Contacts of the helix formed by residues 868 - 885 (chain B) in PDB entry 3LZB
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 868 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B VAL* 3.6 17.8 - - - +
860B GLU* 5.0 2.9 + - - -
866B ILE* 4.0 18.7 - - + +
867B TYR* 1.3 80.3 - - - +
869B HIS* 1.3 65.3 + - - +
870B GLN* 3.2 19.7 + - - +
871B SER* 2.7 30.9 + - - -
872B ASP* 3.1 7.1 + - - -
931B ALA* 5.2 1.4 - - - +
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Residues in contact with HIS 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B GLU* 3.6 60.2 + - + +
808B ARG* 4.0 9.2 - - - +
809B LEU 3.1 40.5 + - - -
810B VAL* 3.7 14.0 - - + +
868B THR* 1.3 76.2 - - - +
870B GLN* 1.3 61.9 + - - +
872B ASP* 3.2 12.1 + - - +
873B VAL* 3.0 28.9 + - - +
937B PHE* 3.8 4.9 - - + -
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Residues in contact with GLN 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B GLU* 5.0 1.4 - - - +
868B THR* 3.1 12.1 + - - +
869B HIS* 1.3 86.4 - - - +
871B SER* 1.3 63.5 + - - +
873B VAL* 3.2 19.2 + - - +
874B TRP 3.3 7.6 + - - -
931B ALA* 3.1 39.6 + - + +
932B ASP* 4.2 11.5 + - - +
934B ARG* 3.1 46.1 + - - +
935B PRO 3.1 15.6 + - - +
936B LYS* 4.4 18.2 + - - +
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Residues in contact with SER 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B VAL* 4.9 0.5 - - - +
858B ALA* 3.9 12.9 + - - +
860B GLU* 4.0 8.3 - - - -
861B SER* 3.4 23.6 + - - -
866B ILE 4.3 1.6 - - - -
867B TYR* 3.5 9.7 - - - +
868B THR* 2.7 38.9 + - - -
870B GLN* 1.3 74.7 - - - +
872B ASP* 1.3 66.9 + - - +
874B TRP* 3.2 5.2 + - - +
875B SER* 3.2 23.7 + - - -
934B ARG* 3.9 7.5 - - - +
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Residues in contact with ASP 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B MET* 3.7 25.2 - - + +
809B LEU 4.6 1.2 - - - +
810B VAL* 3.4 10.9 - - - +
811B HIS* 2.7 30.4 + - - +
812B ARG* 3.1 25.3 + - - -
813B ASP 4.6 0.3 + - - -
814B LEU* 4.2 6.1 - - + +
868B THR 3.1 12.1 + - - +
869B HIS* 3.4 14.6 + - - +
870B GLN 3.2 0.2 - - - -
871B SER* 1.3 75.3 + - - +
873B VAL* 1.3 61.3 + - - +
875B SER* 3.3 8.4 + - - -
876B TYR* 2.8 29.3 + - - +
937B PHE* 3.7 6.2 - - + -
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Residues in contact with VAL 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805B GLU* 5.8 0.2 - - - +
869B HIS 3.0 18.5 + - - +
870B GLN* 3.3 19.3 - - - +
871B SER 3.2 0.4 - - - -
872B ASP* 1.3 77.8 - - - +
874B TRP* 1.3 63.1 + - - +
876B TYR* 3.0 4.8 + - - +
877B GLY 3.0 17.5 + - - -
926B CYS* 3.7 32.3 - - + +
934B ARG* 4.1 8.5 - - + -
935B PRO* 3.3 29.2 - - + +
937B PHE* 3.7 31.6 - - + +
940B LEU* 4.3 4.5 - - + -
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Residues in contact with TRP 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B LYS 5.5 1.0 + - - -
856B TRP 3.5 19.0 + - - -
857B MET 3.4 14.4 + - - -
