Contacts of the helix formed by residues 898 - 915 (chain B) in PDB entry 2R4B
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 898 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840B VAL* 3.6 16.8 - - - +
890B GLU* 4.9 2.3 + - - -
896B LYS* 3.3 13.0 + - + +
897B PHE* 1.3 80.1 - - - +
899B HIS* 1.3 66.9 + - - +
900B GLN* 3.3 17.8 + - - +
901B SER* 2.7 27.9 + - - -
902B ASP 3.2 5.2 + - - -
961B ALA* 5.3 1.9 - - - +
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Residues in contact with HIS 899 (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 MET* 6.4 0.2 - - - +
835B GLU* 3.5 57.9 + - + +
838B ARG* 3.6 29.8 + - - -
839B LEU 3.1 41.7 + - - -
840B VAL* 3.9 9.3 - - + +
898B THR* 1.3 73.6 - - - +
900B GLN* 1.3 63.7 + - + +
902B ASP* 3.1 26.2 + - - +
903B VAL* 3.2 15.2 + - - +
967B PHE* 3.6 4.1 - - + -
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Residues in contact with GLN 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B GLU* 4.9 4.2 - - - +
898B THR* 3.1 10.5 + - - +
899B HIS* 1.3 82.1 - - + +
901B SER* 1.3 60.4 + - - +
903B VAL* 3.3 28.0 + - - +
904B TRP 3.4 1.7 + - - -
961B ALA* 3.0 42.5 + - + +
962B ASP* 4.5 6.3 - - - +
964B ARG* 2.9 45.0 + - - +
965B PRO 3.6 7.5 + - - +
966B LYS* 3.2 39.9 - - - +
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Residues in contact with SER 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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840B VAL* 4.8 0.7 - - - +
888B ALA* 3.5 21.4 + - - +
890B GLU* 3.6 9.1 + - - -
891B CYS* 3.6 14.2 - - - -
896B LYS 4.4 0.4 - - - -
897B PHE* 3.5 13.8 - - - -
898B THR* 2.7 39.2 + - - -
900B GLN* 1.3 73.7 - - - +
902B ASP* 1.3 62.2 + - - +
903B VAL 3.2 0.7 - - - -
904B TRP* 3.5 5.5 - - - +
905B SER* 3.2 22.7 + - - -
964B ARG* 3.7 8.3 - - - +
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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
----------------------------------------------------------
831B MET* 3.3 18.7 - - + +
839B LEU 4.6 0.9 - - - +
840B VAL* 3.5 17.1 - - - +
841B HIS* 2.9 27.2 + - - +
842B ARG* 3.1 27.4 + - - -
843B ASP 4.7 0.2 + - - -
844B LEU* 3.7 6.3 - - - +
897B PHE* 5.7 0.3 - - - -
898B THR 3.2 4.0 + - - -
899B HIS* 3.1 17.0 + - - +
901B SER* 1.3 75.9 + - - +
903B VAL* 1.3 58.7 + - - +
905B SER* 3.4 9.6 + - - -
906B TYR* 2.9 26.7 + - - +
967B PHE* 3.5 16.7 - - + -
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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
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899B HIS 3.2 14.1 + - - +
900B GLN* 3.4 20.2 - - - +
901B SER 3.2 0.6 - - - -
902B ASP* 1.3 76.1 - - - +
904B TRP* 1.3 66.0 + - - +
906B TYR* 3.1 5.3 + - - +
907B GLY 3.0 18.7 + - - -
956B CYS* 3.5 24.8 - - + +
964B ARG* 3.9 14.4 - - + -
965B PRO* 3.4 28.7 - - + +
967B PHE* 3.6 30.5 - - + +
970B LEU* 4.0 6.5 - - + -
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Residues in contact with TRP 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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885B LYS 5.0 1.4 + - - -
886B TRP 3.7 11.1 - - - -
887B MET 3.4 14.3 + - - -
888B ALA* 3.5 16.4 - - + -
889B LEU* 3.9 21.5 - - + -
900B GLN 3.4 3.8 + - - -
