Contacts of the helix formed by residues 868 - 885 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810C VAL* 3.7 18.8 - - - +
860C GLU* 5.0 2.4 + - - -
866C ILE* 4.1 19.5 - - + -
867C TYR* 1.3 80.4 - - - +
869C HIS* 1.3 64.9 + - - +
870C GLN* 3.1 19.8 + - - +
871C SER* 2.7 28.2 + - - -
872C ASP* 3.1 6.4 + - - -
931C ALA* 5.3 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 869 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801C MET* 6.4 0.2 - - - +
805C GLU* 3.6 61.2 + - + +
808C ARG* 4.1 7.9 - - - +
809C LEU 3.1 39.8 + - - -
810C VAL* 3.7 13.6 - - + +
868C THR* 1.3 76.0 - - - +
870C GLN* 1.3 62.0 + - - +
872C ASP* 3.2 13.0 + - - +
873C VAL* 3.1 28.2 + - - +
937C PHE* 3.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 870 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805C GLU* 5.0 1.4 - - - +
868C THR* 3.0 11.3 + - - +
869C HIS* 1.3 85.3 - - - +
871C SER* 1.3 62.7 + - - +
873C VAL* 3.2 18.5 + - - +
874C TRP 3.3 7.3 + - - -
931C ALA* 3.1 40.8 + - + +
932C ASP* 4.2 10.8 - - - +
934C ARG* 3.1 46.7 + - - +
935C PRO 3.1 16.3 + - - +
936C LYS* 4.4 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 871 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810C VAL* 4.9 0.3 - - - +
858C ALA* 4.0 10.9 + - - +
860C GLU* 4.0 8.3 + - - -
861C SER* 3.5 23.3 + - - -
866C ILE 4.3 2.2 - - - -
867C TYR* 3.5 10.5 - - - +
868C THR* 2.7 38.6 + - - -
870C GLN* 1.3 75.7 - - - +
872C ASP* 1.3 66.6 + - - +
874C TRP* 3.2 13.0 + - - +
875C SER* 3.2 16.8 + - - -
934C ARG* 3.9 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 872 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801C MET* 3.7 19.6 - - + +
809C LEU 4.6 1.2 - - - +
810C VAL* 3.4 11.6 - - - +
811C HIS* 2.8 34.8 + - - +
812C ARG* 3.1 25.6 + - - -
813C ASP 4.6 0.3 + - - -
814C LEU* 4.0 5.6 - - + +
868C THR 3.1 11.6 + - - +
869C HIS* 3.4 14.8 + - - +
870C GLN 3.2 0.4 - - - -
871C SER* 1.3 75.3 + - - +
873C VAL* 1.3 60.3 + - - +
875C SER* 3.3 9.7 + - - -
876C TYR* 2.8 28.8 + - - +
937C PHE* 3.7 6.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 873 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869C HIS 3.1 17.6 + - - +
870C GLN* 3.4 19.5 - - - +
871C SER 3.1 0.4 - - - -
872C ASP* 1.3 77.3 - - - +
874C TRP* 1.3 62.9 + - - +
876C TYR* 3.0 12.7 + - - +
877C GLY 3.0 10.2 + - - -
926C CYS* 3.8 31.9 - - + +
934C ARG* 4.1 8.7 - - + -
935C PRO* 3.2 29.6 - - + +
937C PHE* 3.7 32.8 - - + +
940C LEU* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 874 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855C LYS 5.5 1.0 + - - -
856C TRP 3.6 18.7 + - - -
857C MET 3.4 11.6 + - - -
858C ALA* 3.4 20.0 - - + -
859C LEU* 4.2 17.0 - - + -
870C GLN 3.3 5.6 + - - +
871C SER 3.2 10.5 + - - +
873C VAL* 1.3 77.5 - - - +
875C SER* 1.3 55.1 + - - +
877C GLY* 2.8 23.4 + - - -
878C VAL* 3.2 17.2 + - + +
891C TYR* 5.0 5.9 + - - -
903C LEU* 3.8 36.3 - - + +
908C ARG* 4.2 7.2 - - - -
926C CYS 3.4 12.1 + - - +
927C TRP* 3.2 60.7 + + + -
928C MET 3.7 3.4 - - - -
929C ILE* 4.6 3.8 - - + -
934C ARG* 3.4 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 875 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812C ARG 5.5 3.6 + - - -
813C ASP* 6.0 0.2 - - - -
814C LEU* 3.6 31.2 + - - +
856C TRP* 3.0 25.9 + - - +
857C MET* 4.6 3.3 - - - -
871C SER 3.2 12.6 + - - -
872C ASP* 3.6 12.0 + - - -
873C VAL 3.3 0.2 - - - -
874C TRP* 1.3 77.2 - - - +
876C TYR* 1.3 57.0 + - - +
878C VAL* 3.3 6.4 + - - +
879C THR* 2.8 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 876 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794C CYS* 2.7 31.8 + - - +
797C ILE* 3.7 32.3 - - + -
798C ALA* 3.8 16.2 - - + +
801C MET* 4.6 0.2 - - + -
814C LEU* 3.6 13.5 - - + -
872C ASP 2.8 14.4 + - - +
873C VAL 3.0 11.4 + - - +
875C SER* 1.3 74.4 - - - +
877C GLY* 1.3 60.9 + - - +
879C THR* 3.1 6.5 + - - -
880C VAL* 2.9 47.8 + - + +
922C ILE* 5.8 0.2 - - + -
926C CYS* 4.2 6.1 - - - -
937C PHE* 3.7 18.2 - + + -
940C LEU* 3.7 26.9 - - + -
