Contacts of the strand formed by residues 857 - 869 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A VAL* 4.2 20.0 - - + -
850A GLY 3.7 13.7 - - - +
851A PHE* 4.1 8.5 - - + -
855A GLY 3.2 4.4 + - - +
856A THR* 1.3 77.0 - - - +
858A VAL* 1.4 68.1 + - - +
859A ALA 4.1 6.7 - - - +
890A TYR* 6.1 1.8 - - + -
891A LYS 4.7 10.3 - - - +
892A ILE* 4.4 22.0 - - + -
893A PRO* 4.1 11.0 - - - +
927A TRP* 5.0 6.3 - - + -
928A MET* 4.7 17.5 - - + -
931A VAL* 5.3 5.8 - - + -
946A ASN* 3.0 24.8 + - + +
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Residues in contact with VAL 858 (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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723A GLY* 3.9 22.2 - - - -
726A GLU* 5.3 5.4 - - + +
727A ALA* 4.2 18.2 - - + -
850A GLY 3.1 10.3 + - - +
851A PHE* 5.0 2.0 - - - -
852A MET* 4.6 20.9 - - + -
856A THR* 4.7 8.3 - - + +
857A VAL* 1.4 82.7 - - - +
859A ALA* 1.3 56.3 + - + +
892A ILE 5.6 0.2 - - - -
893A PRO* 4.2 12.1 - - + -
894A ASN* 2.4 35.9 + - - +
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Residues in contact with ALA 859 (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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720A LEU* 4.6 2.5 - - + +
723A GLY* 3.9 23.1 - - - -
724A PHE* 4.0 24.2 - - + +
849A VAL* 3.5 2.8 - - - +
850A GLY 2.7 33.9 + - - +
857A VAL* 4.1 2.2 - - - +
858A VAL* 1.3 82.7 - - + +
860A LEU* 1.4 62.0 + - - +
892A ILE* 5.5 2.2 - - - -
894A ASN* 3.2 17.9 - - + +
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Residues in contact with LEU 860 (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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720A LEU* 5.0 1.3 - - - +
724A PHE* 4.3 3.7 - - - -
847A TYR* 4.8 0.2 - - + -
848A LYS 3.4 14.1 - - - +
849A VAL* 4.2 7.9 - - + -
857A VAL* 5.3 0.2 - - + -
859A ALA* 1.4 76.7 - - - +
861A GLU* 1.3 74.7 + - - +
862A VAL* 3.2 23.6 - - + -
886A MET* 4.7 10.1 - - + +
892A ILE* 3.6 23.8 - - + +
894A ASN 3.1 9.4 + - - +
895A ILE* 3.3 15.4 - - + +
896A ARG 3.1 21.8 + - - +
924A ALA* 4.9 3.4 - - + -
927A TRP* 3.1 51.1 - - + +
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Residues in contact with GLU 861 (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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720A LEU* 5.1 6.7 - - + +
724A PHE* 4.7 13.7 - - + -
846A ARG 4.2 0.2 - - - +
847A TYR* 3.5 3.5 - - - -
848A LYS* 2.9 57.3 + - + +
860A LEU* 1.3 75.1 - - - +
862A VAL* 1.3 66.4 + - - +
863A ASP* 4.5 15.0 - - - +
896A ARG* 3.3 36.0 + - + +
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Residues in contact with VAL 862 (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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845A ALA* 4.3 4.3 - - + -
846A ARG 3.4 13.7 - - - +
847A TYR* 4.0 11.7 - - + -
860A LEU* 3.2 34.5 - - + -
861A GLU* 1.3 73.3 - - - +
863A ASP* 1.3 68.0 + - - +
864A HIS* 3.8 30.5 - - + +
886A MET* 4.1 13.7 - - + -
896A ARG 2.8 12.1 + - - -
897A GLY* 3.4 5.0 - - - -
898A THR 3.4 20.6 + - - -
923A ILE* 4.3 13.9 - - + -
924A ALA* 5.8 1.1 - - + +
927A TRP* 4.3 6.5 - - + +
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Residues in contact with ASP 863 (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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712A GLU* 5.3 0.3 - - - +
845A ALA* 3.1 26.0 - - - -
846A ARG* 3.0 24.3 + - + +
861A GLU* 4.5 15.2 - - - +
