Contacts of the strand formed by residues 822 - 826 (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 PHE 822 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788B ALA* 3.5 44.4 - - + -
789B LEU* 3.9 17.7 - - + -
792B GLY* 4.9 2.7 - - - -
793B ALA 3.9 17.0 - - - +
794B ALA* 4.0 23.3 - - + -
795B LYS* 3.4 22.3 + - - +
820B GLY 3.8 1.4 + - - -
821B GLU* 1.3 72.0 - - - +
823B VAL* 1.3 59.2 + - - +
824B ILE* 3.6 32.3 - - - -
825B GLU* 3.8 5.8 - - + -
901B LYS* 3.8 25.6 - - + -
902B PHE 3.6 13.9 - - - -
903B THR* 4.6 4.5 - - - +
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Residues in contact with VAL 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B ALA* 3.4 3.5 - - - +
795B LYS* 2.8 35.3 + - + +
797B VAL* 4.7 4.0 - - + -
817B ILE* 4.1 34.1 - - + -
821B GLU 3.8 3.8 - - - +
822B PHE* 1.3 74.5 - - - +
824B ILE* 1.3 71.0 + - + +
887B ILE* 3.8 19.3 - - + -
902B PHE* 2.8 20.0 + - + +
904B ALA* 3.8 24.0 - - + +
914B LEU* 4.3 19.3 - - + -
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Residues in contact with ILE 824 (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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794B ALA* 4.3 13.5 - - + -
797B VAL* 4.3 16.4 - - + -
811B LEU* 4.2 13.0 - - + -
822B PHE* 3.6 15.9 - - - -
823B VAL* 1.3 89.7 - - + +
825B GLU* 1.3 69.7 + - - +
874B ASN* 3.9 13.0 - - + +
875B LEU* 4.3 4.0 - - + -
876B SER* 3.8 32.8 - - - +
879B ILE* 4.1 10.3 - - + -
902B PHE* 2.8 50.0 + - + +
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Residues in contact with GLU 825 (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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311B ARG* 4.4 5.9 + - - +
312B LYS* 5.4 0.7 - - - -
313B ASN* 4.4 10.0 + - - -
789B LEU* 3.5 18.3 - - + +
794B ALA* 5.5 0.2 - - - +
822B PHE* 3.8 6.1 - - + -
824B ILE* 1.3 78.4 - - - +
826B TYR* 1.3 60.9 + - - +
827B THR* 3.7 24.0 - - + +
874B ASN* 2.8 30.8 + - - +
876B SER* 3.4 4.0 + - - -
899B ARG* 2.9 53.8 + - - +
900B ILE 3.1 20.0 - - - +
901B LYS* 4.4 0.9 - - - +
902B PHE* 4.5 0.4 - - - -
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Residues in contact with TYR 826 (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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313B ASN* 3.8 8.5 + - - +
825B GLU* 1.3 76.0 - - - +
827B THR* 1.3 62.7 + - - +
855B TYR* 2.7 38.1 + - - +
857B PHE* 3.7 30.3 - + + -
867B VAL* 3.9 14.3 - - + +
869B ALA* 3.8 17.5 - - + +
876B SER* 3.3 35.9 - - - -
877B ARG* 3.9 6.9 - - - -
900B ILE* 3.0 37.3 + - + +
902B PHE* 3.8 23.0 - + + -
916B PHE* 5.5 0.4 - + - -
2536B ARG* 3.5 32.3 + - - -
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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