944C PHE* 3.5 25.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 877 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873C VAL 3.0 6.3 + - - -
874C TRP 2.8 8.8 + - - -
876C TYR* 1.3 78.4 - - - +
878C VAL* 1.3 57.2 + - - +
880C VAL* 3.5 6.7 + - - +
881C TRP* 3.0 25.6 + - - +
923C MET* 3.9 7.3 - - - +
926C CYS* 4.0 18.2 - - - -
927C TRP* 3.5 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 878 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855C LYS 3.8 16.8 - - - +
856C TRP* 3.4 31.2 - - + +
874C TRP* 3.2 22.7 + - + +
875C SER 3.6 6.3 - - - +
876C TYR 3.2 0.2 - - - -
877C GLY* 1.3 73.8 - - - +
879C THR* 1.3 61.0 + - - +
881C TRP* 3.0 9.2 + - - +
882C GLU* 2.8 27.7 + - + +
890C PRO* 3.8 27.1 - - + -
891C TYR* 5.4 1.6 - - - +
909C LEU* 4.2 11.4 - - + -
927C TRP* 3.8 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 879 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C ILE* 4.2 26.7 - - + -
814C LEU* 3.6 12.6 + - + +
815C ALA* 3.5 20.2 - - - -
816C ALA* 3.8 23.1 - - + +
819C VAL* 4.7 2.9 - - + -
856C TRP* 4.4 0.4 - - - +
875C SER 2.8 15.6 + - - -
876C TYR* 3.3 11.7 - - - -
878C VAL* 1.3 77.0 - - - +
880C VAL* 1.3 64.8 + - + +
882C GLU* 3.1 14.8 + - - +
883C LEU* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 880 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794C CYS* 3.8 14.1 - - + -
797C ILE* 6.2 0.7 - - + -
876C TYR* 2.9 54.4 + - + +
877C GLY* 3.7 6.7 - - - +
879C THR* 1.3 76.0 - - + +
881C TRP* 1.3 54.2 + - - +
883C LEU* 3.0 13.3 + - + +
884C MET* 2.8 59.8 + - + +
919C VAL* 5.3 0.9 - - + -
923C MET* 4.0 19.1 - - + -
944C PHE* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 881 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877C GLY 3.0 10.1 + - - +
878C VAL* 3.0 14.5 + - - +
880C VAL* 1.3 74.2 - - - +
882C GLU* 1.3 70.7 + - - +
884C MET* 3.2 3.4 + - - +
885C THR* 3.0 43.5 + - + +
888C SER* 3.6 24.7 - - - -
889C LYS 3.6 14.6 - - - -
890C PRO* 3.3 34.8 - - + -
891C TYR 4.6 0.7 - - - -
909C LEU* 3.7 31.3 - - + +
910C PRO* 2.7 48.1 + - + -
912C PRO* 3.7 11.2 - - + +
923C MET* 3.0 36.3 - - + +
927C TRP* 4.4 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 882 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775C LEU* 4.0 16.0 - - + +
778C VAL* 5.3 0.9 - - + -
816C ALA* 2.9 42.7 + - + +
817C ARG* 4.9 0.3 + - - +
856C TRP* 3.1 42.9 + - + -
878C VAL* 2.8 20.0 + - + +
879C THR* 3.3 13.4 - - - +
881C TRP* 1.3 80.9 - - + +
883C LEU* 1.3 60.9 + - - +
885C THR* 3.1 7.0 + - - -
886C PHE 3.0 4.0 + - - -
887C GLY* 2.7 34.5 + - - -
888C SER 4.2 14.6 - - - +
890C PRO* 4.7 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 883 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774C LEU* 3.7 27.8 - - + -
778C VAL* 4.2 16.7 - - + +
790C LEU* 3.8 25.4 - - + +
793C TRP* 4.0 28.9 - - + -
794C CYS* 4.4 16.2 - - - -
797C ILE* 4.1 17.3 - - + -
816C ALA* 4.3 15.9 - - + -
879C THR* 3.0 20.7 + - + +
880C VAL* 3.0 10.8 + - + +
882C GLU* 1.3 78.3 - - - +
884C MET* 1.3 62.0 + - + +
886C PHE* 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 884 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790C LEU* 4.4 11.0 - - + +
791C LEU* 4.1 20.0 - - + -
794C CYS* 3.4 33.0 - - - -
880C VAL* 2.8 33.6 + - + +
881C TRP* 3.9 4.3 - - - +
883C LEU* 1.3 74.0 - - + +
885C THR* 1.3 57.7 + - - +
886C PHE* 3.4 3.3 - - - -
912C PRO* 3.9 12.2 - - + +
913C PRO* 5.5 0.9 - - - +
914C ILE* 2.8 32.3 - - - +
915C CYS* 3.6 23.6 - - - -
919C VAL* 4.5 7.0 - - + -
923C MET* 4.8 1.6 - - - -
944C PHE* 4.6 0.7 - - + -
955C LEU* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 885 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C LYS* 5.5 0.3 - - - +
881C TRP* 3.0 46.6 + - + +
882C GLU* 3.1 10.0 + - - -
884C MET* 1.3 74.6 - - - +
886C PHE* 1.3 74.4 + - - +
888C SER* 3.2 37.2 + - - -
912C PRO* 3.7 22.2 - - + -
913C PRO* 5.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
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