Contacts of the helix formed by residues 873 - 890 (chain B) in PDB entry 3BBT
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 873 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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815B VAL* 3.5 18.8 - - - +
865B GLU* 3.3 26.5 - - - +
871B LYS* 3.9 14.4 - - + +
872B PHE* 1.3 76.1 - - - +
874B HIS* 1.3 75.5 + - - +
875B GLN* 3.5 12.3 + - + +
876B SER* 2.5 39.5 + - - +
877B ASP 3.2 6.2 + - - -
936B ALA* 5.3 2.2 - - + -
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Residues in contact with HIS 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B MET* 6.1 1.4 - - - +
810B GLU* 3.5 60.9 + - + +
813B ARG* 3.7 33.3 + - - +
814B LEU 3.9 6.4 + - - -
815B VAL* 3.4 25.4 - - + +
873B THR* 1.3 82.6 + - - +
875B GLN* 1.3 60.3 - - + +
877B ASP* 3.3 12.8 + - - +
878B VAL* 3.3 24.9 + - - +
942B PHE* 3.6 6.0 - - + -
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Residues in contact with GLN 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B GLU* 4.9 2.1 - - - +
873B THR* 3.2 9.8 + - + +
874B HIS* 1.3 81.3 - - + +
876B SER* 1.3 62.9 + - - +
877B ASP 3.2 0.2 - - - -
878B VAL* 3.3 29.3 + - - +
879B TRP 3.5 1.2 + - - -
936B ALA* 3.2 39.6 + - + +
937B ASP* 4.7 5.8 + - - +
939B ARG* 2.8 51.4 + - - +
940B PRO 3.1 14.4 + - - +
941B LYS* 3.7 31.1 + - - +
942B PHE* 5.1 0.5 + - - -
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Residues in contact with SER 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B VAL* 4.9 0.3 - - - +
863B ALA* 4.0 9.6 + - - +
865B GLU* 4.1 3.1 - - - -
866B CYS* 3.4 28.6 - - - -
872B PHE* 3.7 6.8 - - - +
873B THR* 2.5 47.9 + - - +
875B GLN* 1.3 74.6 - - - +
877B ASP* 1.3 65.2 + - - +
878B VAL 3.2 0.7 - - - -
879B TRP* 3.4 16.5 - - - +
880B SER* 3.4 10.6 + - - -
939B ARG* 3.5 8.3 - - - +
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Residues in contact with ASP 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B MET* 3.4 28.3 - - + +
815B VAL* 3.5 15.9 - - - +
816B HIS* 2.7 29.1 + - - +
817B ARG* 3.0 26.9 + - - -
818B ASP 4.4 0.5 + - - -
819B LEU* 3.9 7.9 + - - +
873B THR 3.2 5.8 + - - +
874B HIS* 3.3 14.4 + - - +
876B SER* 1.3 78.0 + - - +
878B VAL* 1.3 57.9 + - - +
880B SER* 3.4 8.5 + - - -
881B TYR* 3.0 25.8 + - - +
942B PHE* 3.7 4.8 - - + -
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Residues in contact with VAL 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874B HIS 3.4 15.0 - - - +
875B GLN* 3.4 31.2 - - - +
876B SER 3.2 0.4 - - - -
877B ASP* 1.3 74.7 - - - +
879B TRP* 1.3 65.7 + - - +
881B TYR* 3.1 5.3 + - - +
882B GLY 3.0 17.5 + - - -
931B CYS* 3.5 28.4 - - + +
939B ARG* 4.3 3.8 - - + -
940B PRO* 3.4 26.7 - - + +
942B PHE* 3.7 26.7 - - + +
945B LEU* 4.0 8.5 - - + -
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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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860B LYS 5.0 1.6 + - - -
861B TRP 3.3 20.5 + - - -
862B MET 3.4 14.9 + - - -
