Contacts of the strand formed by residues 900 - 908 (chain B) in PDB entry 2QEP
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 900 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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891B TYR* 4.2 27.4 - - + -
892B LEU 3.6 6.3 - - - +
893B LYS* 3.3 27.3 - - + +
898B ASN 3.9 2.2 + - - -
899B GLU* 1.3 74.8 - - - +
901B ARG* 1.3 75.6 + - - +
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Residues in contact with ARG 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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835B TRP* 3.4 60.8 + - + +
838B GLY* 4.9 13.9 - - - -
839B CYS 4.9 4.5 + - - -
840B VAL* 4.3 18.6 - - + -
891B TYR* 3.4 6.2 - - - -
892B LEU* 2.9 39.6 + - + +
899B GLU* 3.6 17.8 + - - +
900B THR* 1.3 80.0 - - - +
902B THR* 1.3 68.1 + - - +
903B VAL* 4.0 3.4 - - + -
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Residues in contact with THR 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B VAL* 3.1 24.3 - - - +
876B VAL* 6.4 0.4 - - + -
889B SER* 4.9 9.2 - - - +
890B PHE 3.3 13.9 - - - +
891B TYR* 3.8 20.2 - - + -
901B ARG* 1.3 74.0 - - - +
903B VAL* 1.3 65.3 + - - +
904B THR* 4.4 14.6 + - - +
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Residues in contact with VAL 903 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B TRP* 4.8 5.2 - - + -
834B VAL* 4.3 7.6 - - + -
839B CYS 4.1 15.0 - - - +
840B VAL* 3.7 14.6 - - + +
842B ILE* 4.0 33.0 - - + -
889B SER* 3.7 0.5 - - - -
890B PHE* 2.8 51.6 + - + +
892B LEU* 3.9 34.8 - - + -
901B ARG* 4.0 4.0 - - + -
902B THR* 1.3 77.7 - - - +
904B THR* 1.3 64.8 + - - +
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Residues in contact with THR 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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840B VAL 2.9 12.7 + - - -
841B VAL* 3.3 4.5 - - - -
842B ILE 2.8 24.7 + - - +
887B VAL* 3.6 21.5 - - + -
888B ARG 3.4 5.2 - - - +
889B SER* 4.3 11.3 + - - +
902B THR* 4.4 10.2 + - - +
903B VAL* 1.3 74.5 - - - +
905B GLN* 1.3 61.6 + - - +
906B PHE* 3.4 30.3 + - + -
933B CYS* 4.3 14.4 - - - -
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Residues in contact with GLN 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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842B ILE* 3.4 27.8 - - + +
844B MET* 3.4 21.8 - - + -
859B TYR* 2.7 32.8 + - - +
860B TRP* 3.8 9.4 - - - -
887B VAL* 3.3 5.9 - - - +
888B ARG* 2.8 73.3 + - - +
890B PHE* 3.6 24.0 - - + -
903B VAL 4.0 1.0 + - - -
904B THR* 1.3 73.1 - - - +
906B PHE* 1.3 67.1 + - - +
907B HIS* 3.9 1.4 + - - +
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Residues in contact with PHE 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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841B VAL* 3.9 25.1 - - + -
842B ILE 2.8 12.7 + - - +
843B VAL* 3.5 2.3 - - - -
844B MET* 2.9 27.2 + - - +
885B PHE* 6.0 0.9 - + - -
886B LEU 3.7 2.9 - - - -
887B VAL* 3.5 25.4 - - + -
904B THR* 3.4 25.1 - - + -
905B GLN* 1.3 73.9 - - - +
907B HIS* 1.3 59.5 + - - +
926B PHE* 3.8 15.8 - + + -
929B LYS* 3.7 17.5 - - + -
930B VAL* 3.5 41.7 - - + -
933B CYS* 3.5 34.5 - - + -
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Residues in contact with HIS 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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844B MET* 3.3 41.8 - - + +
846B THR 2.5 26.9 + - - -
847B PRO* 4.6 6.1 - - + -
848B LEU* 5.0 4.0 - - + -
860B TRP* 4.4 4.9 - + - -
885B PHE* 3.3 2.8 - - - -
886B LEU* 2.8 40.7 + - + +
888B ARG* 3.2 41.1 + - - +
905B GLN* 4.7 3.6 - - - +
906B PHE* 1.3 71.3 - - - +
908B PHE* 1.3 66.0 + - - +
909B LEU* 3.6 24.6 - - + +
926B PHE* 3.9 3.7 - - - -
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Residues in contact with PHE 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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844B MET 2.8 16.4 + - - +
845B LEU* 3.8 8.8 - - + -
846B THR 3.8 14.9 + - - +
884B ASP* 3.2 33.4 - - + -
885B PHE* 4.1 1.6 - + + -
907B HIS* 1.3 82.5 - - - +
909B LEU* 1.3 61.2 + - - +
910B SER* 3.7 11.2 - - - -
911B TRP* 3.6 40.7 + + + -
917B PRO* 4.2 16.6 - - + -
922B SER* 4.1 2.7 - - - -
923B LEU* 3.6 44.6 - - + -
926B PHE* 3.6 38.5 - + + -
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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