901B SER 3.5 11.2 - - - +
903B VAL* 1.3 77.6 - - - +
905B SER* 1.3 58.8 + - - +
907B GLY 2.9 17.8 + - - -
908B VAL* 3.1 26.7 + - + +
921B TYR* 4.7 6.4 + - - -
933B LEU* 3.8 30.1 - - + -
938B ARG* 4.0 16.8 - - - -
956B CYS 3.1 13.9 + - - +
957B TRP* 3.3 47.2 + + + -
958B MET 3.6 18.2 - - - -
959B ILE* 5.1 0.7 - - - -
964B ARG* 3.3 30.3 - - - +
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Residues in contact with SER 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 ARG 5.2 5.2 + - - -
843B ASP* 5.8 0.2 - - - -
844B LEU* 3.5 31.6 + - - +
886B TRP* 2.7 26.3 + - - +
887B MET* 4.6 2.6 - - - -
901B SER 3.2 11.9 + - - -
902B ASP* 3.4 13.0 + - - -
903B VAL 3.2 0.6 - - - -
904B TRP* 1.3 77.8 - - - +
906B TYR* 1.3 52.3 + - - +
908B VAL* 3.3 5.5 + - - +
909B THR* 2.7 38.2 + - - -
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Residues in contact with TYR 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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824B CYS* 2.5 29.3 + - - -
827B ILE* 3.7 21.8 - - + -
828B ALA* 3.5 31.9 - - + +
831B MET* 4.9 0.2 - - + -
844B LEU* 3.6 11.8 - - + +
902B ASP 2.9 14.9 + - - +
903B VAL 3.1 8.3 + - - +
905B SER* 1.3 76.3 - - - +
907B GLY* 1.3 57.5 + - - +
909B THR* 3.2 3.8 + - - -
910B ILE* 2.8 51.3 + - + +
956B CYS* 4.3 6.1 - - - -
967B PHE* 3.8 19.7 - + + -
970B LEU* 3.8 25.4 - - + -
974B PHE* 3.4 29.2 - + - -
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Residues in contact with GLY 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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903B VAL 3.0 6.9 + - - -
904B TRP 2.9 9.9 + - - -
906B TYR* 1.3 76.9 - - - +
908B VAL* 1.3 60.4 + - - +
910B ILE* 3.4 12.8 - - - +
911B TRP* 3.0 24.1 + - - +
953B MET* 4.1 2.9 - - - +
956B CYS* 3.9 15.9 - - - -
957B TRP* 3.4 19.7 - - - -
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Residues in contact with VAL 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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885B LYS 3.6 22.7 - - - +
886B TRP* 3.5 30.3 - - + +
904B TRP* 3.1 30.6 + - + +
905B SER 3.3 6.0 + - - +
907B GLY* 1.3 74.4 - - - +
909B THR* 1.3 57.1 + - - +
911B TRP* 3.3 6.1 - - - +
912B GLU* 3.0 26.9 + - - +
920B PRO* 3.8 17.7 - - + -
921B TYR* 5.2 1.8 - - - +
939B LEU* 4.0 13.7 - - + -
957B TRP* 3.7 15.5 - - + +
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Residues in contact with THR 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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827B ILE* 4.4 24.7 - - + -
844B LEU* 3.7 8.7 + - + +
845B ALA* 3.3 23.8 + - - +
846B ALA* 3.6 24.9 - - + +
849B VAL* 4.5 4.0 - - + -
886B TRP* 4.1 0.9 - - - -
905B SER 2.7 21.1 + - - -
906B TYR* 3.4 9.0 - - - -
908B VAL* 1.3 74.7 - - - +
910B ILE* 1.3 65.5 + - + +
912B GLU* 3.2 25.9 - - - +
913B LEU* 3.2 9.9 + - + +
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Residues in contact with ILE 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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824B CYS* 3.8 24.7 - - + -
827B ILE* 5.2 2.0 - - + -
906B TYR* 2.8 54.3 + - + +
907B GLY* 3.4 16.2 - - - +
909B THR* 1.3 73.4 - - + +
