GLU 892 (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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879A LYS* 3.8 26.7 + - + +
891A TYR* 1.3 75.7 - - - +
893A TRP* 1.3 59.5 + - - +
894A THR 3.9 0.4 + - - -
898A GLU 3.4 1.4 - - - +
899A LEU* 3.4 7.8 - - - -
900A ARG* 2.8 75.1 + - - +
902A GLU* 4.1 39.4 - - + +
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Residues in contact with TRP 893 (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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821A LEU* 3.5 54.7 - - + -
822A GLY* 4.4 12.8 - - - +
823A LYS 5.3 0.9 + - - -
824A ASP* 2.9 26.6 + - + +
828A TYR* 3.9 22.4 - + - -
850A VAL* 4.0 22.7 - - + -
861A VAL* 4.0 4.7 - - + -
862A ALA* 3.7 21.5 - - + -
878A GLY 5.2 3.4 + - - -
879A LYS* 5.6 0.8 - - - +
891A TYR 4.3 0.2 + - - -
892A GLU* 1.3 74.1 - - - +
894A THR* 1.3 68.8 + - - +
897A LYS* 3.6 48.9 - - + +
898A GLU 3.5 21.8 - - - -
899A LEU* 3.7 15.0 - - + -
900A ARG* 5.1 2.1 + - - -
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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