Contacts of the helix formed by residues 866 - 883 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A VAL* 4.0 9.8 - - - +
858A GLU* 4.7 4.3 - - + +
864A ILE* 5.1 10.5 - - + -
865A TYR* 1.3 75.3 - - - +
867A ILE* 1.3 75.4 + - - +
868A LYS* 3.4 26.1 + - + +
869A SER* 3.1 40.1 + - - +
870A ASP* 3.6 10.0 + - - +
930A SER* 5.1 5.6 - - - -
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Residues in contact with ILE 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A MET* 4.2 13.2 - - + -
803A GLU* 3.6 54.1 - - + +
807A CYS 3.8 22.9 - - - +
808A VAL* 4.3 8.6 - - + +
866A THR* 1.3 87.2 + - - +
868A LYS* 1.3 69.5 + - + +
869A SER 3.1 0.7 - - - -
870A ASP* 3.3 16.0 + - - +
871A VAL* 3.3 13.5 + - + +
936A PHE* 3.5 17.3 - - + -
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Residues in contact with LYS 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A THR* 3.1 20.9 - - + +
867A ILE* 1.3 85.5 - - + +
869A SER* 1.3 61.8 + - - +
870A ASP 3.3 0.4 - - - -
871A VAL* 3.3 18.6 - - + +
930A SER* 3.2 28.4 + - - +
931A ARG* 3.8 28.4 - - - +
933A ARG* 3.2 44.4 + - + +
934A PRO 5.2 1.6 - - - +
935A SER* 5.5 9.0 - - - +
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Residues in contact with SER 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A ALA* 3.8 20.6 + - - +
858A GLU* 3.1 16.2 + - - +
859A SER* 3.9 9.9 - - - -
864A ILE 3.3 10.4 + - - -
865A TYR* 4.4 4.0 - - - -
866A THR* 3.1 34.7 + - - +
868A LYS* 1.3 77.3 - - - +
870A ASP* 1.3 65.1 + - - +
871A VAL 3.2 0.4 - - - -
872A TRP* 3.2 18.7 - - - +
873A SER* 3.3 9.0 + - - -
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Residues in contact with ASP 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A MET* 3.9 21.0 - - + +
808A VAL* 3.6 14.3 - - - +
809A HIS* 2.8 51.2 + - - +
812A LEU* 3.5 7.4 - - + +
865A TYR* 5.0 4.7 - - - -
866A THR 3.7 8.2 - - - +
867A ILE* 3.3 12.3 + - + +
869A SER* 1.3 78.1 - - - +
871A VAL* 1.3 55.7 + - - +
872A TRP 3.2 0.2 - - - -
873A SER* 3.1 11.9 + - - -
874A TYR* 2.7 33.8 + - - +
936A PHE* 3.6 2.7 - - + -
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Residues in contact with VAL 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A ILE 3.4 15.9 - - - +
868A LYS* 3.3 20.9 - - + +
870A ASP* 1.3 77.7 - - - +
872A TRP* 1.3 62.7 + - - +
874A TYR* 3.2 3.8 + - - +
875A GLY 3.0 17.5 + - - -
925A CYS* 3.2 36.9 - - + +
933A ARG* 3.9 9.9 - - + -
934A PRO* 3.4 28.3 - - + +
935A SER* 4.9 0.7 - - - -
936A PHE* 3.5 26.2 - - + +
939A LEU* 5.0 3.8 - - + -
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Residues in contact with TRP 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A LYS 4.9 1.6 + - - -
854A TRP 3.7 5.1 - - - -
855A MET 2.7 32.8 + - - +
856A ALA* 3.6 10.5 - - + -
857A PRO* 3.5 28.3 - - + -
868A LYS 3.7 2.2 + - - -
869A SER 3.2 10.9 + - - +
871A VAL* 1.3 79.3 - - - +
873A SER* 1.3 63.4 + - - +