911B TRP* 1.3 60.7 + - - +
913B LEU* 3.2 12.9 + - + +
914B MET* 3.0 33.3 + - + +
952B VAL* 4.8 0.9 - - + -
953B MET* 3.6 32.3 - - + +
956B CYS* 5.6 0.4 - - - -
974B PHE* 3.4 33.7 - - + -
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Residues in contact with TRP 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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907B GLY 3.0 15.0 + - - +
908B VAL 3.3 11.4 - - - +
910B ILE* 1.3 76.1 - - - +
912B GLU* 1.3 69.3 + - - +
914B MET* 3.3 1.6 + - - +
915B THR* 3.0 44.2 + - + +
918B GLY* 3.6 17.0 - - - -
919B LYS 3.8 14.6 - - - -
920B PRO* 3.5 31.0 - - + -
921B TYR 5.0 0.4 - - - -
939B LEU* 3.7 34.9 - - + +
940B PRO* 2.8 49.7 + - + -
942B PRO* 3.7 18.7 - - + +
950B TYR* 5.3 0.2 - + - -
953B MET* 3.8 17.9 - - - -
957B TRP* 4.3 3.1 - + + -
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Residues in contact with GLU 912 (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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805B LEU* 3.6 25.7 - - + +
845B ALA* 5.1 0.2 - - - +
846B ALA* 2.8 39.6 + - + +
847B ARG* 4.6 1.7 + - - +
886B TRP* 2.9 41.0 + - + +
908B VAL 3.0 15.1 + - - +
909B THR* 3.2 13.6 - - - +
911B TRP* 1.3 77.1 - - + +
913B LEU* 1.3 55.4 + - - +
915B THR* 3.1 12.0 + - - -
917B GLY* 2.7 32.6 + - - -
918B GLY 3.8 15.8 - - - +
920B PRO* 4.4 5.4 - - + -
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Residues in contact with LEU 913 (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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804B LEU* 3.5 41.7 - - + -
808B VAL* 4.2 18.4 - - + +
820B LEU* 3.4 27.8 - - + +
823B TRP* 4.3 16.2 - - + -
824B CYS* 5.0 5.4 - - - -
827B ILE* 3.9 19.5 - - + -
846B ALA* 4.1 17.7 - - + -
909B THR* 3.4 12.1 - - + +
910B ILE* 3.2 15.5 + - + +
911B TRP 3.2 0.8 - - - -
912B GLU* 1.3 75.4 - - - +
914B MET* 1.3 62.5 + - + +
916B PHE* 2.9 22.2 + - - +
917B GLY 4.6 1.6 - - - +
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Residues in contact with MET 914 (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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820B LEU* 4.3 12.6 - - - +
821B LEU* 4.5 5.2 - - + -
824B CYS* 3.5 32.3 - - - -
910B ILE* 3.0 13.8 + - + +
911B TRP 3.8 3.6 - - - +
913B LEU* 1.3 77.2 - - + +
915B THR* 1.3 58.6 + - - +
916B PHE* 3.2 9.5 + - - -
942B PRO* 3.9 9.1 - - + +
943B PRO* 5.6 1.0 - - - +
944B ILE* 3.4 27.7 - - + +
945B CYS* 3.6 18.6 - - - -
949B VAL* 4.0 19.3 - - + -
953B MET* 3.1 27.6 - - + -
974B PHE* 4.7 1.3 - - + -
985B LEU* 3.8 32.5 - - + -
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Residues in contact with THR 915 (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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812B LYS* 5.3 3.3 + - - -
911B TRP* 3.0 47.1 + - + +
912B GLU* 3.1 4.0 + - - -
914B MET* 1.3 74.6 - - - +
916B PHE* 1.3 72.8 + - - +
917B GLY 3.5 0.3 + - - -
918B GLY* 2.9 36.0 + - - -
942B PRO* 3.9 21.5 - - + -
943B PRO* 5.3 4.7 - - + -
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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
------------------------------------------------------------
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