Contacts of the strand formed by residues 842 - 848 (chain A) in PDB entry 1HXK
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 THR 842 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A VAL* 5.1 10.2 - - + +
798A ILE* 3.8 21.7 - - + +
838A GLU* 3.1 3.6 - - - +
839A ASP* 2.7 42.6 + - - +
841A ASN* 1.3 76.1 - - - +
843A ARG* 1.3 63.9 + - - +
896A LEU* 3.5 29.4 - - + -
897A GLU 3.5 7.2 - - - +
898A LYS* 2.9 24.1 + - + +
899A VAL* 3.9 2.9 - - - +
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Residues in contact with ARG 843 (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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798A ILE* 4.1 3.4 - - - -
836A PHE* 3.5 29.8 - - + -
837A ILE 3.3 13.5 - - - +
838A GLU* 2.9 35.4 + - + -
842A THR* 1.3 76.0 - - - +
844A LEU* 1.3 63.4 + - - +
845A THR* 3.4 22.0 + - - +
895A VAL 3.7 0.5 - - - +
896A LEU* 3.5 5.4 - - - +
897A GLU* 2.9 43.1 + - + +
899A VAL* 3.7 20.2 - - + +
904A ARG* 4.2 1.6 - - - +
905A PRO* 6.2 0.4 - - - +
912A GLY* 5.7 0.2 - - - -
913A TYR 2.7 29.1 + - - +
914A LEU* 3.9 9.1 - - - +
915A THR* 4.2 5.6 - - - +
918A ALA* 6.0 0.2 - - - +
985A MET* 3.1 33.3 - - - +
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Residues in contact with LEU 844 (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* 5.1 0.2 - - + -
708A VAL* 4.1 13.9 - - + -
794A LEU* 4.0 24.9 - - + -
796A THR* 3.7 27.6 - - + -
798A ILE* 3.7 15.6 - - + +
836A PHE* 3.1 4.0 - - - +
837A ILE* 3.0 33.5 + - + -
843A ARG* 1.3 73.9 - - - +
845A THR* 1.3 62.0 + - - +
862A LEU* 3.7 12.8 - - + +
894A LEU* 3.7 24.7 - - + -
895A VAL 3.4 15.0 - - - +
896A LEU* 3.8 22.9 - - + -
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Residues in contact with THR 845 (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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835A MET 3.4 13.9 - - - +
836A PHE* 3.3 15.7 - - + +
843A ARG* 3.4 19.2 + - - +
844A LEU* 1.3 73.8 - - - +
846A LEU* 1.3 62.2 + - - +
847A LEU* 3.7 31.5 - - + +
893A ARG 3.7 1.4 - - - +
894A LEU* 3.6 6.3 - - - +
895A VAL* 2.8 48.3 + - - +
897A GLU* 4.6 2.1 + - - -
914A LEU* 4.0 15.9 - - + -
918A ALA* 4.3 8.5 - - + +
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Residues in contact with LEU 846 (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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710A PHE* 4.9 3.8 - - + -
776A ILE* 5.3 0.2 - - + -
792A MET* 4.4 9.9 - - + -
794A LEU* 4.5 12.8 - - + -
834A GLY* 3.3 2.6 - - - -
835A MET* 2.8 54.0 + - + +
844A LEU 4.2 0.4 - - - -
845A THR* 1.3 73.7 - - - +
847A LEU* 1.3 60.4 + - - +
848A THR* 4.4 2.1 - - + +
862A LEU* 4.4 11.2 - - + +
863A GLU 5.9 0.9 - - - +
864A ILE* 3.9 29.8 - - + -
892A TYR* 3.8 29.8 - - + -
893A ARG 3.5 14.4 - - - +
894A LEU* 4.0 20.4 - - + -
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Residues in contact with LEU 847 (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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813A PHE* 4.8 2.0 - - + -
833A SER* 3.5 11.7 - - - +
834A GLY* 4.3 4.7 - - - -
845A THR* 3.7 31.0 - - + +
846A LEU* 1.3 75.9 - - - +
848A THR* 1.3 60.7 + - - +
892A TYR* 3.1 28.9 - - - +
893A ARG* 2.9 20.1 + - + +
895A VAL* 3.8 22.0 - - + -
914A LEU* 4.3 12.3 - - + -
918A ALA* 3.6 24.0 - - - +
921A ALA* 4.1 4.0 - - + -
922A SER* 3.9 19.5 - - - +
925A LEU* 3.7 15.7 - - + -
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Residues in contact with THR 848 (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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831A ILE* 3.8 14.8 + - + +
832A PRO 3.6 0.5 + - - +
833A SER* 2.9 33.7 + - - +
846A LEU* 4.4 5.2 - - + +
847A LEU* 1.3 78.5 - - - +
849A GLY* 1.3 60.5 + - - +
850A GLN* 2.8 30.1 + - - +
864A ILE* 3.6 30.3 - - + -
891A ILE 3.7 3.4 - - - -
892A TYR* 3.8 8.5 - - + -
922A SER* 5.3 1.4 + - - -
925A LEU* 3.7 9.7 - - - +
926A LEU* 4.1 12.8 - - - +
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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