Contacts of the helix formed by residues 866 - 883 (chain B) in PDB entry 4XUF
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 866 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B VAL* 3.9 11.2 - - - +
858B GLU* 4.9 5.8 - - + +
864B ILE* 4.0 13.2 - - + +
865B TYR* 1.3 75.6 - - - +
867B ILE* 1.3 74.3 + - - +
868B LYS* 3.5 23.6 + - + +
869B SER* 3.1 37.3 + - - +
870B ASP* 3.6 10.2 + - - +
930B SER* 5.0 7.2 - - - -
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Residues in contact with ILE 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B MET* 4.9 4.0 - - + -
803B GLU* 3.7 42.8 - - + +
807B CYS 3.6 23.6 - - - +
808B VAL* 4.2 10.6 - - + +
866B THR* 1.3 86.1 + - - +
868B LYS* 1.3 69.7 + - + +
869B SER 3.1 0.2 - - - -
870B ASP* 3.3 20.5 + - - +
871B VAL* 3.5 2.3 + - - +
936B PHE* 3.2 44.9 - - + -
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Residues in contact with LYS 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803B GLU* 6.0 0.4 - - - +
866B THR* 3.2 16.8 - - + +
867B ILE* 1.3 85.8 - - + +
869B SER* 1.3 61.5 + - - +
870B ASP 3.3 0.2 - - - -
871B VAL* 3.3 20.0 - - + +
930B SER* 3.2 36.3 + - - +
931B ARG* 3.9 20.7 + - - +
933B ARG* 3.2 41.5 + - + +
934B PRO 5.4 2.2 - - - +
935B SER* 5.8 4.0 - - - -
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Residues in contact with SER 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B MET* 5.6 0.3 - - - -
856B ALA* 3.4 18.0 + - - +
858B GLU* 4.2 6.7 - - - -
859B SER* 3.1 24.2 + - - -
864B ILE 4.3 1.3 - - - -
865B TYR* 4.5 5.6 - - - -
866B THR* 3.1 34.3 + - - +
867B ILE 3.1 0.6 - - - -
868B LYS* 1.3 77.3 - - - +
870B ASP* 1.3 65.0 + - - +
871B VAL 3.2 0.4 - - - -
872B TRP* 3.2 19.6 - - - +
873B SER* 3.3 8.5 + - - -
933B ARG* 4.2 1.8 - - - +
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Residues in contact with ASP 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799B MET* 4.5 2.8 - - - +
808B VAL* 3.9 8.1 - - - +
809B HIS* 2.8 50.6 + - - +
810B ARG* 5.2 0.2 - - - -
812B LEU* 3.6 10.3 - - + +
865B TYR* 5.2 3.6 - - - -
866B THR 3.6 12.1 + - - +
867B ILE* 3.3 15.8 + - - +
869B SER* 1.3 78.2 + - - +
871B VAL* 1.3 55.4 + - - +
872B TRP 3.2 0.7 - - - -
873B SER* 3.1 12.2 + - - -
874B TYR* 2.6 35.7 + - - +
936B PHE* 3.7 15.7 - - + -
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Residues in contact with VAL 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B ILE 3.7 4.7 - - - +
868B LYS* 3.3 30.5 - - + +
869B SER 3.2 0.2 - - - -
870B ASP* 1.3 77.9 - - - +
872B TRP* 1.3 57.6 + - - +
874B TYR* 3.2 8.1 + - - +
875B GLY 2.9 22.7 + - - -
925B CYS* 3.2 37.2 - - + +
933B ARG* 3.9 9.6 - - + -
934B PRO* 3.4 29.4 - - + +
935B SER* 5.0 0.7 - - - -
936B PHE* 4.1 20.8 - - + +
939B LEU* 4.9 3.6 - - + -
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Residues in contact with TRP 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853B LYS 5.1 0.8 + - - -
854B TRP 3.6 7.4 - - - -
855B MET 2.7 34.2 + - - +
856B ALA* 3.5 13.2 - - + -
857B PRO* 3.5 33.9 - - + -
868B LYS 3.8 1.6 + - - -
869B SER 3.2 11.3 + - - +
871B VAL* 1.3 78.9 - - - +
