Contacts of the helix formed by residues 859 - 877 (chain A) in PDB entry 4BIC
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 859 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800A VAL* 3.5 17.0 - - - +
829A LEU* 4.0 8.1 - - - -
857A GLY 3.4 5.0 + - - -
858A TYR* 1.3 74.7 - - - +
860A LYS* 1.3 66.3 - - - -
861A ALA* 3.1 4.0 - - - -
862A ALA* 2.9 21.8 + - - +
863A ASP* 3.9 2.1 + - - -
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Residues in contact with LYS 860 (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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795A HIS* 3.1 86.0 + - + +
796A ASP* 4.9 3.6 + - - +
798A GLN* 3.3 23.4 + - - +
800A VAL* 3.4 5.3 - - + +
829A LEU* 3.9 21.2 - - + +
859A GLY* 1.3 70.1 - - - -
861A ALA* 1.4 60.2 + - - +
863A ASP* 3.3 10.3 + - - +
864A ILE* 3.6 7.1 - - - +
928A CYS* 6.5 0.7 - - + -
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Residues in contact with ALA 861 (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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849A GLU* 4.3 0.4 - - - +
859A GLY* 2.9 1.9 + - - -
860A LYS* 1.4 75.4 - - - +
862A ALA* 1.3 63.7 + - - +
864A ILE* 3.1 22.2 + - - +
865A TRP 3.2 5.7 + - - -
923A PRO* 3.5 33.2 - - + +
926A ARG* 2.9 35.0 + - + +
927A ALA 5.4 0.7 - - - -
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Residues in contact with ALA 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A ALA* 3.9 25.4 + - + +
849A GLU* 3.9 4.3 + - - +
850A ILE* 4.1 8.7 - - + -
858A TYR* 3.7 31.6 - - + -
859A GLY 2.9 16.3 + - - +
861A ALA* 1.3 76.7 - - - +
863A ASP* 1.4 58.5 + - - +
865A TRP* 3.4 3.8 + - - +
866A SER* 3.1 30.8 + - - -
926A ARG* 3.8 0.4 - - - +
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Residues in contact with ASP 863 (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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791A LEU* 3.8 16.5 - - + +
795A HIS* 2.7 28.7 + - + +
800A VAL* 3.5 8.5 - - - +
801A HIS* 2.8 30.5 + - - +
802A ARG* 2.9 30.0 + - - -
804A ILE* 4.2 7.2 - - + +
858A TYR* 5.7 0.2 - - - -
859A GLY 3.9 1.1 + - - -
860A LYS 3.3 11.5 + - - +
861A ALA 3.2 0.6 - - - -
862A ALA* 1.4 74.8 - - - +
864A ILE* 1.3 55.9 + - - +
866A SER* 3.3 7.2 + - - -
867A LEU* 2.7 34.6 + - - +
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Residues in contact with ILE 864 (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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788A LEU* 4.5 3.8 - - + -
791A LEU* 4.5 10.5 - - + -
795A HIS* 4.2 17.3 - - + -
860A LYS 3.6 12.3 - - - +
861A ALA* 3.1 11.8 + - - +
863A ASP* 1.3 73.7 - - - +
865A TRP* 1.3 57.8 + - - +
867A LEU* 3.3 7.0 + - + +
868A GLY 2.9 22.2 + - - -
917A LYS 4.8 0.4 - - - +
918A CYS* 3.5 23.6 - - - +
926A ARG* 4.2 6.5 - - + -
927A ALA 3.5 26.0 - - - +
928A CYS* 4.6 3.1 - - - -
929A ALA* 4.0 27.1 - - + +
932A LEU* 3.6 22.7 - - + -
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Residues in contact with TRP 865 (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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844A GLN 5.4 0.4 + - - -
845A TYR 3.2 19.9 - - - -
846A MET 3.4 11.1 + - - -
847A ALA* 3.5 19.5 - - + -
848A PRO* 3.6 27.6 - - + -
861A ALA 3.2 5.7 + - - -
862A ALA 3.6 8.3 - - - +
863A ASP 3.3 0.2 - - - -
864A ILE* 1.3 76.8 - - - +
