Contacts of the strand formed by residues 857 - 869 (chain B) in PDB entry 2CKJ
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 857 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849B VAL* 4.2 18.6 - - + -
850B GLY 3.7 9.4 - - - +
851B PHE* 3.9 12.1 - - + -
855B GLY 3.3 3.1 + - - +
856B THR* 1.4 79.8 - - - +
858B VAL* 1.3 67.9 + - - +
859B ALA 4.0 7.6 - - - +
890B TYR* 5.9 2.2 - - + -
891B LYS 4.9 8.6 - - - +
892B ILE* 4.3 24.0 - - + -
893B PRO* 4.2 11.5 - - - +
927B TRP* 4.8 7.4 - - + -
928B MET* 4.6 18.4 - - + -
931B VAL* 5.6 4.0 - - + -
946B ASN* 3.2 24.0 + - + +
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Residues in contact with VAL 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B GLY* 4.0 23.3 - - - -
726B GLU* 5.1 6.3 - - + +
727B ALA* 4.4 15.9 - - + -
850B GLY 3.0 10.8 + - - +
851B PHE* 4.8 2.2 - - - -
852B MET* 4.5 24.9 - - + -
856B THR* 4.8 8.5 - - + +
857B VAL* 1.3 82.0 - - - +
859B ALA* 1.3 58.2 + - + +
892B ILE* 5.6 0.7 - - - -
893B PRO* 3.5 15.7 - - + +
894B ASN* 2.5 36.4 + - - +
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Residues in contact with ALA 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720B LEU* 4.6 2.5 - - + +
723B GLY* 3.9 24.9 - - - -
724B PHE* 3.7 25.7 - - + +
849B VAL* 3.3 4.0 - - - +
850B GLY 2.7 35.4 + - - +
857B VAL* 4.0 2.8 - - - +
858B VAL* 1.3 81.7 - - + +
860B LEU* 1.3 62.2 + - - +
892B ILE* 5.5 0.9 - - - -
894B ASN* 3.3 17.3 - - + +
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Residues in contact with LEU 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720B LEU* 4.9 2.2 - - - +
724B PHE* 4.2 3.5 - - - -
847B TYR* 4.8 0.9 - - + -
848B LYS 3.4 12.6 - - - +
849B VAL* 4.4 7.6 - - + -
857B VAL* 5.3 0.2 - - + -
859B ALA* 1.3 78.0 - - - +
861B GLU* 1.3 79.2 + - - +
862B VAL* 3.5 21.8 - - + -
886B MET* 4.8 10.8 - - + +
892B ILE* 3.4 22.9 - - + -
894B ASN 3.2 7.3 + - - -
895B ILE* 3.4 17.8 - - + -
896B ARG 3.1 23.7 + - - +
927B TRP* 3.1 51.4 - - + +
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Residues in contact with GLU 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720B LEU* 5.1 9.3 - - + +
724B PHE* 4.5 11.3 - - + -
846B ARG 4.3 0.2 - - - +
847B TYR* 3.3 3.8 - - - -
848B LYS* 2.7 68.6 + - + +
860B LEU* 1.3 77.7 - - - +
862B VAL* 1.4 67.0 + - - +
863B ASP* 4.1 16.6 - - - +
896B ARG* 3.5 34.3 + - + +
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Residues in contact with VAL 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B ALA* 4.4 4.3 - - + -
846B ARG 3.6 9.6 - - - +
847B TYR* 4.2 8.3 - - + -
860B LEU* 3.5 22.0 - - + -
861B GLU* 1.4 78.3 - - - +
863B ASP* 1.3 68.1 + - - +
864B HIS* 3.8 25.4 - - + +
886B MET* 3.9 22.7 - - + -
896B ARG 3.1 8.3 + - - +
897B GLY* 3.6 3.3 - - - -
898B THR 3.4 23.0 + - - +
923B ILE* 4.2 16.4 - - + -
924B ALA* 6.2 0.2 - - + -
927B TRP* 4.3 8.3 - - + +
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Residues in contact with ASP 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712B GLU* 5.2 0.3 - - - +
845B ALA* 3.2 24.5 - - - -
