Contacts of the strand formed by residues 887 - 894 (chain B) in PDB entry 5KJH
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 887 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B VAL* 3.8 24.0 - - + -
879B ILE* 3.6 34.5 - - + -
885B GLY* 4.4 0.5 - - - -
886B ASN* 1.4 86.1 + - - +
888B MET* 1.3 62.3 + - - +
889B PRO* 4.5 0.2 - - - +
902B PHE* 3.5 30.1 - - + -
903B THR 3.3 9.2 - - - +
904B ALA* 4.1 2.0 - - - -
905B ILE* 3.8 11.1 - - - +
908B ILE* 3.8 17.3 - - + -
914B LEU* 4.3 13.7 - - + -
915B PHE 3.2 18.5 + - - +
916B PHE* 3.4 25.0 - - + +
917B ASN 4.8 0.9 + - - -
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Residues in contact with MET 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B ILE* 1.3 76.8 - - - +
889B PRO* 1.4 92.0 - - + +
890B LYS* 5.0 2.6 - - + +
901B LYS 3.7 0.5 - - - +
902B PHE* 3.5 5.5 - - - -
903B THR* 2.8 34.6 + - - +
905B ILE* 3.5 32.3 - - + -
917B ASN* 5.8 3.1 - - + +
2538B VAL* 4.1 7.2 - - + -
2539B PRO* 3.9 30.1 - - + -
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Residues in contact with PRO 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857B PHE* 3.7 20.2 - - + -
888B MET* 1.4 113.7 - - + +
890B LYS* 1.3 63.4 + - - +
900B ILE* 4.2 4.9 - - + -
901B LYS 3.3 7.4 - - - +
902B PHE* 3.7 17.7 - - + -
916B PHE* 3.7 33.9 - - + -
917B ASN 4.7 5.8 - - - +
2537B GLY 4.9 0.2 - - - +
2538B VAL* 3.6 21.9 - - + +
2539B PRO* 4.9 0.2 - - + -
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Residues in contact with LYS 890 (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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738B GLN* 3.2 28.7 + - - +
749B VAL* 4.7 2.0 + - - +
752B ASN* 3.1 34.1 + - - -
888B MET* 5.0 3.4 - - + +
889B PRO* 1.3 76.6 - - - +
891B ILE* 1.3 74.1 + - - +
892B MET* 3.7 19.9 + - - -
899B ARG 3.6 0.7 - - - +
900B ILE* 3.6 3.4 - - - +
901B LYS* 3.0 49.2 + - + +
903B THR* 5.9 0.9 - - - +
2538B VAL* 3.9 8.7 - - + +
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Residues in contact with ILE 891 (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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676B HIS* 3.3 35.6 + - + -
677B ALA* 6.1 6.1 - - + +
752B ASN* 4.1 3.5 - - - +
857B PHE* 5.2 0.2 - - + -
858B THR 4.2 11.2 - - - +
859B LEU* 3.7 29.6 - - + +
890B LYS* 1.3 82.8 - - - +
892B MET* 1.3 63.1 + - - +
898B TRP* 4.0 21.8 - - + -
899B ARG 3.4 7.4 - - - +
900B ILE* 4.2 17.9 - - + -
2538B VAL* 3.6 32.8 - - + +
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Residues in contact with MET 892 (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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676B HIS* 4.3 2.2 - - - -
749B VAL* 6.0 1.8 - - - -
752B ASN* 3.5 12.6 - - - -
753B ARG 3.5 32.5 - - - +
754B GLU* 3.9 8.7 - - + +
786B ASN* 3.7 15.0 - - - +
789B LEU* 4.0 8.1 - - + -
890B LYS* 3.9 24.2 - - - +
891B ILE* 1.3 75.8 - - - +
893B TYR* 1.3 61.3 + - - +
894B VAL* 3.6 17.0 + - + +
898B TRP* 3.3 6.6 - - - -
899B ARG 2.8 33.7 + - - -
901B LYS* 3.8 44.2 - - + +
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Residues in contact with TYR 893 (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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676B HIS* 3.7 21.4 + + + -
679B ARG* 5.0 6.5 - - - -
710B GLU* 3.4 24.6 + - + +
711B ARG* 5.3 3.6 + - - +
752B ASN 3.0 6.9 + - - -
753B ARG* 3.1 49.9 - - + +
754B GLU 2.9 26.5 + - - +
892B MET* 1.3 72.1 - - - +
894B VAL* 1.3 58.6 + - - +
895B ASN* 4.3 6.1 - - - -
896B HIS* 2.8 59.4 + + - +
897B GLU 3.6 2.7 - - - -
898B TRP* 3.4 36.1 - + - +
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Residues in contact with VAL 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754B GLU* 3.6 16.6 - - + +
789B LEU* 3.7 28.0 - - + -
790B GLN* 3.5 42.4 - - + +
892B MET* 3.8 11.2 - - + +
893B TYR* 1.3 78.5 - - - +
895B ASN* 1.3 70.2 + - - +
896B HIS 3.2 0.2 - - - -
897B GLU* 2.7 31.4 + - - +
899B ARG* 4.0 25.1 - - - +
2620B SER* 4.8 1.2 + - - +
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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