Contacts of the strand formed by residues 885 - 894 (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 PHE 885 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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881B TRP* 3.3 34.7 + + + -
882B CYS* 3.0 39.7 + - - +
883B GLU 3.5 0.2 - - - -
884B ASP* 1.3 86.8 - - + +
886B LEU* 1.3 63.4 + - - +
887B VAL* 5.6 2.5 - - + -
906B PHE* 6.0 0.7 - + - -
907B HIS 3.3 8.5 - - - +
908B PHE* 4.0 2.2 - + + -
909B LEU* 4.1 2.9 - - - -
922B SER* 3.4 25.1 - - - -
925B ASP* 3.6 21.3 - - + -
926B PHE* 3.3 52.9 - + + -
929B LYS* 3.5 27.1 - - + -
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Residues in contact with LEU 886 (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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878B GLU* 4.2 9.6 - - + +
879B HIS 3.4 14.8 - - - +
880B ILE* 3.8 26.2 - - + +
881B TRP* 4.4 2.9 - - - +
885B PHE* 1.3 76.3 - - - +
887B VAL* 1.3 67.2 + - - +
888B ARG* 3.3 50.9 - - + +
906B PHE* 3.7 0.3 - - - -
907B HIS* 2.8 44.8 + - + +
909B LEU* 3.7 26.5 - - + -
926B PHE* 5.0 0.3 - - - -
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Residues in contact with VAL 887 (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 SER 4.1 0.3 - - - +
878B GLU* 3.4 3.6 - - - +
879B HIS* 2.8 37.4 + - + +
881B TRP* 3.6 24.9 - - + +
885B PHE* 5.6 2.0 - - + -
886B LEU* 1.3 80.5 - - - +
888B ARG* 1.3 69.1 + - - +
889B SER* 4.9 3.4 - - - +
904B THR* 3.6 29.6 - - + -
905B GLN 3.3 5.4 - - - +
906B PHE* 3.5 32.5 - - + -
929B LYS* 5.8 0.4 - - + -
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Residues in contact with ARG 888 (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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860B TRP* 3.3 42.7 - - - +
875B LEU* 4.1 10.1 - - + -
877B SER 3.3 6.1 - - - +
878B GLU* 3.0 31.1 + - + -
886B LEU* 3.3 22.6 - - + +
887B VAL* 1.3 79.0 - - - +
889B SER* 1.3 63.1 + - - +
890B PHE* 3.9 16.2 - - + -
903B VAL 3.9 0.3 - - - +
904B THR* 3.4 5.4 - - - +
905B GLN* 2.8 64.0 + - - +
907B HIS* 3.2 33.9 + - - +
909B LEU* 5.4 0.2 - - - +
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Residues in contact with SER 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B LEU* 3.8 2.8 - - - +
876B VAL* 2.8 33.8 + - - +
877B SER* 2.8 32.7 + - - +
887B VAL* 4.9 3.1 - - - +
888B ARG* 1.3 75.4 + - - +
890B PHE* 1.3 63.2 + - - +
902B THR* 4.9 10.7 - - - +
903B VAL 3.7 3.1 - - - -
904B THR* 4.3 13.1 + - - +
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Residues in contact with PHE 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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831B TRP* 4.5 15.9 - + + -
842B ILE* 5.7 0.9 - - + -
859B TYR* 5.7 1.1 - + - -
860B TRP* 3.4 41.7 - + + -
861B PRO* 3.9 3.6 - - + -
873B VAL* 3.9 20.6 - - + -
874B ASN 3.0 14.6 - - - +
875B LEU* 3.3 28.7 - - + -
876B VAL* 4.3 1.8 - - - -
888B ARG* 3.9 11.7 - - + -
889B SER* 1.3 74.1 - - - +
891B TYR* 1.3 63.2 + - - +
892B LEU* 4.0 1.3 - - - -
902B THR* 3.3 12.3 - - - +
903B VAL* 2.8 49.1 + - + +
905B GLN* 3.6 37.0 - - + -
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Residues in contact with TYR 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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872B GLU* 3.0 8.1 - - - +
873B VAL* 3.5 0.3 - - - -
874B ASN* 2.8 53.2 + - + +
876B VAL* 3.3 35.7 - - + +
890B PHE* 1.3 73.6 - - - +
892B LEU* 1.3 58.9 + - - +
893B LYS* 3.7 1.3 + - + +
900B THR* 4.2 20.6 - - + -
901B ARG 3.4 6.3 - - - +
902B THR* 3.8 25.1 - - + -
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Residues in contact with LEU 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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831B TRP* 3.6 25.4 - - + +
834B VAL* 3.8 28.9 - - + -
835B TRP* 3.4 38.8 - - + +
839B CYS 5.6 0.4 - - - +
871B TYR* 4.0 21.1 - - + -
872B GLU 3.4 2.0 - - - +
873B VAL* 4.0 16.8 - - + +
890B PHE* 4.0 2.5 + - + -
891B TYR* 1.3 70.3 - - - +
893B LYS* 1.3 58.3 + - - +
900B THR* 4.4 1.1 - - - -
901B ARG* 2.9 36.3 + - + +
903B VAL* 3.9 22.2 - - + -
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Residues in contact with LYS 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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835B TRP* 4.7 0.7 - - - -
870B ILE 3.5 1.2 - - - +
871B TYR* 3.5 3.7 - - - -
872B GLU* 2.7 66.9 + - + +
891B TYR* 3.7 2.9 + - + +
892B LEU* 1.3 71.9 - - - +
894B ASN* 1.3 70.1 + - - +
895B LEU* 3.5 26.0 + - + -
898B ASN* 3.7 30.8 + - - +
899B GLU 3.4 11.4 - - - +
900B THR* 3.3 21.3 - - + +
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Residues in contact with ASN 894 (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* 3.2 49.4 - - + +
870B ILE* 3.8 10.9 - - - +
871B TYR* 4.0 17.2 + - + -
892B LEU 4.0 1.8 + - - -
893B LYS* 1.3 69.8 - - - +
895B LEU* 1.3 53.8 + - - +
896B GLN* 2.9 24.7 + - - +
897B THR* 3.2 29.6 + - - +
898B ASN* 2.5 37.4 + - - -
899B GLU 3.1 6.6 + - - +
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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