875A GLY* 3.0 11.3 + - - -
876A ILE* 3.1 25.7 + - + +
889A TYR* 4.4 15.0 + - - -
902A ILE* 4.1 20.6 - - + -
905A GLY* 6.4 0.9 - - - -
906A PHE 4.9 9.4 - - - -
925A CYS 3.3 19.2 + - - +
926A TRP* 3.2 41.9 + + + -
927A ALA 3.9 5.4 - - - -
928A PHE* 4.7 2.0 - + - -
933A ARG* 3.5 26.0 - - - +
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Residues in contact with SER 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A HIS 5.6 0.3 + - - -
812A LEU* 3.7 36.0 + - - +
854A TRP* 2.5 28.1 + - - +
855A MET* 4.4 2.4 - - - -
869A SER 3.3 10.2 + - - -
870A ASP* 3.1 16.1 + - - -
872A TRP* 1.3 78.6 - - - +
874A TYR* 1.3 57.5 + - - +
876A ILE* 3.4 4.7 + - - +
877A LEU* 2.8 28.4 + - - +
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Residues in contact with TYR 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A ALA* 2.5 35.0 + - + +
795A VAL* 3.6 32.1 - - + -
796A ALA* 3.3 20.8 - - + +
799A MET* 5.0 0.4 - - + -
812A LEU* 3.8 8.0 - - + +
870A ASP 2.7 15.7 + - - +
871A VAL* 3.3 9.2 - - - +
873A SER* 1.3 72.4 - - - +
875A GLY* 1.3 55.1 + - - +
877A LEU* 3.4 10.7 - - + +
878A LEU* 2.5 62.5 + - + +
881A ILE* 6.3 0.9 - - + -
921A ILE* 5.0 2.2 - - + -
925A CYS* 4.4 7.2 - - - -
936A PHE* 3.7 22.4 - + + -
939A LEU* 3.5 24.7 - - + -
943A LEU* 4.0 7.8 - - + +
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Residues in contact with GLY 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A VAL 3.0 10.1 + - - -
872A TRP 3.0 1.4 + - - -
874A TYR* 1.3 78.0 - - - +
876A ILE* 1.3 59.1 + - - +
878A LEU* 3.3 9.9 + - - +
879A TRP 3.1 16.5 + - - -
922A MET* 3.8 6.4 - - - +
925A CYS* 3.9 16.4 - - - -
926A TRP* 3.3 31.4 - - - -
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Residues in contact with ILE 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853A LYS 3.2 28.7 - - - +
854A TRP* 3.5 22.7 - - + -
872A TRP* 3.1 29.5 + - + +
873A SER 3.7 5.4 - - - +
875A GLY* 1.3 72.8 - - - +
877A LEU* 1.3 64.1 + - - +
879A TRP* 3.1 13.1 + - - +
880A GLU* 3.3 13.9 + - - +
888A PRO* 3.6 23.1 - - + +
889A TYR* 4.1 22.4 - - + +
908A MET* 4.3 3.1 - - - -
926A TRP* 3.5 27.6 - - + +
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Residues in contact with LEU 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A LEU* 4.9 0.2 - - + -
795A VAL* 3.7 33.7 - - + -
812A LEU* 3.8 22.9 - - + +
813A ALA* 3.5 10.5 - - - +
814A ALA* 3.4 36.6 - - + +
817A VAL* 4.8 6.3 - - + -
854A TRP* 4.6 0.4 - - - -
873A SER 2.8 18.1 + - - +
874A TYR* 3.4 11.9 - - + +
876A ILE* 1.3 78.4 - - - +
878A LEU* 1.3 62.5 + - - +
880A GLU* 3.2 20.7 - - - +
881A ILE* 3.2 36.1 - - + +
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Residues in contact with LEU 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A ALA* 3.6 24.5 - - + -
874A TYR* 2.5 36.6 + - + +
875A GLY* 3.4 8.7 - - - +
876A ILE 3.2 0.2 - - - -
877A LEU* 1.3 73.8 - - - +
879A TRP* 1.3 60.9 + - - +