858B ALA* 3.4 20.0 - - + -
859B LEU* 4.2 15.0 - - + -
870B GLN 3.3 5.4 + - - +
871B SER 3.2 12.0 + - - +
873B VAL* 1.3 77.1 - - - +
875B SER* 1.3 57.1 + - - +
877B GLY 2.9 17.7 + - - -
878B VAL* 3.2 16.9 + - + +
891B TYR* 5.0 7.0 + - - -
903B LEU* 3.9 30.7 - - + -
908B ARG* 4.1 11.4 - - - -
926B CYS 3.4 12.1 + - - +
927B TRP* 3.1 51.6 + + + -
928B MET 3.1 24.7 - - - -
929B ILE* 4.6 3.4 - - + -
934B ARG* 3.3 26.9 - - - -
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Residues in contact with SER 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B ARG 5.5 3.6 + - - -
813B ASP* 5.8 0.2 - - - -
814B LEU* 3.7 32.6 + - - +
856B TRP* 3.1 26.5 + - - +
857B MET* 4.6 3.6 - - - +
871B SER 3.2 12.5 + - - -
872B ASP* 3.7 11.9 + - - -
874B TRP* 1.3 77.3 - - - +
876B TYR* 1.3 57.2 + - - +
878B VAL* 3.2 6.2 + - - +
879B THR* 2.9 30.7 + - - -
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Residues in contact with TYR 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B CYS* 2.7 29.9 + - - -
797B ILE* 3.7 34.1 - - + -
798B ALA* 3.8 16.4 - - + +
814B LEU* 3.8 11.9 - - + +
872B ASP 2.8 14.4 + - - +
873B VAL 3.0 9.2 + - - +
875B SER* 1.3 74.3 - - - +
877B GLY* 1.3 60.7 + - - +
879B THR* 3.1 6.3 + - - -
880B VAL* 2.9 49.5 + - + +
922B ILE* 5.7 0.4 - - + -
926B CYS* 4.2 7.2 - - - -
937B PHE* 3.7 20.6 - + + -
940B LEU* 3.8 27.1 - - + +
944B PHE* 3.5 25.5 - + - -
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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
----------------------------------------------------------
873B VAL 3.0 6.5 + - - -
874B TRP 2.9 9.0 + - - -
876B TYR* 1.3 80.0 - - - +
878B VAL* 1.3 57.1 + - - +
880B VAL* 3.5 6.3 + - - +
881B TRP* 3.0 25.5 + - - +
923B MET* 3.9 7.9 - - - +
926B CYS* 4.0 17.5 - - - -
927B TRP* 3.5 19.3 - - - -
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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
----------------------------------------------------------
855B LYS 3.8 15.9 - - - +
856B TRP* 3.4 31.4 - - + +
874B TRP* 3.2 23.6 + - + +
875B SER 3.6 6.5 - - - +
876B TYR 3.2 0.6 - - - -
877B GLY* 1.3 72.4 - - - +
879B THR* 1.3 61.6 + - - +
881B TRP* 3.0 9.4 + - + +
882B GLU* 2.8 27.8 + - + +
890B PRO* 3.8 24.5 - - + -
891B TYR* 5.4 1.6 - - - +
909B LEU* 4.1 14.4 - - + -
927B TRP* 3.7 16.2 - - - +
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Residues in contact with THR 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ILE* 4.2 28.9 - - + -
814B LEU* 3.8 7.1 - - + +
815B ALA* 3.5 23.1 + - - +
816B ALA* 3.7 24.2 - - + +
819B VAL* 4.7 2.9 - - + -
875B SER 2.9 15.4 + - - -
876B TYR* 3.1 12.8 + - + -
878B VAL* 1.3 76.6 - - - +
880B VAL* 1.3 64.2 + - + +
882B GLU* 3.1 15.1 + - - +
883B LEU* 3.0 23.3 + - + +
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Residues in contact with VAL 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794B CYS* 3.9 14.8 - - - -
