Contacts of the helix formed by residues 905 - 926 (chain B) in PDB entry 3U3F
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 GLY 905 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B LEU* 4.3 8.8 - - - +
902B PRO* 2.7 21.7 + - - +
904B GLU* 1.3 70.5 - - - +
906B TYR* 1.3 64.9 + - - -
907B VAL 3.1 2.9 - - - -
908B VAL* 3.0 22.1 + - - +
909B VAL* 3.4 14.2 + - - +
901D LEU* 4.1 23.7 - - - +
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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
----------------------------------------------------------
898B LEU* 3.7 37.1 + - + -
901B LEU* 3.7 28.2 + - + -
902B PRO 4.0 5.6 - - - -
903B PRO* 3.2 41.9 + - + +
905B GLY* 1.3 76.8 - - - +
907B VAL* 1.3 63.0 + - - +
909B VAL* 3.0 24.0 - - + +
910B VAL* 3.3 13.0 + - - +
957B MET* 3.7 18.2 - - + -
960B ALA* 4.5 25.1 - - + -
961B GLN* 4.4 10.1 - - + -
973B LYS* 3.8 25.2 - - + +
976B MET* 4.7 7.6 - - + -
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Residues in contact with VAL 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B GLU* 3.5 13.5 - - - +
905B GLY 3.1 0.2 - - - -
906B TYR* 1.3 78.3 - - - +
908B VAL* 1.3 58.9 + - + +
910B VAL* 3.5 2.8 + - - +
911B LYS* 2.9 51.7 + - - +
957B MET* 4.0 8.9 - - + +
958B ARG* 4.0 15.0 - - - +
961B GLN* 3.0 27.8 - - - +
274F LEU* 4.1 23.0 - - + +
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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
----------------------------------------------------------
904B GLU 5.2 1.3 - - - +
905B GLY* 3.0 17.4 + - - +
907B VAL* 1.3 77.1 - - + +
909B VAL* 1.3 67.9 + - - +
911B LYS* 2.9 27.8 + - - +
912B ASN* 3.1 9.5 + - - -
893D GLU* 5.3 0.4 - - - +
897D GLU* 3.1 30.7 - - + +
901D LEU* 5.1 4.0 - - + -
908D VAL* 3.7 25.8 - - + -
909D VAL* 3.9 6.7 - - + +
912D ASN* 3.2 30.4 - - - +
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Residues in contact with VAL 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B LEU* 3.7 25.4 - - + -
897B GLU* 3.6 26.0 - - + +
898B LEU* 4.3 7.0 - - + -
901B LEU* 3.4 32.3 - - + -
905B GLY 3.4 1.7 + - - +
906B TYR* 3.0 23.3 - - + +
908B VAL* 1.3 77.4 - - - +
910B VAL* 1.3 62.4 - - + +
912B ASN* 3.0 30.5 - - - +
913B VAL* 3.2 12.1 + - - +
976B MET* 5.0 0.9 - - + -
908D VAL* 4.7 9.0 - - + -
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Residues in contact with VAL 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894B LEU* 4.2 2.2 - - + -
906B TYR 3.3 17.4 + - - +
907B VAL 3.9 2.7 - - - +
908B VAL 3.1 0.4 - - - -
909B VAL* 1.3 76.5 - - + +
911B LYS* 1.3 60.8 + - - +
912B ASN 3.0 1.6 - - - -
913B VAL* 3.2 6.1 + - - +
914B GLY* 2.7 28.8 + - - -
950B LEU* 4.6 4.7 - - + -
953B LEU* 4.0 25.1 - - + -
954B ILE* 4.0 20.0 - - + -
957B MET* 4.0 11.9 - - + -
976B MET* 3.7 26.7 - - + -
271F MET* 4.5 0.5 - - - +
274F LEU* 4.0 17.5 - - + -
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Residues in contact with LYS 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B VAL* 2.9 37.8 + - - +
908B VAL* 2.9 17.6 + - - +
910B VAL* 1.3 74.8 - - - +
912B ASN* 1.3 56.9 + - - +
914B GLY* 3.4 1.4 + - - -
915B LEU* 2.8 38.0 + - + +
893D GLU* 2.8 38.6 + - - +
912D ASN* 3.3 17.5 - - - +
271F MET* 3.9 6.8 - - + +
274F LEU* 2.7 49.7 + - + +
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Residues in contact with ASN 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B ALA* 5.1 6.1 - - + -