873B SER* 1.3 57.1 + - - +
875B GLY* 3.0 3.6 + - - -
876B ILE* 2.9 39.6 + - + +
889B TYR* 4.0 17.6 + - - -
902B ILE* 4.5 16.2 - - + -
905B GLY 6.5 0.4 - - - -
906B PHE 4.9 8.1 - - - -
907B LYS* 6.0 0.9 - - + -
925B CYS 3.3 14.2 + - - +
926B TRP* 3.2 55.7 + + + -
927B ALA 4.2 4.5 - - - -
928B PHE* 4.9 1.3 - + - -
933B ARG* 3.7 13.0 - - - +
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Residues in contact with SER 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B HIS 5.5 0.5 + - - -
810B ARG 5.7 0.7 + - - -
812B LEU* 3.7 37.3 + - - +
854B TRP* 2.7 25.8 + - - +
855B MET* 4.5 3.5 - - - +
869B SER* 3.3 9.3 + - - -
870B ASP* 3.1 16.8 + - - -
872B TRP* 1.3 78.4 - - - +
874B TYR* 1.3 57.4 + - - +
876B ILE* 3.4 4.6 + - - +
877B LEU* 2.8 28.4 + - - +
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Residues in contact with TYR 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B ALA* 2.3 36.0 + - + +
795B VAL* 3.6 20.9 - - + -
796B ALA* 3.2 36.1 - - + +
799B MET* 5.5 0.2 - - + -
812B LEU* 3.8 11.2 - - + +
870B ASP 2.6 19.9 + - - +
871B VAL* 3.4 9.2 - - - +
872B TRP 3.1 0.2 - - - -
873B SER* 1.3 74.0 - - - +
875B GLY* 1.3 54.1 + - - +
877B LEU* 3.2 8.0 + - + +
878B LEU* 2.6 63.8 + - + +
925B CYS* 4.5 5.8 - - - -
936B PHE* 4.4 15.3 - + + -
939B LEU* 4.1 25.1 - - + -
943B LEU* 3.9 6.7 - - + +
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Residues in contact with GLY 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B VAL 2.9 13.6 + - - -
872B TRP 3.0 1.0 + - - -
874B TYR* 1.3 79.2 - - - +
876B ILE* 1.3 59.6 + - - +
878B LEU* 3.3 15.1 + - - +
879B TRP 3.2 14.2 + - - -
922B MET* 4.1 3.8 - - - +
925B CYS* 4.0 11.9 - - - -
926B TRP* 3.2 32.6 - - - -
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Residues in contact with ILE 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853B LYS 3.4 25.6 - - - +
854B TRP* 3.5 28.0 - - + +
872B TRP* 2.9 35.6 + - + +
873B SER 3.7 6.1 - - - +
875B GLY* 1.3 72.9 - - - +
877B LEU* 1.3 67.4 + - - +
879B TRP* 3.1 18.4 + - + +
880B GLU* 3.3 7.6 + - - +
888B PRO* 4.0 16.4 - - + -
889B TYR* 4.0 18.8 - - + +
908B MET* 4.7 3.6 - - - -
926B TRP* 3.5 27.6 - - + +
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Residues in contact with LEU 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B LEU* 5.2 3.8 - - + -
795B VAL* 4.4 23.8 - - + -
812B LEU* 3.8 22.9 - - + -
813B ALA* 3.3 36.3 - - - +
814B ALA* 4.2 6.3 - - + +
817B VAL* 4.7 5.8 - - + -
854B TRP* 4.7 2.0 - - - -
873B SER 2.8 15.1 + - - +
874B TYR* 3.3 13.9 - - + +
876B ILE* 1.3 75.2 - - - +
878B LEU* 1.3 66.3 + - - +
880B GLU* 2.8 24.0 + - - +
881B ILE* 3.1 40.3 + - + -
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Residues in contact with LEU 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B ALA* 3.6 31.2 - - + -
874B TYR* 2.6 52.0 + - + +
875B GLY* 3.3 14.6 - - - +
876B ILE 3.2 0.2 - - - -
877B LEU* 1.3 75.8 - - - +
879B TRP* 1.3 60.4 + - - +
881B ILE* 3.4 4.7 + - + -
882B PHE* 3.2 41.0 + - + -
918B ILE* 5.1 6.7 - - + +
921B ILE* 3.7 27.1 - - + -
922B MET* 3.2 23.0 - - + +
