Contacts of the helix formed by residues 900 - 911 (chain B) in PDB entry 5QSY
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 TYR 900 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837B VAL* 2.8 45.2 + - + -
838B PHE* 4.4 7.4 - + - -
862B LEU* 4.5 3.0 - - + +
865B ARG* 3.1 24.8 + - + +
866B ARG* 3.9 36.1 - - + +
869B LEU* 3.4 29.6 - - + -
896B TYR* 3.3 36.2 + + + +
899B ASP* 1.3 98.6 + - + +
901B GLY* 1.3 54.7 + - - +
902B ASP* 3.1 3.8 - - - +
903B ILE* 2.6 35.9 + - + +
904B ILE* 3.2 15.7 + - + -
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Residues in contact with GLY 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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893B TYR* 4.5 2.2 - - - -
896B TYR 3.1 7.0 + - - -
897B TYR* 3.1 47.3 + - - -
900B TYR* 1.3 73.4 - - - +
902B ASP* 1.3 57.2 + - - +
904B ILE* 4.0 6.4 - - - +
905B LYS* 2.8 35.0 + - - +
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Residues in contact with ASP 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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866B ARG* 2.8 42.4 + - - -
897B TYR* 4.4 6.9 + - - +
898B ASN 5.2 1.7 - - - +
899B ASP 4.3 0.9 - - - +
900B TYR 2.7 6.6 + - - +
901B GLY* 1.3 71.7 - - - -
903B ILE* 1.3 67.1 + - - +
905B LYS* 4.0 3.2 - - - +
906B GLU* 3.1 35.3 + - - +
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Residues in contact with ILE 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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866B ARG* 4.1 24.9 - - + +
869B LEU* 3.8 23.3 - - + -
870B ALA* 4.1 25.6 - - + -
873B SER* 3.5 24.2 - - - +
900B TYR* 2.6 15.5 + - - +
902B ASP* 1.3 88.5 - - - +
904B ILE* 1.3 62.3 + - - +
906B GLU* 3.4 14.4 + - - +
907B THR* 2.9 27.5 + - - -
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Residues in contact with ILE 904 (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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838B PHE* 4.5 11.7 - - + -
869B LEU* 4.4 12.3 - - + -
889B ILE* 4.9 5.8 - - + +
890B PHE* 3.7 21.3 - - + -
892B HIS 4.1 7.9 - - - +
893B TYR* 3.4 48.0 - - + -
896B TYR 4.6 3.8 - - - +
900B TYR* 3.2 30.3 + - + -
901B GLY 4.0 2.7 - - - +
903B ILE* 1.3 75.9 - - - +
905B LYS* 1.3 59.0 + - - +
907B THR* 3.0 7.8 + - - -
908B LEU* 2.9 41.7 + - + +
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Residues in contact with LYS 905 (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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893B TYR* 3.2 33.4 - - + +
897B TYR* 3.8 25.5 + - + +
901B GLY 2.8 23.6 + - - +
902B ASP* 4.3 3.8 - - - +
904B ILE* 1.3 73.8 - - - +
906B GLU* 1.3 50.9 + - - +
908B LEU* 4.6 6.3 - - + +
909B SER* 2.8 35.6 + - - -
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Residues in contact with GLU 906 (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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877B ILE* 4.4 6.7 - - + +
902B ASP* 3.1 24.1 + - - +
903B ILE* 3.8 16.7 - - - +
904B ILE 3.2 0.2 - - - -
905B LYS* 1.3 74.8 - - - +
907B THR* 1.3 59.0 + - - +
909B SER* 3.8 7.3 - - - -
910B LYS* 3.6 29.5 + - + +
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Residues in contact with THR 907 (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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873B SER* 3.5 16.0 + - - +
876B ILE* 3.8 34.1 - - + -
877B ILE* 3.4 29.9 - - + +
883B MET* 4.7 2.9 - - + -
889B ILE* 6.1 0.4 - - + -
890B PHE* 4.7 13.5 - - + -
903B ILE 2.9 13.6 + - - -
904B ILE* 3.0 10.3 + - - -
906B GLU* 1.3 75.3 - - - +
908B LEU* 1.3 64.8 + - - +
909B SER 3.0 1.6 + - - -
910B LYS 3.3 1.2 + - - -
911B THR* 3.2 30.1 + - - -
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Residues in contact with LEU 908 (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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883B MET* 3.3 35.1 - - + +
890B PHE* 3.5 33.2 - - + -
893B TYR* 4.4 17.0 - - + -
904B ILE* 2.9 37.6 + - + +
905B LYS* 4.3 5.2 - - + +
907B THR* 1.3 72.8 - - - +
909B SER* 1.3 66.0 + - - +
911B THR 4.7 4.7 + - - +
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Residues in contact with SER 909 (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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905B LYS* 2.8 22.2 + - - -
906B GLU* 3.8 11.4 - - - -
907B THR 3.0 0.6 - - - -
908B LEU* 1.3 80.5 - - - +
910B LYS* 1.3 79.6 + - - +
911B THR 3.4 6.4 + - - +
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Residues in contact with LYS 910 (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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877B ILE* 4.9 17.0 - - + -
906B GLU* 3.6 20.2 + - + +
907B THR 3.3 4.4 + - - +
909B SER* 1.3 84.8 + - - +
911B THR* 1.3 66.5 + - - +
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Residues in contact with THR 911 (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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876B ILE* 4.1 23.7 - - + +
877B ILE* 4.1 19.2 - - - +
879B ASP* 5.3 7.2 - - - +
883B MET* 4.3 26.2 - - + -
907B THR* 3.2 17.1 + - - +
908B LEU 4.8 4.8 - - - +
909B SER 3.4 8.4 + - - +
910B LYS* 1.3 81.1 - - - +
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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