846B ARG* 3.0 24.9 + - + +
861B GLU* 4.1 17.7 - - - +
862B VAL* 1.3 74.6 - - - +
864B HIS* 1.3 61.9 + - - +
865B PHE* 3.3 23.4 - - + -
896B ARG* 5.4 2.4 + - - +
898B THR* 2.6 35.3 + - - +
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Residues in contact with HIS 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B PHE* 4.3 13.5 - + + -
844B LEU 4.1 2.0 - - - -
845B ALA* 4.2 10.8 - - - +
862B VAL* 3.8 30.9 + - + +
863B ASP* 1.3 71.2 - - - +
865B PHE* 1.3 62.0 + - - +
879B MET* 3.1 24.5 - - + -
882B ALA* 5.3 8.5 + - + +
883B LEU* 3.5 22.0 - - + +
886B MET* 4.5 16.9 - - + +
898B THR* 2.9 27.8 + - - +
899B GLY* 3.1 2.4 - - - -
900B ARG 2.8 29.8 + - - -
919B GLN 5.8 0.7 - - - -
920B GLY 4.9 6.5 - - - -
923B ILE* 4.1 20.8 - - + +
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Residues in contact with PHE 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699B ILE* 4.2 12.4 - - + +
703B ILE* 4.6 28.5 - - + -
708B PHE* 5.4 2.0 - + - -
843B PHE* 3.5 2.1 - - - -
844B LEU* 2.7 55.0 + - + +
846B ARG* 4.4 30.7 - - + -
863B ASP* 3.3 32.1 - - + -
864B HIS* 1.3 76.2 - - - +
866B SER* 1.3 60.6 + - - +
900B ARG* 3.9 25.4 - - + +
902B CYS* 3.8 25.1 - - - -
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Residues in contact with SER 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B ILE* 4.5 0.4 - - - -
841B HIS* 3.9 17.9 - - - -
842B PRO 3.5 9.9 + - - -
843B PHE* 3.5 24.4 - - - -
865B PHE* 1.3 63.8 - - - +
867B ASN* 1.3 59.3 + - - +
868B VAL* 3.5 0.7 + - - +
875B SER 5.1 1.0 + - - -
879B MET* 4.0 12.4 - - - +
900B ARG 3.0 21.1 - - - -
901B LEU* 3.5 15.7 - - - +
902B CYS* 3.3 26.2 + - - -
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Residues in contact with ASN 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697B ILE 3.9 10.7 + - - -
699B ILE* 3.4 32.0 - - + +
841B HIS* 3.9 6.8 - - - -
842B PRO* 3.3 27.4 + - + +
866B SER* 1.3 68.6 - - - +
868B VAL* 1.3 68.3 + - - +
869B GLY* 3.2 3.8 + - - -
902B CYS* 3.9 7.0 - - - +
904B THR* 3.1 23.0 + - - +
906B LEU* 3.6 26.5 - - - +
909B ASN* 3.4 18.9 + - - -
1332B ARG 5.1 5.5 + - - -
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Residues in contact with VAL 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B TYR* 3.8 15.3 - - + -
841B HIS* 4.2 5.8 - - + +
866B SER 3.5 3.8 + - - +
867B ASN* 1.3 77.9 + - - +
869B GLY* 1.3 59.0 + - - +
871B THR 3.3 23.6 - - - +
872B GLN* 4.2 1.8 - - - +
875B SER* 3.4 33.8 + - - +
901B LEU* 3.8 29.2 - - + -
902B CYS 3.0 18.1 + - - +
908B SER* 3.8 1.2 + - - -
909B ASN* 2.9 37.6 + - - +
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Residues in contact with GLY 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709B TYR* 3.6 16.3 + - - -
867B ASN* 3.2 7.4 + - - -
868B VAL* 1.3 76.3 - - - +
870B ASN* 1.3 59.9 + - - -
871B THR 3.5 5.6 + - - -
902B CYS 3.9 1.0 + - - -
903B LYS* 4.0 0.7 - - - +
904B THR* 3.1 34.6 + - - +
906B LEU* 3.3 13.0 - - - -
907B PRO 4.1 6.1 - - - -
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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