Contacts of the helix formed by residues 826 - 846 (chain B) in PDB entry 5XA0
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 LYS 826 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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825B SER* 1.3 73.8 - - - +
827B ASP* 1.3 61.8 + - - +
829B ILE* 3.2 14.7 - - + +
830B LYS* 2.6 48.4 + - + +
833B PHE* 3.9 14.4 - - + -
877B GLY* 4.7 7.8 - - - +
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Residues in contact with ASP 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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825B SER 3.2 8.0 - - - +
826B LYS* 1.3 75.7 - - - +
828B GLU* 1.3 66.7 + - + +
829B ILE* 4.3 1.1 - - + +
830B LYS* 2.6 29.9 + - - +
831B GLU* 3.6 2.3 + - - +
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Residues in contact with GLU 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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827B ASP* 1.3 76.8 - - + +
829B ILE* 1.3 66.1 + - - +
830B LYS 3.0 0.9 + - - -
831B GLU* 3.1 21.0 + - - +
832B ARG 4.1 1.0 + - - -
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Residues in contact with ILE 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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735B TYR* 5.7 10.1 - - + -
826B LYS* 3.2 14.1 + - + +
827B ASP* 4.3 0.8 - - + +
828B GLU* 1.3 77.7 - - - +
830B LYS* 1.3 61.9 + - - +
832B ARG* 3.0 14.4 + - - +
833B PHE* 3.0 15.3 + - - +
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Residues in contact with LYS 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826B LYS* 2.6 39.7 + - + +
827B ASP 2.6 24.8 + - - +
829B ILE* 1.3 73.3 - - - +
831B GLU* 1.3 54.1 + - - +
833B PHE* 2.3 26.6 + - + +
834B ALA* 2.8 13.5 + - - +
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Residues in contact with GLU 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 ASP 3.6 1.9 + - - +
828B GLU* 3.1 14.1 + - - +
830B LYS* 1.3 78.8 - - - +
832B ARG* 1.3 63.0 + - - +
834B ALA* 3.5 12.3 + - - +
835B GLN* 3.7 9.2 + - - +
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Residues in contact with ARG 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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717B GLN* 4.1 25.8 - - + -
731B SER* 6.3 2.5 - - - -
828B GLU 4.1 0.6 + - - -
829B ILE* 3.0 13.0 + - - +
831B GLU* 1.3 79.4 - - - +
833B PHE* 1.3 63.4 + - - +
835B GLN* 3.0 18.6 + - - +
836B THR* 3.1 11.8 + - - -
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Residues in contact with PHE 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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826B LYS* 3.9 12.8 - - + -
829B ILE 3.0 6.5 + - - +
830B LYS* 2.3 36.8 + - + +
832B ARG* 1.3 69.5 - - - +
834B ALA* 1.3 55.7 + - - +
836B THR* 3.0 11.2 + - - -
837B MET* 2.9 28.3 + - - +
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Residues in contact with ALA 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 LYS 2.8 11.8 + - - +
831B GLU* 3.9 10.8 - - - +
832B ARG 3.2 0.2 - - - -
833B PHE* 1.3 72.2 - - - +
835B GLN* 1.3 57.9 + - - +
837B MET* 3.1 7.1 + - - +
838B GLU* 2.9 31.3 + - - +
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Residues in contact with GLN 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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720B LYS* 5.8 8.1 - - + -
831B GLU 3.7 6.5 + - - +
832B ARG* 3.0 11.8 + - - +
834B ALA* 1.3 78.5 - - - +
836B THR* 1.3 57.6 + - - +
838B GLU* 4.4 5.3 - - - +
839B PHE* 3.0 28.8 + - - +
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Residues in contact with THR 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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832B ARG 3.1 10.0 + - - -
833B PHE* 3.0 14.3 + - - -
835B GLN* 1.3 79.6 - - - +