863B ALA* 3.6 15.7 - - + -
864B LEU* 4.4 13.9 - - + -
875B GLN 3.5 3.0 + - - -
876B SER 3.4 12.9 + - - +
878B VAL* 1.3 77.8 - - - +
880B SER* 1.3 61.8 + - - +
882B GLY 3.0 11.3 + - - -
883B VAL* 3.2 18.5 + - + +
896B TYR* 4.7 5.3 + - - -
908B LEU* 3.7 39.9 - - + +
913B ARG* 3.9 12.6 - - - -
931B CYS 3.3 14.7 + - - +
932B TRP* 3.3 59.9 + + + -
933B MET 3.9 2.2 - - - -
934B ILE* 5.2 1.8 - - + -
939B ARG* 3.4 28.9 - - - +
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Residues in contact with SER 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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817B ARG 5.1 5.5 + - - -
818B ASP* 5.4 0.3 - - - -
819B LEU* 3.3 32.0 + - - +
861B TRP* 2.6 30.1 + - - +
862B MET* 4.4 2.6 - - - +
876B SER 3.4 8.9 + - - -
877B ASP* 3.4 13.0 + - - -
878B VAL 3.3 0.6 - - - -
879B TRP* 1.3 77.6 - - - +
881B TYR* 1.3 53.7 + - - +
883B VAL* 3.4 5.4 + - - +
884B THR* 2.6 37.6 + - - -
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Residues in contact with TYR 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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799B CYS* 2.6 35.6 + - - +
802B ILE* 3.7 24.2 - - + -
803B ALA* 3.7 30.0 - - + +
819B LEU* 3.8 11.4 - - + +
877B ASP 3.0 14.5 + - - +
878B VAL 3.1 9.8 + - - +
880B SER* 1.3 74.3 - - - +
882B GLY* 1.3 61.2 - - - +
884B THR* 3.2 4.1 + - - -
885B ILE* 2.9 62.2 + - + +
931B CYS* 4.6 1.6 - - - -
942B PHE* 3.8 19.3 - + + -
945B LEU* 3.7 26.5 - - + -
949B PHE* 3.5 15.8 - + - -
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Residues in contact with GLY 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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878B VAL 3.0 6.7 + - - -
879B TRP 3.0 9.0 + - - -
881B TYR* 1.3 76.6 - - - +
883B VAL* 1.3 56.5 + - - +
885B ILE* 3.3 16.1 - - - +
886B TRP* 3.1 26.7 + - - +
928B MET* 4.3 3.6 - - - +
931B CYS* 4.0 15.3 - - - -
932B TRP* 3.3 19.4 - - - -
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Residues in contact with VAL 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B LYS 3.8 19.1 - - - +
861B TRP* 3.6 31.2 - - + +
879B TRP* 3.2 31.8 + - + +
880B SER 3.8 2.0 - - - +
882B GLY* 1.3 73.2 - - - +
884B THR* 1.3 66.6 + - - +
886B TRP* 3.2 7.0 + - + +
887B GLU* 2.9 23.8 + - - +
895B PRO* 3.8 19.3 - - + -
896B TYR* 5.3 1.3 - - - +
914B LEU* 4.1 13.5 - - + -
932B TRP* 3.5 15.7 - - + +
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Residues in contact with THR 884 (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 ILE* 4.4 25.1 - - + -
819B LEU* 3.1 23.6 + - + +
820B ALA* 3.2 9.6 - - - +
821B ALA* 3.6 23.1 - - + +
824B VAL* 4.4 5.8 - - + -
880B SER 2.6 25.1 + - - -
881B TYR* 3.4 9.6 - - - -
883B VAL* 1.3 76.1 - - - +
885B ILE* 1.3 61.6 + - + +
887B GLU* 3.3 15.5 + - - +
888B LEU* 3.2 25.2 + - + +
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Residues in contact with ILE 885 (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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799B CYS* 3.7 26.9 - - + -
