Contacts of the helix formed by residues 826 - 838 (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 826 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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772B PRO 4.6 0.7 - - - +
773B LYS* 3.8 40.2 - - + +
801B ILE* 4.9 6.0 - - + +
820B GLN* 4.3 7.0 + - - +
822B PRO* 3.9 5.5 - - - +
823B LEU* 2.9 27.7 + - + +
825B ALA* 1.3 87.5 - - + +
827B VAL* 1.3 56.2 + - - +
828B ALA* 3.2 2.2 - - - -
829B ASP* 2.9 24.6 + - - +
830B PHE* 2.8 34.1 + - - +
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Residues in contact with VAL 827 (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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822B PRO* 4.3 4.0 - - + -
823B LEU 3.3 11.1 + - - +
824B PRO 3.7 11.0 + - - +
825B ALA 3.9 0.2 - - - -
826B THR* 1.3 75.9 - - - +
828B ALA* 1.3 64.1 + - - +
830B PHE* 3.0 10.0 + - - +
831B TRP* 2.9 42.6 + - + +
857B TYR* 3.2 37.9 - - + -
859B TYR* 3.8 16.6 - - + -
868B TYR* 3.5 32.1 - - + -
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Residues in contact with ALA 828 (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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795B HIS* 3.7 34.5 - - + +
826B THR* 5.1 0.7 - - - -
827B VAL* 1.3 79.3 - - - +
829B ASP* 1.3 63.8 + - - +
831B TRP* 3.3 3.6 + - - +
832B GLN* 3.0 24.7 + - - +
868B TYR* 4.1 19.6 - - + +
869B HIS* 3.9 19.7 - - + +
871B TYR* 4.3 3.6 - - - -
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Residues in contact with ASP 829 (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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773B LYS* 4.6 12.0 - - - +
789B LEU* 3.6 26.3 - - + +
794B SER* 4.4 7.5 + - - -
795B HIS* 4.2 17.2 - - - +
796B SER* 4.7 5.9 + - - -
800B TYR 4.3 8.4 - - - +
801B ILE* 3.6 18.0 - - + +
825B ALA 4.3 3.8 - - - +
826B THR* 2.9 33.8 + - - +
828B ALA* 1.3 77.5 - - - +
830B PHE* 1.3 56.0 + - - +
832B GLN* 3.2 11.8 + - - +
833B MET 2.9 23.6 + - - -
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Residues in contact with PHE 830 (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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801B ILE* 3.7 11.3 - - + +
819B THR* 4.3 11.4 - - + -
820B GLN 5.1 0.7 - - - -
822B PRO* 3.4 33.2 - - + -
826B THR* 2.8 12.7 + - - +
827B VAL 3.2 8.1 - - - +
829B ASP* 1.3 76.7 - - - +
831B TRP* 1.3 69.5 + + - +
833B MET* 3.1 15.9 + - + +
834B VAL* 2.9 46.3 + - + +
842B ILE* 3.7 23.1 - - + -
859B TYR* 3.4 36.6 - + + -
942B ILE* 3.9 24.9 - - + -
944B HIS* 4.4 5.2 - + - -
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Residues in contact with TRP 831 (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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827B VAL* 2.9 34.8 + - + +
828B ALA* 3.3 2.0 + - - +
830B PHE* 1.3 74.1 - + - +
832B GLN* 1.3 61.2 + - - +
834B VAL* 3.3 29.0 + - + +
835B TRP* 2.9 28.4 + - - +
842B ILE* 4.6 7.4 - - + -
859B TYR* 3.0 53.8 + + - -
860B TRP* 4.6 2.7 - - + -
868B TYR* 3.3 26.3 - + + -
871B TYR* 3.9 24.6 - - + -
873B VAL* 3.4 33.2 - - + -
890B PHE* 4.5 15.5 - + + -
892B LEU* 3.6 25.5 - - + +
903B VAL* 4.8 7.9 - - + -
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Residues in contact with GLN 832 (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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789B LEU* 3.4 29.9 - - + +
