Contacts of the helix formed by residues 859 - 877 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800B VAL* 3.6 12.8 - - - +
829B LEU* 4.0 13.5 - - - -
857B GLY 3.3 7.5 + - - -
858B TYR* 1.3 74.0 - - - +
860B LYS* 1.4 66.0 + - - +
861B ALA* 3.3 3.6 - - - -
862B ALA* 3.1 19.9 + - - +
863B ASP* 3.8 2.9 + - - -
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Residues in contact with LYS 860 (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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795B HIS* 3.2 62.6 + - + +
796B ASP* 5.0 3.2 + - - +
798B GLN* 2.7 26.5 + - - -
800B VAL* 3.5 9.2 - - + +
829B LEU* 3.9 25.9 - - + +
859B GLY* 1.4 69.0 - - - -
861B ALA* 1.3 56.3 + - - +
863B ASP* 3.0 28.1 + - - +
864B ILE* 3.4 5.5 - - + +
928B CYS* 6.6 0.2 - - + -
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Residues in contact with ALA 861 (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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849B GLU* 4.2 0.2 - - - +
859B GLY 3.3 1.1 - - - -
860B LYS* 1.3 77.0 - - - +
862B ALA* 1.4 62.2 + - - +
864B ILE* 3.2 9.6 + - - -
865B TRP 3.1 13.7 + - - -
923B PRO* 3.6 34.5 - - + +
926B ARG* 3.0 39.0 + - + +
927B ALA 5.5 1.3 - - - -
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Residues in contact with ALA 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B TYR 4.9 0.2 - - - +
847B ALA* 4.0 8.9 + - + +
849B GLU* 3.7 13.0 + - - +
850B ILE* 3.9 28.5 - - + -
857B GLY 4.7 0.2 - - - +
858B TYR* 4.1 15.0 - - + -
859B GLY 3.1 17.7 + - - +
861B ALA* 1.4 77.5 - - - +
863B ASP* 1.4 57.3 + - - +
865B TRP* 3.4 4.5 + - - +
866B SER* 3.1 29.0 + - - -
926B ARG* 4.0 2.7 - - - +
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Residues in contact with ASP 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B LEU* 3.9 19.6 - - + +
795B HIS* 2.7 29.9 + - + +
800B VAL* 3.5 9.5 - - - +
801B HIS* 3.0 24.8 + - - +
802B ARG* 3.0 28.8 + - - -
803B ASP 4.6 0.5 + - - -
804B ILE* 4.3 5.5 + - + +
858B TYR* 5.8 0.3 - - - -
859B GLY 4.5 2.1 - - - +
860B LYS 3.0 11.5 + - - +
862B ALA* 1.4 76.3 - - - +
864B ILE* 1.3 53.1 + - - +
866B SER* 3.3 8.8 + - - -
867B LEU* 2.8 33.2 + - - +
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Residues in contact with ILE 864 (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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788B LEU* 5.1 1.8 - - + -
791B LEU* 5.3 3.8 - - + -
795B HIS* 3.6 22.0 - - + +
860B LYS* 3.4 19.7 - - + +
861B ALA* 3.2 9.0 + - - +
863B ASP* 1.3 74.1 - - + +
865B TRP* 1.3 64.9 + - - +
867B LEU* 3.3 12.8 + - + +
868B GLY 3.1 16.8 + - - -
917B LYS 4.9 0.4 - - - +
918B CYS* 3.5 23.5 - - + +
926B ARG* 4.2 7.9 - - + -
927B ALA 3.6 26.9 - - - +
928B CYS* 4.6 1.8 - - - -
929B ALA* 4.3 16.4 - - + +
932B LEU* 3.7 26.0 - - + -
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Residues in contact with TRP 865 (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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844B GLN 5.1 1.0 + - - -
845B TYR 3.3 24.0 - - - -
846B MET 3.0 19.8 + - - -
847B ALA* 3.5 14.6 - - + -
848B PRO* 3.6 32.8 - - + -
861B ALA 3.1 6.3 + - - -
862B ALA 3.5 8.7 - - - +
863B ASP 3.3 0.4 - - - -
864B ILE* 1.3 75.9 - - - +
866B SER* 1.3 53.2 + - - +
868B GLY* 2.8 22.9 + - - -
869B CYS* 3.1 28.0 + - - -