802B ILE* 5.2 1.3 - - + -
881B TYR* 2.9 58.0 + - + +
882B GLY* 3.3 15.3 - - - +
884B THR* 1.3 75.7 - - + +
886B TRP* 1.3 58.7 + - - +
888B LEU* 3.1 13.7 + - + +
889B MET* 2.9 33.3 + - + +
927B VAL* 5.2 1.6 - - + -
928B MET* 3.8 30.1 - - + -
931B CYS* 5.4 0.7 - - - -
949B PHE* 3.7 27.4 - - + -
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Residues in contact with TRP 886 (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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882B GLY 3.1 19.6 + - - +
883B VAL* 3.2 8.0 + - - +
885B ILE* 1.3 74.2 - - - +
887B GLU* 1.3 73.9 - - + +
889B MET* 3.3 1.4 + - - +
890B THR* 3.0 45.1 + - + +
893B GLY* 3.3 28.0 - - - -
894B LYS 4.0 11.7 - - - -
895B PRO* 3.7 15.5 - - + -
896B TYR 5.0 0.4 - - - -
914B LEU* 3.8 41.0 - - + +
915B PRO* 2.9 39.8 + - + -
917B PRO* 3.5 22.5 - - + +
928B MET* 3.7 18.4 - - + -
932B TRP* 4.2 5.8 - + + -
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Residues in contact with GLU 887 (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 LEU* 3.6 26.5 - - + +
783B VAL* 4.5 1.1 - - + +
821B ALA* 3.3 31.4 + - + +
822B ARG 5.0 0.5 + - - -
861B TRP* 2.8 43.3 + - - -
883B VAL 2.9 11.6 + - - +
884B THR* 3.3 15.2 - - - +
886B TRP* 1.3 78.0 - - + +
888B LEU* 1.3 58.8 + - - +
890B THR* 3.1 10.7 + - - -
892B GLY* 2.8 31.3 + - - -
893B GLY 3.7 17.8 - - - +
895B PRO* 4.3 9.3 - - + +
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Residues in contact with LEU 888 (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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779B LEU* 3.7 27.4 - - + -
783B VAL* 4.5 14.6 - - + +
795B LEU* 3.3 28.9 - - + +
798B TRP* 4.1 21.1 - - + -
799B CYS* 4.6 6.7 - - - -
802B ILE* 4.0 25.4 - - + -
821B ALA* 4.1 16.6 - - + -
884B THR* 3.2 18.6 - - + +
885B ILE* 3.1 18.8 + - + +
887B GLU* 1.3 75.9 - - - +
889B MET* 1.3 65.6 + - + +
891B PHE* 3.1 15.8 + - - -
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Residues in contact with MET 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795B LEU* 4.6 10.8 - - - +
796B LEU* 4.7 3.4 - - + -
799B CYS* 3.7 30.1 - - - -
885B ILE* 2.9 21.4 + - + +
886B TRP 3.8 2.9 - - - +
888B LEU* 1.3 78.4 - - - +
890B THR* 1.3 60.2 + - - +
891B PHE* 3.2 10.2 - - - -
917B PRO* 3.8 21.4 - - + +
918B PRO* 5.6 0.5 - - - +
919B ILE* 3.3 28.3 + - + +
920B CYS* 3.7 9.0 - - - -
924B VAL* 5.1 2.7 - - + -
928B MET* 3.4 21.8 - - + -
949B PHE* 4.6 12.3 - - + -
960B LEU* 4.0 36.3 - - + -
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Residues in contact with THR 890 (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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787B LYS* 4.5 7.3 + - - -
886B TRP* 3.0 47.9 + - + +
887B GLU* 3.1 5.5 + - - -
889B MET* 1.3 75.2 - - - +
891B PHE* 1.3 71.9 + - - +
893B GLY* 3.0 30.5 + - - -
917B PRO* 3.8 20.6 - - + -
918B PRO* 4.8 8.3 - - + -
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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