893B GLU* 5.6 1.0 + - - -
897B GLU* 5.8 1.8 + - - -
908B VAL 3.1 7.3 + - - -
909B VAL* 3.0 12.6 + - - +
911B LYS* 1.3 73.7 - - - +
913B VAL* 1.3 69.8 + - + +
914B GLY 3.0 1.1 - - - -
915B LEU* 2.8 12.5 + - - +
916B THR* 2.8 20.3 + - + +
908D VAL* 3.7 19.2 + - - +
911D LYS* 4.0 20.6 - - - +
912D ASN* 2.5 38.2 + - - +
915D LEU* 3.5 23.2 - - + +
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Residues in contact with VAL 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B LEU* 3.7 5.3 - - + +
890B ALA* 4.0 28.0 - - + +
891B VAL* 4.4 15.0 - - + +
894B LEU* 4.1 18.6 - - + -
909B VAL 3.2 13.6 + - - +
910B VAL* 3.7 7.6 - - - +
912B ASN* 1.3 78.4 - - + +
914B GLY* 1.3 63.5 + - - +
916B THR* 3.2 7.8 + - - -
917B LEU* 3.1 25.8 + - - +
950B LEU* 4.7 1.6 - - + -
953B LEU* 4.4 11.9 - - + -
980B SER* 5.9 0.7 - - - -
983B LEU* 3.6 30.5 - - + -
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Residues in contact with GLY 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910B VAL 2.7 18.9 + - - -
911B LYS 3.5 4.0 - - - -
913B VAL* 1.3 74.6 - - - +
915B LEU* 1.3 54.8 + - - +
917B LEU* 3.4 4.5 + - - +
918B ARG* 3.1 25.8 + - - +
950B LEU* 4.2 16.9 - - - +
267F LEU* 4.3 2.3 - - - +
271F MET* 3.5 26.1 - - - +
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Residues in contact with LEU 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911B LYS* 2.8 27.0 + - + +
912B ASN 2.8 7.7 + - - +
914B GLY* 1.3 70.5 - - - -
916B THR* 1.3 63.6 + - - +
918B ARG* 3.1 17.1 + - - +
919B LYS* 3.3 14.7 + - - +
886D GLU* 5.3 0.4 - - - +
912D ASN* 4.3 16.4 - - + +
915D LEU* 4.1 29.6 - - + +
916D THR* 3.7 26.5 - - + -
919D LYS* 3.2 35.9 + - - +
271F MET* 5.2 12.6 - - + -
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Residues in contact with THR 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883B ASN* 4.8 5.2 - - - +
886B GLU* 4.3 18.2 - - + +
887B LEU* 3.7 22.8 - - - +
890B ALA* 3.9 15.9 - - + +
912B ASN* 2.8 20.6 + - + +
913B VAL* 3.2 11.1 + - - -
915B LEU* 1.3 71.5 - - - +
917B LEU* 1.3 64.9 + - - +
919B LYS* 3.3 12.5 + - - +
920B LEU* 3.2 19.2 + - - +
911D LYS* 5.9 4.7 - - - +
915D LEU* 3.7 28.5 - - + -
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Residues in contact with LEU 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887B LEU* 3.5 17.3 - - + -
913B VAL 3.1 18.9 + - - +
914B GLY 3.5 2.9 - - - +
916B THR* 1.3 76.4 + - - +
918B ARG* 1.3 59.3 + - - +
920B LEU* 3.3 11.3 + - + -
921B ILE* 2.9 48.7 + - + +
946B LEU* 4.0 28.7 - - + +
947B ASN* 4.7 0.7 - - - +
950B LEU* 4.0 27.1 - - + -
983B LEU* 4.6 11.0 - - + -
267F LEU* 3.8 26.9 - - + -
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Residues in contact with ARG 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914B GLY 3.1 10.5 + - - +
915B LEU* 3.1 13.9 + - - +
917B LEU* 1.3 77.3 - - - +
919B LYS* 1.3 57.0 + - - +
921B ILE* 3.8 2.3 - - - +
922B GLY* 2.8 26.7 + - - -
879D LEU* 5.5 9.9 - - - +
883D ASN* 5.6 0.8 - - - +
886D GLU* 6.1 0.2 - - - -
919D LYS* 3.4 45.0 - - - +
264F THR* 4.4 18.7 - - + +
267F LEU* 3.4 28.7 - - + -
268F ASP* 2.9 39.3 + - - -
271F MET* 5.8 3.8 - - - -
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Residues in contact with LYS 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883B ASN* 3.3 22.6 - - + +
886B GLU* 2.6 42.3 + - - +
915B LEU 3.3 9.5 + - - +
916B THR* 3.3 10.3 - - - +