881B PHE* 4.9 4.6 - + - -
894B VAL* 6.0 1.6 - - + -
899B VAL 4.4 8.1 - - - -
900B HIS* 3.6 34.3 - - + -
901B PRO* 4.4 3.8 - - + +
918B CYS 3.5 23.9 + - - -
919B PHE* 3.3 38.1 - + - -
920B GLU 4.4 2.0 - - - -
921B PRO* 4.7 2.2 - - + -
926B ARG* 3.9 14.8 - - - +
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Residues in contact with SER 866 (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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802B ARG 5.6 1.6 - - - -
803B ASP* 5.2 2.8 + - - -
804B ILE* 3.5 31.2 + - - +
845B TYR* 2.9 29.6 + - - +
846B MET* 5.2 0.2 - - - -
862B ALA 3.1 11.3 + - - -
863B ASP* 3.4 11.9 - - - -
865B TRP* 1.3 77.0 - - - +
867B LEU* 1.4 52.4 - - - +
869B CYS* 3.3 8.8 + - - +
870B THR* 2.9 35.5 + - - -
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Residues in contact with LEU 867 (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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784B THR* 4.5 8.3 - - + +
787B ILE* 3.8 41.7 - - + -
788B LEU* 3.7 35.4 - - + -
791B LEU* 4.4 10.3 - - + -
804B ILE* 4.0 8.5 - - - +
863B ASP 2.8 13.8 + - - +
864B ILE* 3.4 13.2 - - + +
866B SER* 1.4 74.1 - - - +
868B GLY* 1.3 56.6 + - - +
870B THR* 3.0 5.2 + - - -
871B ILE* 2.9 42.7 + - + +
914B PHE* 5.0 0.9 - - + -
918B CYS* 4.3 18.8 - - - -
932B LEU* 4.6 3.4 - - + -
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Residues in contact with GLY 868 (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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864B ILE 3.1 6.3 + - - -
865B TRP 2.8 9.9 + - - -
867B LEU* 1.3 75.3 - - - +
869B CYS* 1.3 57.0 + - - +
871B ILE* 3.3 10.4 + - - +
872B ILE* 3.1 31.2 + - - +
915B ILE* 4.4 2.7 - - - +
918B CYS* 3.9 23.1 - - - -
919B PHE* 3.4 13.3 - - - -
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Residues in contact with CYS 869 (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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844B GLN 4.0 6.1 - - - -
845B TYR* 3.5 31.9 - - + -
865B TRP* 3.1 43.1 + - - -
866B SER 3.4 8.1 - - - +
867B LEU 3.2 0.2 - - - -
868B GLY* 1.3 72.8 - - - +
870B THR* 1.4 58.3 + - - +
872B ILE* 3.3 8.1 + - - +
873B GLU* 2.9 26.3 + - - +
880B PRO* 3.7 16.6 - - + +
901B PRO* 4.1 9.4 - - - -
919B PHE* 3.9 12.1 - - - -
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Residues in contact with THR 870 (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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762B LEU* 3.9 25.6 - - + -
787B ILE* 4.1 18.2 - - + -
804B ILE* 3.6 6.4 + - + +
805B LYS* 3.4 25.3 + - - +
806B GLY 4.0 16.2 - - - +
809B VAL* 5.4 0.7 - - + -
845B TYR* 3.8 1.1 - - - -
866B SER 2.9 13.2 + - - -
867B LEU* 3.0 13.9 + - - -
869B CYS* 1.4 74.3 - - - +
871B ILE* 1.3 58.1 + - - +
873B GLU* 3.1 11.8 + - - +
874B MET* 2.8 28.8 + - + +
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Residues in contact with ILE 871 (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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780B ILE* 3.7 22.6 - - + +
784B THR* 3.6 25.1 - - + +
867B LEU* 2.9 30.7 + - + +
868B GLY* 3.3 13.0 + - - +
870B THR* 1.3 76.4 - - - +
872B ILE* 1.4 55.2 + - - +
874B MET* 3.1 12.7 + - + +
875B ALA* 3.0 28.8 + - + +
907B MET* 5.5 1.3 - - + -
914B PHE* 3.7 34.1 - - + -
915B ILE* 3.9 28.9 - - + -
918B CYS* 4.6 2.0 - - - -
