Contacts of the helix formed by residues 895 - 917 (chain C) in PDB entry 6DBT
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 GLU 895 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892C VAL 3.5 0.9 - - - +
893C PRO 2.8 25.8 - - - +
894C SER* 1.3 75.6 + - - +
896C GLU* 1.3 65.0 + - - +
897C ARG 3.6 0.4 - - - -
898C ARG* 3.0 61.6 + - - +
899C GLU* 4.0 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 896 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894C SER* 3.2 7.4 + - - +
895C GLU* 1.3 78.9 - - - +
897C ARG* 1.3 66.3 + - + +
898C ARG 3.2 1.3 - - - -
899C GLU* 2.7 35.9 + - - +
900C ALA* 3.1 13.9 + - - +
945C MET* 4.3 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 897 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833C GLU* 3.0 35.9 + - + +
836C GLU* 4.9 2.6 + - - +
837C VAL* 5.1 3.4 - - - +
838C TYR* 3.2 47.6 + - - +
892C VAL* 4.5 15.7 - - + -
894C SER* 3.5 27.1 - - - +
896C GLU* 1.3 72.2 - - - +
898C ARG* 1.3 65.8 + - - +
900C ALA* 3.2 1.6 + - - +
901C LEU* 3.0 30.8 + - - +
945C MET* 2.5 67.3 + - - +
946C PHE* 5.1 4.9 - - - -
948C TYR* 5.6 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 898 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889C CYS* 2.6 49.2 + - + +
890C GLU* 3.0 33.9 + - - +
892C VAL* 3.6 7.2 + - + +
894C SER 3.5 12.9 + - - +
895C GLU* 3.0 50.1 + - - +
897C ARG* 1.3 77.8 - - - +
899C GLU* 1.3 56.5 + - - +
901C LEU* 3.5 6.1 + - - +
902C LEU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 899 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C GLU 4.0 3.7 + - - +
896C GLU* 2.7 41.0 + - - +
898C ARG* 1.3 79.7 - - - +
900C ALA* 1.3 68.5 + - - +
902C LEU* 3.3 15.5 + - + +
903C LYS* 2.9 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 900 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896C GLU* 3.1 5.6 + - - +
897C ARG 3.2 5.4 + - - +
899C GLU* 1.3 88.7 + - - +
901C LEU* 1.3 57.8 + - - +
903C LYS* 3.2 8.5 + - - +
904C LEU* 2.9 25.2 + - - +
941C LEU* 3.7 23.4 - - + +
945C MET* 3.6 33.7 - - + -
946C PHE* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 901 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829C ILE* 5.3 2.0 - - + -
830C PHE* 4.4 14.6 - - + -
833C GLU* 4.0 28.7 - - + -
885C VAL* 3.5 29.2 - - + +
888C VAL* 4.0 18.2 - - + -
889C CYS* 3.5 20.9 - - - -
892C VAL* 5.3 4.5 - - + -
897C ARG* 3.0 25.0 + - + +
898C ARG* 3.6 2.5 - - - +
900C ALA* 1.3 73.4 - - - +
902C LEU* 1.3 59.2 + - - +
904C LEU* 3.3 15.3 - - + +
905C MET* 2.9 31.2 + - - +
946C PHE* 4.6 14.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 902 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882C ARG* 3.3 49.8 - - + +
885C VAL* 4.1 17.5 - - + -
886C GLU* 5.1 10.8 - - + +
889C CYS* 5.2 2.9 - - - -
898C ARG 2.9 19.0 + - - +
899C GLU* 3.3 15.5 - - + +
900C ALA 3.2 0.2 - - - -
901C LEU* 1.3 76.1 - - - +
903C LYS* 1.3 66.5 + - - +
905C MET* 3.4 1.6 + - - +
906C ASP* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 903 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899C GLU* 2.9 27.2 + - - +