837B MET* 1.3 57.1 + - - +
839B PHE* 3.8 5.1 - - - +
840B VAL* 2.9 26.4 + - - +
866B VAL* 6.4 2.9 - - - -
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Residues in contact with MET 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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833B PHE 2.9 15.2 + - - +
834B ALA* 3.8 6.5 - - - +
836B THR* 1.3 75.3 - - - +
838B GLU* 1.3 60.9 + - - +
840B VAL* 3.4 8.6 - - - +
841B GLU* 2.9 25.5 + - - +
890B ILE* 5.8 11.0 - - + +
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Residues in contact with GLU 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 ALA 2.9 15.7 + - - +
835B GLN* 4.4 4.7 - - - +
837B MET* 1.3 74.4 - - - +
839B PHE* 1.3 59.4 + - - +
841B GLU* 3.4 8.1 + - - +
842B GLU* 2.9 26.5 + - - +
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Residues in contact with PHE 839 (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 GLN 3.0 22.7 + - - +
836B THR* 3.9 7.0 - - - +
838B GLU* 1.3 75.5 - - - +
840B VAL* 1.3 56.9 + - - +
842B GLU* 3.2 10.1 + - - +
843B TYR* 2.8 24.9 + - - +
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Residues in contact with VAL 840 (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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836B THR 2.9 21.3 + - - +
837B MET* 3.4 11.2 - - - +
838B GLU 3.1 0.4 - - - -
839B PHE* 1.3 73.0 - - - +
841B GLU* 1.3 60.5 + - - +
842B GLU 3.1 1.1 - - - -
843B TYR* 3.0 11.6 + - - +
844B LEU* 2.9 26.3 + - - +
894B ILE* 6.1 0.5 - - - -
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Residues in contact with GLU 841 (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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837B MET 2.9 17.5 + - - +
838B GLU* 3.7 8.3 - - - +
840B VAL* 1.3 75.5 - - - +
842B GLU* 1.3 56.2 + - - +
844B LEU* 3.6 9.5 - - - +
845B ARG* 2.9 27.4 + - - +
890B ILE* 6.4 1.8 - - + -
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Residues in contact with GLU 842 (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 GLU 2.9 13.9 + - - +
839B PHE* 3.3 15.3 - - - +
840B VAL 3.1 0.4 - - - -
841B GLU* 1.3 75.7 - - - +
843B TYR* 1.4 56.3 + - - +
845B ARG* 3.8 7.0 - - - +
846B ASP* 3.0 27.5 + - - +
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Residues in contact with TYR 843 (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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839B PHE 2.8 12.7 + - - +
840B VAL* 3.0 15.0 + - - +
842B GLU* 1.4 75.0 - - - +
844B LEU* 1.3 60.8 + - - +
846B ASP* 3.8 14.5 + - - +
863B THR* 6.5 1.1 - - - -
898B VAL* 3.1 21.2 - - + +
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Residues in contact with LEU 844 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840B VAL 2.9 12.3 + - - +
841B GLU* 3.6 13.0 - - - +
843B TYR* 1.3 77.4 - - - +
845B ARG* 1.3 57.5 + - - +
847B VAL* 2.9 24.3 - - - +
848B VAL 4.5 0.3 + - - -
893B ALA 3.9 21.5 - - - +
894B ILE* 4.4 10.5 - - - +
897B CYS* 3.5 12.0 - - + +
898B VAL* 4.0 9.2 - - - -
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Residues in contact with ARG 845 (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 GLU 2.9 18.7 + - - +
842B GLU* 3.5 8.3 + - - +
843B TYR 3.4 0.4 - - - -
844B LEU* 1.3 70.6 - - - +
846B ASP* 1.3 61.5 + - - +
847B VAL 3.0 6.2 + - - -
848B VAL* 3.1 20.7 + - - +
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Residues in contact with ASP 846 (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 GLU 3.0 17.9 + - - +
843B TYR* 3.8 11.7 - - - +
844B LEU 3.4 0.4 - - - -
845B ARG* 1.3 74.4 - - - +
847B VAL* 1.3 60.8 + - - +
848B VAL* 3.1 1.4 + - - +
849B CYS* 3.3 14.6 + - - +
851B ARG* 3.6 21.1 - - + +
859B LYS* 6.3 2.9 - - + -
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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