790B LYS 3.1 25.9 + - - +
793B ASN* 3.6 8.1 - - - +
794B SER* 3.6 22.5 + - - +
795B HIS 4.7 0.7 + - - -
828B ALA 3.0 13.0 + - - +
829B ASP* 3.2 10.6 + - - +
831B TRP* 1.3 75.2 - - - +
833B MET* 1.3 60.4 + - - +
835B TRP* 3.2 0.3 + - - -
836B GLU* 2.7 62.1 + - - +
871B TYR* 3.4 26.1 - - + +
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Residues in contact with MET 833 (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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787B VAL* 3.7 30.3 - - + -
789B LEU* 3.8 13.9 - - + +
801B ILE* 4.1 16.6 - - + -
803B ALA* 3.6 25.6 - - - -
817B ILE* 3.8 15.0 - - + -
819B THR* 4.1 20.6 - - + +
829B ASP 2.9 13.4 + - - +
830B PHE* 3.1 22.4 + - + +
832B GLN* 1.3 76.7 - - - +
834B VAL* 1.3 53.7 + - - +
836B GLU* 4.5 3.6 - - - +
837B SER* 2.8 37.5 + - - +
942B ILE* 3.9 19.1 - - + -
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Residues in contact with VAL 834 (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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830B PHE* 2.9 50.2 + - + +
831B TRP* 3.4 20.9 - - + +
832B GLN 3.2 0.2 - - - -
833B MET* 1.3 79.0 - - - +
835B TRP* 1.3 61.1 + - - +
837B SER* 3.5 3.3 - - - -
838B GLY 3.4 14.6 + - - -
839B CYS* 3.4 31.5 + - + +
842B ILE* 4.6 4.9 - - + -
892B LEU* 3.8 20.6 - - + -
903B VAL* 4.3 10.5 - - + -
942B ILE* 4.5 11.0 - - + -
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Residues in contact with TRP 835 (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 2.9 17.6 + - - +
832B GLN 3.7 2.5 - - - +
834B VAL* 1.3 78.4 - - - +
836B GLU* 1.3 73.0 + - + +
838B GLY* 3.3 12.1 + - - -
871B TYR* 3.7 19.3 - + + -
892B LEU* 3.4 47.3 - - + -
894B ASN* 3.2 46.5 - - + +
897B THR* 5.7 0.8 - - - +
899B GLU* 3.7 40.2 + - + -
901B ARG* 3.4 51.8 + - + +
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Residues in contact with GLU 836 (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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788B LEU 4.1 3.9 - - - +
789B LEU* 3.6 9.4 - - - +
790B LYS* 3.0 46.9 + - - +
793B ASN* 3.7 15.2 - - - +
832B GLN* 2.7 53.1 + - + +
833B MET* 4.4 3.1 - - - +
835B TRP* 1.3 81.3 - - + +
837B SER* 1.3 64.5 + - - +
838B GLY 3.4 0.3 + - - -
871B TYR* 4.2 4.0 + - - +
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Residues in contact with SER 837 (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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787B VAL* 6.3 0.9 - - - -
817B ILE* 4.0 25.1 - - - -
833B MET 2.8 21.9 + - - -
834B VAL 3.5 5.8 - - - -
835B TRP 3.2 0.2 - - - -
836B GLU* 1.3 79.1 - - - +
838B GLY* 1.3 57.1 + - - +
839B CYS* 3.1 18.1 + - - -
939B CYS* 3.9 3.1 - - - +
940B PRO* 3.7 19.3 - - - +
942B ILE* 4.5 0.9 - - - -
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Residues in contact with GLY 838 (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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834B VAL 3.4 1.1 + - - -
835B TRP 3.3 11.7 + - - -
836B GLU 3.2 4.0 + - - -
837B SER* 1.3 77.5 - - - +
839B CYS* 1.3 66.0 + - - +
840B VAL* 3.6 8.5 + - - +
901B ARG* 4.9 14.4 - - - -
939B CYS* 3.5 21.1 - - - +
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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