866A SER* 1.4 55.3 + - - +
868A GLY* 3.0 16.8 + - - -
869A CYS* 3.1 25.3 + - - -
881A PHE* 5.4 1.2 - + - -
894A VAL* 3.5 17.4 - - + +
898A LYS 4.2 7.4 - - - -
899A VAL 3.2 32.1 - - - -
900A HIS* 4.1 6.1 - - + -
901A PRO* 5.3 1.1 - - + -
918A CYS 3.5 19.6 + - - +
919A PHE* 3.4 50.7 - + - -
920A GLU 4.5 2.0 - - - -
921A PRO* 4.8 0.7 - - + -
926A ARG* 4.1 14.6 - - - +
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Residues in contact with SER 866 (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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802A ARG 5.5 3.6 + - - -
803A ASP* 5.6 0.3 - - - -
804A ILE* 3.3 33.7 + - - -
845A TYR* 2.8 26.7 + - - +
846A MET* 4.9 1.6 - - - -
847A ALA 5.0 0.3 + - - -
862A ALA 3.1 13.0 + - - -
863A ASP* 3.5 10.4 + - - -
865A TRP* 1.4 74.2 - - - +
867A LEU* 1.3 64.9 + - - +
869A CYS* 3.2 7.5 + - - +
870A THR* 3.0 26.6 + - - -
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Residues in contact with LEU 867 (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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784A THR* 4.5 13.7 - - + -
787A ILE* 3.7 41.7 - - + -
788A LEU* 3.7 36.8 - - + -
791A LEU* 4.4 7.2 - - + -
804A ILE* 4.0 8.2 - - + +
863A ASP 2.7 18.1 + - - +
864A ILE* 3.3 14.4 - - + +
866A SER* 1.3 71.4 - - - +
868A GLY* 1.3 52.6 + - - +
870A THR* 2.8 25.8 + - - -
871A ILE* 2.9 25.0 + - + +
914A PHE* 5.2 0.4 - - + -
918A CYS* 4.2 18.4 - - - -
932A LEU* 4.4 5.8 - - + -
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Residues in contact with GLY 868 (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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864A ILE 2.9 11.3 + - - -
865A TRP 3.0 6.1 + - - -
867A LEU* 1.3 75.8 - - - +
869A CYS* 1.3 56.4 + - - +
871A ILE* 3.4 9.6 + - - +
872A ILE* 3.1 29.8 + - - +
915A ILE* 4.4 3.0 - - - +
918A CYS* 3.7 24.7 - - - +
919A PHE* 3.3 14.1 - - - -
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Residues in contact with CYS 869 (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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844A GLN 3.9 13.9 - - - -
845A TYR* 3.6 22.9 - - + -
865A TRP* 3.1 43.3 + - - -
866A SER 3.2 7.2 + - - +
868A GLY* 1.3 71.5 - - - +
870A THR* 1.4 59.3 + - - +
872A ILE* 3.4 7.8 + - - +
873A GLU* 3.0 26.0 + - - +
880A PRO* 3.7 16.5 - - + +
881A PHE* 5.5 0.7 - - - -
901A PRO* 4.6 9.0 - - - -
919A PHE* 3.8 12.8 - - - -
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Residues in contact with THR 870 (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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762A LEU* 3.8 25.6 - - + -
787A ILE* 4.0 19.5 - - + -
804A ILE* 3.9 5.0 - - + +
805A LYS* 3.4 27.6 + - - +
806A GLY* 4.2 10.3 - - - +
809A VAL* 5.4 1.3 - - + -
845A TYR* 3.8 1.6 - - - -
866A SER 3.0 11.7 + - - -
867A LEU* 2.8 20.8 + - - -
869A CYS* 1.4 68.6 - - - +
871A ILE* 1.4 57.6 + - - +
873A GLU* 3.2 11.0 + - - +
874A MET* 2.8 31.9 + - + +
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Residues in contact with ILE 871 (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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780A ILE* 3.7 24.4 - - + +
784A THR* 3.7 23.1 - - + +
867A LEU* 2.9 22.8 + - + +
868A GLY* 3.4 12.3 + - - +
870A THR* 1.4 73.8 - - - +
872A ILE* 1.4 51.8 + - - +
874A MET* 3.2 11.7 + - + +