918B ARG* 1.3 79.4 - - - +
920B LEU* 1.3 58.1 + - - +
922B GLY* 2.9 3.0 + - - -
923B SER* 2.8 30.3 + - - -
915D LEU* 4.6 13.9 - - + +
918D ARG* 3.3 50.6 - - + +
268H ASP* 5.0 2.6 + - - -
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Residues in contact with LEU 920 (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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880B VAL* 3.8 11.0 - - + +
883B ASN* 3.5 20.3 - - + +
884B VAL* 3.6 34.8 - - + -
887B LEU* 4.1 24.7 - - + -
916B THR 3.2 7.0 + - - +
917B LEU* 3.4 17.9 - - + +
919B LYS* 1.3 78.6 - - - +
921B ILE* 1.3 65.4 - - - +
922B GLY 2.9 0.3 + - - -
923B SER* 2.9 19.3 + - - +
924B VAL* 2.9 17.6 + - + +
946B LEU* 4.5 5.4 - - + -
987B ALA* 4.5 2.5 - - + -
990B LEU* 3.8 28.3 - - + -
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Residues in contact with ILE 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917B LEU* 2.9 40.6 + - + +
918B ARG* 4.1 4.7 - - - +
920B LEU* 1.3 78.9 - - + +
922B GLY* 1.3 56.5 + - - +
924B VAL* 4.5 1.6 - - - -
925B ASP* 3.1 32.1 + - - +
943B GLN* 3.4 36.9 + - + +
946B LEU* 4.8 6.5 - - + -
947B ASN* 3.2 30.1 - - - +
990B LEU* 5.7 0.9 - - + -
263F ALA* 3.9 20.0 - - + -
264F THR* 4.4 11.7 - - + +
267F LEU* 4.3 7.4 - - + -
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Residues in contact with GLY 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918B ARG 2.8 17.9 + - - -
919B LYS* 3.3 4.3 - - - -
920B LEU 2.9 0.2 - - - -
921B ILE* 1.3 76.0 - - - +
923B SER* 1.3 59.4 + - - +
925B ASP* 3.3 9.3 - - - +
926B ASP* 3.1 33.1 + - - +
264F THR* 5.1 7.0 - - - -
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Residues in contact with SER 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B LEU* 4.4 21.8 - - - -
880B VAL* 4.1 15.1 - - - +
883B ASN* 2.7 27.4 + - - -
919B LYS 2.8 6.4 + - - -
920B LEU* 2.9 13.5 + - - -
922B GLY* 1.3 73.3 - - - +
924B VAL* 1.3 66.0 + - - +
926B ASP* 3.1 27.0 + - - +
927B LEU* 3.6 9.0 + - - +
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Residues in contact with VAL 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B VAL* 3.8 29.6 - - + +
920B LEU* 2.9 19.6 + - + +
921B ILE 4.4 0.2 - - - -
923B SER* 1.3 78.3 + - - +
925B ASP* 1.3 52.8 + - - +
927B LEU* 2.8 28.9 + - + +
928B LEU* 2.9 22.9 - - + +
939B ILE* 4.3 13.5 - - + -
943B GLN* 3.4 27.6 - - + +
990B LEU* 3.8 29.4 - - + -
994B VAL* 4.6 9.0 - - + -
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Residues in contact with ASP 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B ILE* 3.1 27.9 + - - +
922B GLY* 3.3 8.5 - - - +
924B VAL* 1.3 75.9 - - - +
926B ASP* 1.3 60.0 + - - +
927B LEU 3.1 4.3 + - - -
928B LEU* 3.6 20.1 + - - +
929B PRO* 3.9 5.7 - - - +
943B GLN* 3.7 16.2 + - - +
262F SER 5.3 4.8 + - - -
263F ALA* 4.2 10.2 + - - +
264F THR* 3.5 25.1 + - + +
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Residues in contact with ASP 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922B GLY 3.1 17.3 - - - +
923B SER* 3.4 18.0 - - - +
924B VAL 3.1 1.2 - - - -
925B ASP* 1.3 77.1 - - - +
927B LEU* 1.3 60.9 + - + +
929B PRO* 3.6 15.5 - - - +
930B SER* 5.3 0.5 + - - -
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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
------------------------------------------------------------
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