862A VAL* 1.3 73.7 - - - +
864A HIS* 1.3 63.7 + - - +
865A PHE* 3.7 20.6 - - + -
896A ARG* 5.3 3.1 + - - +
898A THR* 2.6 35.5 + - - +
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Residues in contact with HIS 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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843A PHE* 4.2 15.1 - + + -
844A LEU 3.9 2.7 - - - -
845A ALA* 4.0 10.3 - - - +
862A VAL* 3.8 32.8 + - + +
863A ASP* 1.3 72.0 - - - +
865A PHE* 1.3 62.1 + - - +
879A MET* 3.3 20.0 - - + -
882A ALA* 5.7 7.5 + - + +
883A LEU* 3.6 22.2 - - + +
886A MET* 4.8 15.2 - - + +
898A THR* 3.0 25.7 + - - +
899A GLY* 2.9 4.0 - - - -
900A ARG 2.8 30.5 + - - -
919A GLN 6.0 0.7 - - - -
920A GLY 4.8 5.6 - - - -
923A ILE* 4.0 23.3 - - + +
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Residues in contact with PHE 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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699A ILE* 4.2 13.2 - - + +
703A ILE* 4.7 29.8 - - + -
708A PHE* 5.5 1.3 - + - -
843A PHE* 3.3 1.9 - - - -
844A LEU* 2.6 58.9 + - + +
845A ALA* 5.1 0.4 - - - -
846A ARG* 4.3 27.6 - - + -
863A ASP* 3.7 23.3 - - + -
864A HIS* 1.3 77.8 - - - +
866A SER* 1.3 62.2 + - - +
900A ARG* 3.8 28.7 - - + +
902A CYS* 3.8 23.3 - - - -
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Residues in contact with SER 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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699A ILE* 4.5 0.2 - - - -
841A HIS* 3.4 24.0 - - - -
842A PRO 3.3 9.9 - - - -
843A PHE* 3.2 22.3 - - - -
865A PHE* 1.3 65.9 + - - +
867A ASN* 1.3 60.7 + - - +
868A VAL* 3.6 1.0 + - - +
875A SER 5.1 0.5 + - - -
879A MET* 4.0 13.1 + - - +
900A ARG 3.4 16.6 - - - -
901A LEU* 3.8 12.1 - - - +
902A CYS* 3.1 27.7 + - - -
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Residues in contact with ASN 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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697A ILE 3.8 11.7 + - - -
698A THR* 5.0 0.8 - - - +
699A ILE* 3.1 33.9 - - + +
841A HIS* 3.9 6.6 - - - -
842A PRO* 3.2 26.4 + - + +
866A SER* 1.3 72.2 - - - +
868A VAL* 1.3 63.8 + - - +
869A GLY 3.2 4.2 + - - -
902A CYS* 4.3 6.7 - - - -
904A THR* 3.0 23.9 + - - +
906A LEU* 3.7 26.1 - - - +
909A ASN* 3.6 17.4 + - - -
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Residues in contact with VAL 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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709A TYR* 4.0 13.5 - - + -
841A HIS* 4.0 7.3 + - - +
866A SER* 4.0 11.0 - - - +
867A ASN* 1.3 79.0 + - - +
869A GLY* 1.3 68.1 - - - +
871A THR 3.5 19.7 - - - +
872A GLN* 4.1 2.5 - - - +
875A SER* 3.6 32.1 - - - +
901A LEU* 4.1 15.7 - - + -
902A CYS 3.1 24.3 + - - +
908A SER* 4.0 0.5 - - - -
909A ASN* 3.0 34.7 + - - +
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Residues in contact with GLY 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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709A TYR* 3.4 19.1 + - - -
867A ASN* 3.2 8.1 + - - -
868A VAL* 1.3 87.0 - - - +
870A ASN* 1.4 56.7 + - - -
871A THR 3.4 3.6 - - - -
902A CYS 4.0 0.2 + - - -
903A LYS* 4.7 0.2 - - - +
904A THR* 3.3 24.9 + - - +
906A LEU* 3.2 17.5 - - - -
907A PRO 4.1 6.7 - - - -
908A SER* 4.2 0.7 - - - -
909A ASN* 5.2 0.2 - - - -
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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