937B PHE* 5.6 3.1 - - + -
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Residues in contact with ILE 872 (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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868B GLY 3.1 16.8 + - - +
869B CYS* 3.6 10.8 - - - +
870B THR 3.3 0.2 - - - -
871B ILE* 1.4 75.0 - - - +
873B GLU* 1.3 52.2 + - - +
875B ALA* 3.5 2.4 + - + -
876B THR* 2.6 49.6 + - + +
880B PRO* 4.6 11.9 - - + -
881B PHE 5.7 0.2 - - - +
883B GLU* 5.9 1.8 - - - +
901B PRO* 3.9 20.9 - - + -
902B GLU 4.0 10.1 - - - +
903B ILE* 3.9 11.2 - - + -
904B PRO* 3.8 25.8 - - + -
915B ILE* 3.8 28.5 - - + -
919B PHE* 3.9 17.7 - - + -
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Residues in contact with GLU 873 (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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763B SER* 3.2 33.1 - - - -
766B LEU* 3.5 13.1 - - + +
806B GLY* 2.9 26.1 + - - -
807B ASP 4.7 0.2 + - - -
845B TYR* 2.7 31.9 + - + +
869B CYS 2.9 13.0 + - - +
870B THR* 3.2 13.5 - - - +
872B ILE* 1.3 73.4 - - - +
874B MET* 1.3 57.1 + - - +
877B GLY* 2.8 30.7 + - - -
878B LYS 3.4 25.6 - - - +
879B PRO* 5.3 0.4 - - - -
880B PRO* 4.8 1.3 - - + +
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Residues in contact with MET 874 (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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762B LEU* 3.8 33.2 - - + -
766B LEU* 3.6 14.9 - - - +
773B LEU* 2.8 43.0 + - + +
780B ILE* 4.1 31.9 - - + +
783B TYR* 4.4 11.0 - - + -
784B THR* 3.6 21.8 - - - +
787B ILE* 3.8 28.3 - - + -
870B THR* 2.8 21.7 + - + +
871B ILE* 3.1 13.7 + - + +
873B GLU* 1.3 78.4 - - - +
875B ALA* 1.3 53.9 + - - +
876B THR 3.5 0.2 + - - -
877B GLY 3.8 1.9 + - - -
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Residues in contact with ALA 875 (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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772B PRO* 3.3 11.6 - - - +
774B LYS* 3.1 48.1 + - + +
780B ILE* 4.0 10.3 - - + +
871B ILE* 3.0 16.5 + - + +
872B ILE* 3.9 6.7 - - + +
874B MET* 1.3 75.9 - - - +
876B THR* 1.3 57.9 + - - +
904B PRO* 4.1 10.8 - - + -
907B MET* 4.0 17.5 - - + -
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Residues in contact with THR 876 (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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772B PRO* 3.2 20.3 - - - +
774B LYS* 6.2 0.7 - - + -
872B ILE* 2.6 38.0 + - + +
875B ALA* 1.3 74.5 - - - +
877B GLY* 1.3 59.5 + - - +
878B LYS* 3.1 34.2 + - - +
879B PRO 5.1 0.3 + - - -
882B TYR* 4.7 17.1 - - + -
883B GLU* 5.6 1.6 - - - +
902B GLU 5.1 2.5 - - - +
904B PRO* 4.0 21.3 - - + -
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Residues in contact with GLY 877 (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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766B LEU* 4.6 19.5 - - - +
767B ARG* 5.3 6.2 + - - +
771B GLY 4.9 0.9 - - - -
772B PRO* 4.4 12.1 - - - -
873B GLU* 2.8 24.5 + - - -
874B MET 3.8 4.6 + - - -
875B ALA 3.6 1.6 - - - -
876B THR* 1.3 71.6 - - - +
878B LYS* 1.4 60.1 + - - +
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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
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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