881A ILE* 3.5 6.1 + - + +
882A PHE* 3.1 58.5 + - + +
918A ILE* 4.3 10.8 - - + +
921A ILE* 3.6 31.4 - - + -
922A MET* 3.6 21.4 - - + +
943A LEU* 5.1 5.4 - - + -
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Residues in contact with TRP 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875A GLY 3.1 12.1 + - - +
876A ILE* 3.1 10.5 + - - +
878A LEU* 1.3 73.6 - - - +
880A GLU* 1.3 52.4 + - - +
881A ILE 3.0 4.7 - - - -
882A PHE* 3.0 5.0 + - - +
883A SER* 2.7 69.6 + - - -
886A VAL* 3.7 25.6 - - + -
887A ASN 3.6 19.5 - - - -
888A PRO* 3.9 9.2 - - + -
890A PRO* 4.0 14.6 - - + -
908A MET* 3.4 31.0 - - + +
909A ASP* 3.1 30.2 + - - -
910A GLN 5.6 0.4 - - - -
911A PRO* 3.4 32.4 - - + +
922A MET* 3.8 13.2 - - - -
926A TRP* 4.1 14.1 - + + -
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Residues in contact with GLU 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A LEU* 4.3 10.0 - - - +
703A LEU* 3.4 6.6 - - - +
814A ALA* 3.0 39.1 + - + +
854A TRP* 3.0 41.2 + - - -
876A ILE 3.3 6.9 + - - +
877A LEU* 3.2 23.0 - - - +
879A TRP* 1.3 78.4 - - + +
881A ILE* 1.3 59.2 + - - +
883A SER* 2.9 12.1 - - - -
884A LEU 3.3 0.5 + - - -
885A GLY* 2.7 33.5 + - - +
886A VAL 3.9 17.8 - - - +
888A PRO* 4.5 3.1 - - + +
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Residues in contact with ILE 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A LEU* 4.0 22.7 - - + -
703A LEU* 3.9 8.4 - - + +
788A LEU* 3.4 47.6 - - + +
791A PHE* 4.7 10.3 - - + -
792A ALA* 4.3 27.6 - - + +
795A VAL* 5.2 4.7 - - + -
874A TYR* 6.3 0.4 - - + -
877A LEU* 3.2 34.5 + - + +
878A LEU* 3.6 10.5 - - + +
879A TRP 3.0 0.6 - - - -
880A GLU* 1.3 80.1 - - - +
882A PHE* 1.3 70.3 + - + +
883A SER 3.6 0.3 + - - -
884A LEU* 3.6 12.1 + - - +
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Residues in contact with PHE 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785A PHE* 3.6 25.6 - + - -
788A LEU* 3.6 31.0 - - + -
789A LEU* 3.8 24.5 - - + -
792A ALA* 4.6 0.9 - - + -
878A LEU* 3.1 46.9 - - + +
879A TRP 3.0 3.1 + - - -
881A ILE* 1.3 81.5 - - + +
883A SER* 1.3 55.2 + - - +
884A LEU 3.4 2.9 - - - -
911A PRO* 3.5 10.7 - - + +
912A PHE 3.9 0.2 + - - -
913A TYR* 3.2 51.3 + - + +
914A ALA* 3.6 22.4 - - + +
918A ILE* 3.9 20.4 - - + -
922A MET* 5.1 0.2 - - + -
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Residues in contact with SER 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A ARG* 3.1 3.3 + - - -
879A TRP* 2.7 60.1 + - - -
880A GLU* 2.9 15.6 - - - -
882A PHE* 1.3 72.3 - - - +
884A LEU* 1.3 62.8 + - - +
886A VAL* 2.9 33.5 - - - +
911A PRO* 4.0 9.2 - - - -
912A PHE* 5.0 3.6 - - - +
913A TYR* 4.9 5.1 - - - -
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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
------------------------------------------------------------
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