Contacts of the strand formed by residues 895 - 903 (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 ILE 895 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B ILE* 3.8 2.7 - - + +
716B GLU* 3.7 5.2 - - - +
717B LYS* 3.1 40.2 + - + +
720B LEU* 4.7 7.2 - - - +
860B LEU* 3.4 21.3 - - + +
886B MET* 4.3 28.0 - - + -
887B ASP* 5.5 3.1 - - + +
892B ILE* 3.9 36.1 - - + +
893B PRO 5.0 0.4 - - - -
894B ASN* 1.3 75.7 - - - +
896B ARG* 1.3 64.0 - - - +
897B GLY 4.3 0.4 - - - -
955B HIS* 4.0 36.8 - - + -
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Residues in contact with ARG 896 (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* 4.1 15.2 + - - -
714B LYS* 3.6 31.5 - - + +
715B ILE 3.7 3.1 - - - +
716B GLU* 3.3 32.0 + - + +
720B LEU* 4.6 15.2 - - + +
860B LEU 3.1 9.7 + - - +
861B GLU* 3.5 28.5 + - + +
862B VAL 3.1 25.8 + - - +
863B ASP* 5.4 2.4 + - - -
886B MET* 4.1 3.8 - - - -
895B ILE* 1.3 76.4 - - - +
897B GLY* 1.4 61.4 + - - +
898B THR* 4.3 16.6 + - + +
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Residues in contact with GLY 897 (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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714B LYS* 3.0 4.5 - - - +
715B ILE* 2.7 39.2 + - - -
862B VAL 3.6 4.3 - - - -
864B HIS* 5.1 0.4 - - - -
883B LEU* 3.9 8.4 - - - +
886B MET* 3.5 30.4 - - - +
895B ILE* 4.3 0.6 - - - +
896B ARG* 1.4 72.6 - - - +
898B THR* 1.3 61.2 + - - -
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Residues in contact with THR 898 (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* 3.7 26.8 + - - +
713B LEU 3.0 11.9 - - - -
714B LYS* 3.9 12.6 - - + +
862B VAL 3.4 3.8 + - - -
863B ASP* 2.6 36.6 + - - +
864B HIS* 2.9 30.3 + - - -
883B LEU* 3.8 6.3 - - - -
896B ARG* 4.3 20.9 - - + +
897B GLY* 1.3 73.1 - - - -
899B GLY* 1.3 61.1 + - - +
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Residues in contact with GLY 899 (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* 3.9 1.8 - - - -
713B LEU* 2.7 39.4 + - - +
864B HIS 3.1 11.2 - - - -
879B MET* 3.4 21.2 - - - +
883B LEU* 4.6 1.4 - - - +
898B THR* 1.3 78.9 - - - +
900B ARG* 1.3 69.0 + - - +
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Residues in contact with ARG 900 (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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706B ASN* 5.3 3.4 + - - +
708B PHE* 2.9 52.7 + - + -
710B GLY 2.7 36.2 + - - -
711B PRO* 3.4 3.0 - - - +
712B GLU* 3.1 37.5 - - + +
864B HIS 2.8 11.5 + - - -
865B PHE* 3.9 27.9 - - + +
866B SER* 3.0 28.6 - - - +
879B MET* 4.0 1.1 - - - +
899B GLY* 1.3 78.0 - - - -
901B LEU* 1.3 70.2 + - - +
902B CYS* 3.8 1.3 - - - -
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Residues in contact with LEU 901 (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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708B PHE* 2.8 18.5 - - - +
709B TYR* 3.3 42.5 + - + +
710B GLY 5.5 0.2 - - - +
713B LEU* 5.0 9.6 - - + -
866B SER* 3.5 18.2 - - - +
868B VAL* 3.8 14.8 - - + -
872B GLN* 5.2 5.2 - - + +
875B SER* 4.1 13.5 - - - +
876B GLN* 3.7 41.5 - - + +
879B MET* 4.5 11.9 - - + -
900B ARG* 1.3 90.5 - - - +
902B CYS* 1.3 58.8 + - - +
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Residues in contact with CYS 902 (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* 4.3 15.7 - - + +
702B ALA* 3.6 23.3 - - + -
703B ILE* 5.7 1.1 - - - -
708B PHE* 3.2 17.7 - - + -
865B PHE* 3.8 27.1 - - - -
866B SER 3.3 20.7 + - - +
867B ASN* 3.9 5.6 - - - +
868B VAL* 3.0 30.6 + - - +
869B GLY 3.9 0.3 + - - -
900B ARG 4.2 2.2 - - - -
901B LEU* 1.3 71.0 - - - +
903B LYS* 1.4 64.0 + - - +
904B THR* 3.7 3.7 + - + +
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Residues in contact with LYS 903 (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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696B ILE* 4.2 7.8 - - - +
702B ALA* 4.6 1.0 - - - +
707B SER* 3.6 33.3 + - - +
708B PHE* 3.5 10.4 - - - +
709B TYR* 3.2 56.2 + - + +
869B GLY 4.0 0.9 - - - +
870B ASN* 5.4 5.0 + - - +
901B LEU 3.6 0.8 + - - -
902B CYS* 1.4 71.9 - - - +
904B THR* 1.3 66.0 + - - +
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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