875A ALA* 2.8 33.2 + - - +
907A MET* 5.4 1.6 - - + -
914A PHE* 3.6 35.0 - - + -
915A ILE* 3.7 31.0 - - + -
918A CYS* 4.6 3.4 - - - -
937A PHE* 5.7 2.5 - - + -
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Residues in contact with ILE 872 (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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868A GLY 3.1 18.1 + - - +
869A CYS* 3.7 9.0 - - - +
870A THR 3.3 0.2 - - - -
871A ILE* 1.4 77.3 - - - +
873A GLU* 1.3 50.2 + - - +
875A ALA* 3.6 2.4 - - + -
876A THR* 2.8 52.4 + - + +
879A PRO 5.5 0.2 - - - +
880A PRO* 4.4 12.3 - - + -
881A PHE 5.4 0.2 - - - +
901A PRO* 3.8 28.5 - - + +
902A GLU 3.5 25.1 - - - +
903A ILE* 3.8 22.0 - - + -
904A PRO* 4.2 7.2 - - + -
915A ILE* 4.3 11.9 - - + -
919A PHE* 4.0 15.3 - - + -
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Residues in contact with GLU 873 (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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762A LEU* 5.6 0.4 - - - -
763A SER* 3.3 26.3 - - - -
766A LEU* 3.6 14.8 - - + +
806A GLY* 3.0 26.8 + - - -
807A ASP 4.9 0.2 + - - -
845A TYR* 2.6 31.1 + - - +
869A CYS 3.0 13.8 + - - +
870A THR* 3.2 11.4 + - - +
872A ILE* 1.3 72.5 - - - +
874A MET* 1.3 56.6 + - - +
877A GLY* 2.6 37.0 + - - -
878A LYS 3.2 24.9 - - - +
879A PRO* 4.7 6.3 - - - +
880A PRO* 4.5 2.0 - - + -
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Residues in contact with MET 874 (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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762A LEU* 3.8 27.8 - - + -
766A LEU* 3.6 13.7 - - - +
773A LEU* 2.9 44.1 + - + +
779A THR 5.2 0.2 - - - +
780A ILE* 4.0 25.6 - - + +
783A TYR* 4.5 10.8 - - - -
784A THR* 3.2 28.9 - - - +
787A ILE* 4.1 23.8 - - + -
867A LEU* 5.8 0.2 - - + -
870A THR* 2.8 27.4 + - + +
871A ILE* 3.4 20.9 - - + +
873A GLU* 1.3 75.7 - - - +
875A ALA* 1.4 55.2 + - - +
876A THR 3.4 0.2 + - - -
877A GLY 3.5 3.1 + - - -
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Residues in contact with ALA 875 (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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772A PRO* 3.4 10.2 - - - +
774A LYS* 3.1 39.2 + - + +
780A ILE* 4.2 6.0 - - + +
871A ILE* 2.8 20.5 + - + +
872A ILE* 3.7 6.3 - - + +
874A MET* 1.4 70.9 - - - +
876A THR* 1.3 59.2 + - - +
904A PRO* 4.2 12.1 - - + -
907A MET* 3.7 31.0 - - + -
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Residues in contact with THR 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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772A PRO* 3.3 21.3 - - - +
774A LYS* 5.1 5.3 + - - +
872A ILE* 2.8 40.0 + - + +
875A ALA* 1.3 73.0 - - - +
877A GLY* 1.3 63.7 + - - +
878A LYS* 3.2 34.4 + - - +
879A PRO 4.8 1.0 + - - -
902A GLU 5.1 2.5 - - - +
904A PRO* 3.8 26.2 - - + -
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Residues in contact with GLY 877 (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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766A LEU* 4.3 23.7 - - - +
767A ARG* 5.0 3.6 + - - +
771A GLY* 4.2 6.6 - - - -
772A PRO* 3.9 16.6 - - - +
873A GLU* 2.6 22.5 + - - -
874A MET 3.5 4.6 + - - -
876A THR* 1.3 73.1 - - - +
878A LYS* 1.3 63.0 + - - +
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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