900C ALA* 3.5 9.0 - - - +
902C LEU* 1.3 76.2 - - - +
904C LEU* 1.3 57.2 + - - +
906C ASP* 4.2 8.1 - - - +
907C LEU* 2.9 57.9 + - + +
937C GLN* 4.6 28.6 + - - +
941C LEU* 4.3 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 904 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826C PHE* 4.7 9.9 - - + -
829C ILE* 3.8 30.1 - - + -
830C PHE* 6.1 1.6 - - + -
900C ALA 2.9 9.6 + - - +
901C LEU* 3.3 16.2 - - + +
902C LEU 3.1 0.4 - - - -
903C LYS* 1.3 77.8 - - - +
905C MET* 1.3 60.1 + - + +
907C LEU* 3.3 2.2 + - - +
908C TYR* 2.9 27.3 + - - +
938C PHE* 3.4 40.7 - - + -
941C LEU* 3.5 20.9 - - + -
942C LEU* 3.5 20.0 - - + -
946C PHE* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 905 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826C PHE* 4.4 23.6 - - + -
830C PHE* 5.4 3.6 - - + -
879C LEU 3.8 3.8 - - - +
880C MET* 3.5 16.2 - - - -
881C THR 3.3 39.7 - - - +
882C ARG* 4.0 8.7 - - + +
885C VAL* 3.5 35.2 - - + -
901C LEU 2.9 10.1 + - - +
902C LEU 4.3 2.2 - - - +
904C LEU* 1.3 79.2 - - + +
906C ASP* 1.3 58.1 + - - +
908C TYR* 3.5 10.8 - - - +
909C LEU* 2.9 47.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 906 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882C ARG* 5.4 12.9 + - + +
902C LEU* 2.9 28.3 + - + +
903C LYS* 3.6 8.8 - - - +
905C MET* 1.3 79.3 - - - +
907C LEU* 1.3 69.6 + - - +
909C LEU* 3.3 6.9 + - - +
910C GLN* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 907 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903C LYS* 2.9 52.5 + - + +
904C LEU* 3.9 5.2 - - - +
906C ASP* 1.3 84.6 - - - +
908C TYR* 1.3 57.8 + - - +
910C GLN* 3.2 8.7 + - + +
911C MET* 2.9 28.5 + - - +
933C TYR* 6.4 0.2 - - + -
934C ASN* 3.2 35.1 - - - +
937C GLN* 4.2 28.7 - - + +
938C PHE* 4.2 17.7 - - + +
941C LEU* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 908 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C ASP* 3.4 17.7 + - - +
822C ASN* 4.4 13.0 + - + +
826C PHE* 3.8 30.5 - + + -
880C MET* 2.7 49.1 - - + -
904C LEU 2.9 17.2 + - - +
905C MET* 3.5 11.4 - - - +
906C ASP 3.2 0.4 - - - -
907C LEU* 1.3 78.7 - - - +
909C LEU* 1.3 71.5 + - + +
911C MET* 3.1 20.5 - - - +
912C LYS* 2.9 45.2 + - + +
915C TRP* 4.3 11.7 - + - -
938C PHE* 3.6 11.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 909 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C MET* 3.3 28.5 - - + +
881C THR* 4.7 9.6 - - + -
882C ARG* 4.7 8.1 - - + +
905C MET* 2.9 32.4 + - + +
906C ASP* 3.8 6.1 - - - +
908C TYR* 1.3 88.0 - - + +
910C GLN* 1.3 62.1 + - - +
912C LYS* 4.6 4.9 - - + +
913C PRO* 3.0 28.0 - - - +
927C GLN* 4.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 910 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906C ASP* 2.9 25.7 + - - +
907C LEU* 3.2 16.1 + - + +
909C LEU* 1.3 80.3 + - - +
911C MET* 1.3 56.7 + - - +
913C PRO* 4.4 0.9 - - - +
914C VAL* 3.2 16.3 - - - +
927C GLN* 2.5 58.8 + - - +
930C GLN* 5.5 3.3 - - - +
934C ASN* 3.3 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 911 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907C LEU 2.9 7.9 + - - +
