Contacts of the strand formed by residues 887 - 893 (chain K) in PDB entry 6R8Y
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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883K SER* 3.4 4.3 - - - -
884K ILE* 2.6 43.1 + - - +
885K ASN* 5.3 2.0 - - + +
886K SER* 1.3 88.0 - - - +
888K VAL* 1.3 65.9 + - - +
889K ARG* 3.0 39.3 + - - +
905K HIS 3.1 8.5 - - - -
906K TYR* 3.4 32.5 - - + -
908K ASN* 4.8 0.2 - - - -
911K ALA* 4.6 1.5 - - - +
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Residues in contact with VAL 888 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881K LEU* 3.6 33.0 - - + -
882K ALA 3.7 2.9 - - - +
883K SER* 3.7 14.6 - - - +
887K THR* 1.3 75.4 - - - +
889K ARG* 1.3 63.1 + - - +
904K ASN* 3.2 3.3 - - - -
905K HIS* 2.9 39.0 + - + +
908K ASN* 4.4 9.2 - - - +
911K ALA* 4.2 5.2 - - + -
914K LEU* 4.2 12.1 - - + -
921K ILE* 5.1 0.4 - - + -
923K VAL* 4.1 27.4 - - + -
933K LEU* 4.8 11.9 - - + -
942K PHE* 4.0 7.1 - - + -
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Residues in contact with ARG 889 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866K VAL* 3.6 24.0 - - - +
867K LYS* 4.8 10.9 + - - +
880K LEU 3.7 1.4 - - - +
881K LEU* 3.4 4.8 - - - +
882K ALA* 2.8 39.3 + - - +
884K ILE* 3.4 37.5 - - + +
887K THR* 3.0 33.4 + - - +
888K VAL* 1.3 75.1 - - - +
890K LEU* 1.3 59.4 + - - +
891K TYR* 3.8 20.0 + - + -
901K THR* 5.3 1.6 - - + -
903K CYS 3.3 4.5 - - - +
904K ASN* 3.0 21.3 - - - +
424L ARG* 2.9 47.8 - - - +
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Residues in contact with LEU 890 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876K PHE* 3.6 35.7 - - + -
879K LYS* 3.4 38.4 - - + +
880K LEU 3.3 20.9 - - - +
881K LEU* 3.8 14.6 - - + +
888K VAL 4.4 0.2 + - - -
889K ARG* 1.3 73.3 - - - +
891K TYR* 1.3 55.7 + - - +
901K THR* 3.5 2.9 - - - -
902K GLU* 2.5 47.4 + - + +
903K CYS* 2.8 34.9 + - - +
935K TYR* 4.6 5.2 - - + -
942K PHE* 4.2 4.9 - - + -
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Residues in contact with TYR 891 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848K ILE* 3.5 28.9 - - + -
864K LYS* 3.8 17.9 - - + +
866K VAL* 3.2 30.1 - - - +
879K LYS* 3.3 8.3 - - - +
880K LEU* 2.8 44.9 + - + +
882K ALA* 4.6 3.6 - - + -
884K ILE* 4.1 4.0 - - + +
889K ARG* 3.8 31.7 + - + -
890K LEU* 1.3 74.2 - - - +
892K GLU* 1.3 60.7 + - - +
899K LEU* 3.9 25.6 - - + -
900K ARG 3.1 30.3 - - - +
901K THR* 3.4 26.3 - - + +
902K GLU* 4.3 2.5 - - - -
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Residues in contact with GLU 892 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879K LYS* 4.8 13.5 - - + -
891K TYR* 1.3 74.8 - - - +
893K TRP* 1.3 60.0 + - - +
894K THR* 3.7 12.4 + - + +
898K GLU 3.4 5.7 - - - +
899K LEU* 3.7 5.3 - - - +
900K ARG* 2.6 75.8 + - + +
901K THR 3.7 5.7 - - - +
902K GLU* 2.8 42.7 + - + +
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Residues in contact with TRP 893 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821K LEU* 3.5 55.0 - - + -
822K GLY* 4.3 10.7 - - - +
823K LYS 5.4 1.3 + - - -
824K ASP* 3.3 28.6 + - + +
828K TYR* 3.7 26.1 - + - -
850K VAL* 4.6 9.2 - - + -
861K VAL* 4.0 6.5 - - + -
862K ALA* 3.9 18.2 - - + -
878K GLY 4.8 3.6 + - - +
879K LYS* 5.5 0.8 - - - +
891K TYR 4.3 0.2 + - - -
892K GLU* 1.3 72.6 - - - +
894K THR* 1.3 70.3 + - - +
897K LYS* 3.3 52.0 - - + +
898K GLU* 3.5 24.2 - - - -
899K LEU* 4.2 15.7 - - + -
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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