797B ILE* 6.3 0.9 - - + -
876B TYR* 2.9 54.8 + - + +
877B GLY* 3.7 6.5 - - - +
879B THR* 1.3 75.5 - - + +
881B TRP* 1.3 58.4 + - - +
883B LEU* 3.0 11.9 + - + +
884B MET* 2.8 54.7 + - + +
919B VAL* 5.5 0.7 - - + -
923B MET* 4.0 18.6 - - + -
944B PHE* 4.4 9.9 - - + -
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Residues in contact with TRP 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877B GLY 3.0 10.1 + - - +
878B VAL* 3.0 15.6 + - - +
880B VAL* 1.3 77.0 - - - +
882B GLU* 1.3 66.7 + - - +
884B MET* 3.2 3.0 + - - +
885B THR* 3.0 44.2 + - + +
888B SER* 3.6 25.1 - - - -
889B LYS 3.5 14.8 - - - -
890B PRO* 3.4 33.9 - - + -
891B TYR 4.6 1.1 - - - -
909B LEU* 3.7 31.3 - - + +
910B PRO* 2.7 47.6 + - + -
912B PRO* 3.7 10.3 - - + +
923B MET* 3.0 34.7 - - + +
927B TRP* 4.4 0.9 - + - -
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Residues in contact with GLU 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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775B LEU* 4.0 21.3 - - + +
778B VAL* 5.3 0.4 - - - -
815B ALA* 4.9 0.3 - - - +
816B ALA* 3.0 41.3 + - + +
817B ARG* 4.9 0.5 + - - +
856B TRP* 3.0 42.3 + - + -
878B VAL* 2.8 19.1 + - + +
879B THR* 3.3 13.0 - - - +
881B TRP* 1.3 79.4 - - + +
883B LEU* 1.3 60.8 + - - +
885B THR* 3.1 7.1 + - - -
886B PHE 3.0 4.0 + - - -
887B GLY* 2.7 30.5 + - - -
888B SER 4.2 15.3 - - - +
890B PRO* 4.6 1.1 - - + -
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Residues in contact with LEU 883 (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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774B LEU* 3.8 27.1 - - + -
778B VAL* 4.2 16.7 - - + +
790B LEU* 3.4 26.5 - - + +
793B TRP* 4.0 29.2 - - + -
794B CYS* 4.4 16.8 - - - -
797B ILE* 4.1 16.8 - - + -
816B ALA* 4.0 18.2 - - + -
879B THR* 3.0 16.9 + - + +
880B VAL* 3.0 9.2 + - + +
882B GLU* 1.3 81.0 - - - +
884B MET* 1.3 60.2 + - + +
886B PHE* 2.9 23.0 + - - -
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Residues in contact with MET 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B LEU* 4.5 13.0 - - + +
791B LEU* 4.2 8.7 - - + -
794B CYS* 3.4 33.9 - - - -
880B VAL* 2.8 31.1 + - + +
881B TRP* 3.2 5.1 + - - +
883B LEU* 1.3 75.3 - - + +
885B THR* 1.3 59.2 - - - +
886B PHE* 3.4 2.7 - - - -
912B PRO* 3.9 12.0 - - + +
913B PRO* 5.7 0.5 - - - +
914B ILE* 2.7 34.5 - - + +
915B CYS* 3.7 23.6 - - - -
919B VAL* 4.5 6.3 - - + -
923B MET* 4.7 2.0 - - - -
944B PHE* 4.5 0.9 - - + -
955B LEU* 3.6 42.0 - - + -
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Residues in contact with THR 885 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881B TRP* 3.0 45.9 + - + +
882B GLU* 3.1 10.6 + - - -
884B MET* 1.3 74.8 - - - +
886B PHE* 1.3 75.6 + - - +
888B SER* 3.2 36.8 + - - -
912B PRO* 3.7 22.0 - - + -
913B PRO* 5.5 3.4 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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