925B CYS* 4.8 1.3 - - - -
943B LEU* 5.1 4.3 - - + -
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Residues in contact with TRP 879 (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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875B GLY 3.2 7.6 + - - +
876B ILE* 3.1 14.1 + - + +
877B LEU 3.0 0.4 - - - -
878B LEU* 1.3 80.1 - - - +
880B GLU* 1.3 56.4 + - + +
881B ILE 3.1 0.5 + - - -
882B PHE 3.1 2.3 + - - -
883B SER* 2.6 72.3 + - - -
886B VAL* 3.4 35.4 - - + -
887B ASN 3.8 7.6 - - - -
888B PRO* 3.9 9.9 - - + -
890B PRO* 3.7 25.8 - - + -
908B MET* 3.4 29.1 - - + +
909B ASP 3.5 19.8 + - - -
910B GLN 4.7 0.2 - - - -
911B PRO* 3.3 32.7 - - + +
922B MET* 3.7 10.7 - - - +
926B TRP* 4.3 10.5 - + + -
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Residues in contact with GLU 880 (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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700B LEU* 3.8 19.8 - - - +
703B LEU* 3.6 8.3 - - - +
704B ARG* 5.1 1.0 + - - -
814B ALA* 3.3 34.4 + - + +
815B ARG* 5.2 0.2 + - - -
841B ASN* 5.5 0.2 + - - -
854B TRP* 3.0 44.7 + - - -
876B ILE 3.3 3.7 + - - +
877B LEU* 2.8 14.5 + - - +
879B TRP* 1.3 76.0 - - + +
881B ILE* 1.3 60.4 + - - +
883B SER* 3.4 7.4 - - - -
885B GLY* 2.9 29.4 + - - +
886B VAL 3.7 18.6 - - - +
887B ASN* 4.9 0.9 - - - -
888B PRO* 3.8 14.0 - - + +
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Residues in contact with ILE 881 (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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699B LEU* 4.2 20.6 - - + -
703B LEU* 4.0 9.1 - - + +
788B LEU* 3.7 38.7 - - + +
791B PHE* 4.5 6.3 - - + -
792B ALA* 3.8 32.3 - - + +
795B VAL* 5.3 1.1 - - + -
814B ALA* 5.9 0.4 - - + -
877B LEU* 3.1 37.2 + - + +
878B LEU* 3.5 10.5 - - - +
879B TRP 3.0 1.0 - - - -
880B GLU* 1.3 80.8 - - + +
882B PHE* 1.3 72.2 + - + +
883B SER 3.3 1.6 + - - -
884B LEU* 3.6 18.5 + - - +
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Residues in contact with PHE 882 (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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785B PHE* 3.5 24.9 - + - -
788B LEU* 4.0 32.3 - - + -
789B LEU* 3.5 26.2 - - + -
792B ALA* 4.5 3.4 - - + -
878B LEU* 3.2 36.6 - - + +
879B TRP 3.1 3.5 + - - -
881B ILE* 1.3 86.0 - - + +
883B SER* 1.3 59.0 + - - +
884B LEU 3.4 1.1 - - - -
911B PRO* 3.4 10.4 - - + +
912B PHE 3.9 0.2 + - - -
913B TYR* 3.3 52.2 + - - -
914B ALA* 3.8 20.4 - - + +
918B ILE* 4.1 15.3 - - + -
922B MET* 4.1 7.9 - - + -
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Residues in contact with SER 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B ARG* 4.2 2.4 + - - -
879B TRP* 2.6 65.6 + - - -
880B GLU* 3.4 6.4 - - - -
882B PHE* 1.3 78.4 - - - +
884B LEU* 1.3 69.3 + - - +
886B VAL* 3.2 23.0 + - - +
911B PRO* 4.3 6.7 - - - -
912B PHE* 5.1 2.5 - - - +
913B TYR* 4.7 5.9 - - - -
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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
------------------------------------------------------------
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