908C TYR* 3.1 28.3 - - + +
910C GLN* 1.3 79.8 - - - +
912C LYS* 1.3 67.2 + - - +
914C VAL* 3.2 12.3 - - - +
915C TRP* 3.6 7.5 - - + -
931C TYR* 3.2 44.7 - - + +
934C ASN* 4.6 6.7 - - - +
935C SER* 3.6 39.0 - - - +
938C PHE* 3.4 37.9 - - + -
961C THR* 6.0 0.4 - - - +
962C LEU* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 912 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818C CYS* 5.5 0.7 - - - -
819C ASP* 3.0 24.2 - - - -
877C ARG* 5.9 2.9 - - - +
880C MET* 3.8 17.3 - - + -
908C TYR* 2.9 38.1 + - + +
909C LEU* 4.8 4.3 - - + -
911C MET* 1.3 73.1 - - - +
913C PRO* 1.3 70.2 - - + +
914C VAL 2.8 11.2 + - - -
915C TRP* 3.0 50.8 + - + -
916C ARG* 3.5 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 913 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909C LEU* 3.0 29.8 - - + +
910C GLN 4.6 4.0 - - - +
911C MET 3.8 0.7 - - - -
912C LYS* 1.3 93.6 - - + +
914C VAL* 1.3 52.0 + - - +
915C TRP 3.2 0.7 - - - -
916C ARG* 4.0 9.2 - - + +
917C SER* 2.2 38.2 + - - +
924C CYS* 4.6 4.7 - - - -
927C GLN* 4.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 914 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910C GLN 3.2 25.8 - - - +
911C MET 3.2 14.6 - - - +
912C LYS 2.8 0.8 + - - -
913C PRO* 1.3 78.6 - - + +
915C TRP* 1.3 56.9 + - - +
917C SER* 3.4 15.0 + - - -
920C PRO* 3.8 17.0 - - + +
924C CYS* 4.6 7.4 - - - +
927C GLN* 3.5 24.0 - - + +
928C LEU* 4.2 26.7 - - + +
931C TYR* 3.7 25.8 - - + -
965C VAL* 5.6 3.8 - - + -
969C VAL* 5.6 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 915 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813C LEU* 5.2 7.0 - - + -
815C ALA* 4.6 4.9 + - + -
818C CYS* 3.2 37.3 - - + +
819C ASP* 3.2 25.8 - - - -
822C ASN* 4.4 2.0 - - - -
908C TYR* 4.3 11.0 - + - -
911C MET* 3.6 16.4 - - + -
912C LYS* 3.0 46.3 + - + +
914C VAL* 1.3 78.0 - - + +
916C ARG* 1.3 84.3 + - + +
917C SER 3.1 11.7 + - - +
920C PRO* 5.7 0.7 - - - +
931C TYR* 4.2 12.3 - + - -
961C THR* 3.6 24.9 - - - -
965C VAL* 4.9 11.7 - - + -
969C VAL* 5.6 2.5 - - - -
975C ILE* 3.3 57.4 + - + +
976C GLY 4.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 916 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815C ALA* 4.0 23.5 + - + +
816C LEU* 4.1 19.8 + - - +
817C HIS 5.4 0.2 + - - -
818C CYS* 4.4 9.1 - - - -
819C ASP* 5.2 3.2 + - - -
877C ARG* 6.5 0.7 - - - -
912C LYS* 3.5 34.0 + - - +
913C PRO* 3.8 4.9 + - + -
915C TRP* 1.3 89.4 - - + +
917C SER* 1.3 65.2 + - - +
918C THR* 3.2 6.1 + - - -
976C GLY* 5.3 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 917 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913C PRO 2.2 30.2 + - - -
914C VAL 3.4 10.1 + - - -
915C TRP 3.1 7.5 - - - +
916C ARG* 1.3 77.4 - - - +
918C THR* 1.3 65.7 + - - +
919C CYS 3.2 1.4 + - - -
920C PRO* 3.7 23.8 - - - +
923C ASP* 3.6 10.0 + - - -
924C CYS* 2.7 29.4 - - - -
974C SER* 4.0 6.4 + - - -
976C GLY 4.5 2.3 + - - -
----------------------------------------------------------
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