Contacts of the helix formed by residues 853 - 876 (chain C) in PDB entry 6V3O
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 LEU 853 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735C GLU* 5.6 2.9 - - - +
737C ARG* 3.8 40.6 - - + +
740C GLU* 3.6 39.5 - - + +
741C TYR* 4.2 24.7 - - + +
744C SER* 5.4 2.2 - - - +
849C VAL* 3.7 15.3 - - + +
850C ALA* 2.9 16.2 + - + +
852C GLU* 1.3 84.4 - - + +
854C LYS* 1.3 63.1 + - - +
855C PRO* 3.4 2.7 - - - -
856C PHE* 3.3 27.2 + - + +
857C GLY 3.3 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 854 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845C ASP* 3.7 19.4 - - + +
846C GLU* 3.0 34.9 + - - +
849C VAL* 3.3 28.5 - - + +
850C ALA 3.3 11.6 + - - +
851C GLU* 3.1 40.9 + - - +
853C LEU* 1.3 77.8 - - - +
855C PRO* 1.3 68.4 - - + +
857C GLY* 3.1 3.7 + - - +
858C LYS* 3.0 40.6 + - - +
861C ARG* 4.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 855 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851C GLU 3.5 12.8 - - - +
852C GLU* 4.0 8.3 - - - +
853C LEU 3.6 3.4 - - - -
854C LYS* 1.3 91.4 - - + +
856C PHE* 1.3 61.4 + - - +
858C LYS* 3.2 16.7 + - + +
859C GLN* 3.1 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 856 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731C VAL* 3.9 31.6 - - + -
735C GLU* 3.8 42.0 - - + +
737C ARG 5.7 0.2 - - - -
738C PHE* 4.0 11.2 - + - -
741C TYR* 4.0 31.6 - + + -
852C GLU 5.5 0.2 + - - -
853C LEU* 3.3 21.9 + - + +
854C LYS 3.2 0.6 - - - -
855C PRO* 1.3 79.6 - - - +
857C GLY* 1.3 62.4 + - - +
859C GLN* 3.3 12.1 + - + +
860C LEU* 3.2 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 857 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C TYR* 3.5 28.2 + - - -
845C ASP* 3.6 6.7 - - - -
853C LEU 3.3 4.8 + - - -
854C LYS 3.1 7.3 + - - -
856C PHE* 1.3 78.1 - - - +
858C LYS* 1.3 64.9 + - - +
860C LEU* 3.1 7.6 + - - +
861C ARG* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 858 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854C LYS* 3.0 40.0 + - - +
855C PRO* 3.2 14.9 + - + +
857C GLY* 1.3 75.7 - - - +
859C GLN* 1.3 65.6 + - - +
861C ARG* 3.3 28.1 + - - +
862C ASP* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 859 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855C PRO* 3.1 22.2 + - + +
856C PHE* 3.6 12.3 - - + +
857C GLY 3.1 0.2 - - - -
858C LYS* 1.3 82.6 - - - +
860C LEU* 1.3 61.2 + - + +
862C ASP* 3.1 22.7 + - - +
863C LYS* 2.9 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 860 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731C VAL* 3.7 34.3 - - + -
738C PHE* 4.9 1.3 - - + -
741C TYR* 3.8 23.1 - - + +
786C PHE* 3.7 16.3 - - + -
788C LEU* 4.0 22.4 - - + -
791C TRP* 3.5 10.9 - - + -
792C LEU* 4.8 4.9 - - + -
856C PHE* 3.2 39.7 + - + +
857C GLY* 3.1 7.9 + - - +
859C GLN* 1.3 76.9 - - + +
861C ARG* 1.3 57.2 + - - +
863C LYS* 3.4 18.2 + - + +
864C TYR* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 861 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C TYR* 4.1 3.4 + - - -
786C PHE* 3.8 20.6 - - + -
838C PRO* 3.6 34.0 - - + +
841C ALA* 4.2 4.3 + - + +
842C GLY* 3.8 20.1 + - - +
845C ASP* 3.1 36.8 + - - +
854C LYS* 4.7 1.4 + - - +
857C GLY 3.0 17.0 + - - +
858C LYS* 3.4 42.1 - - - +
859C GLN 3.2 0.2 - - - -
860C LEU* 1.3 75.4 - - - +
862C ASP* 1.3 65.3 + - - +
864C TYR* 3.0 17.6 + - + +
865C VAL* 3.1 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 862 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858C LYS* 2.9 19.4 + - - +
859C GLN* 3.1 34.3 + - - +
861C ARG* 1.3 76.4 - - - +
863C LYS* 1.3 62.4 + - + +
864C TYR 3.2 0.2 + - - -
865C VAL* 3.2 12.0 + - - +
866C GLU* 2.9 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 863 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727C GLU* 2.5 33.6 + - - +
731C VAL* 4.2 18.8 - - - -
791C TRP* 3.8 10.8 - - + -
792C LEU* 4.3 17.3 - - + -
859C GLN* 2.9 24.0 + - - +
860C LEU* 3.5 17.9 - - + +
861C ARG 3.3 0.2 - - - -
862C ASP* 1.3 75.3 - - + +
864C TYR* 1.3 55.6 + - - +
866C GLU* 3.9 13.3 + - - +
867C THR* 2.6 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 864 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785C ARG 4.7 3.6 - - - -
786C PHE* 3.6 33.2 - + + -
787C HIS* 5.7 1.1 - + + -
791C TRP* 3.6 32.8 - + + -
833C PHE* 3.5 31.8 + + - -
836C GLY* 3.4 30.4 + - - -
838C PRO* 3.4 33.5 - - + +
860C LEU 3.0 12.6 + - - +
861C ARG* 3.0 14.5 + - - +
863C LYS* 1.3 77.3 - - - +
865C VAL* 1.3 64.9 + - + +
867C THR* 3.3 3.5 + - - -
868C GLN* 3.0 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 865 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838C PRO* 4.6 12.6 - - + -
861C ARG* 3.1 14.6 + - + +
862C ASP* 3.4 15.0 - - - +
864C TYR* 1.3 85.7 - - + +
866C GLU* 1.3 73.4 + - + +
868C GLN* 3.9 7.5 - - - +
869C GLN* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 866 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795C GLY* 5.2 1.8 - - - -
862C ASP* 2.9 32.5 + - - +
863C LYS* 3.9 14.3 - - - +
865C VAL* 1.3 81.0 - - + +
867C THR* 1.3 63.8 + - - +
869C GLN* 4.1 3.6 - - - +
870C LEU* 3.2 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 867 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791C TRP* 3.9 18.2 - - + +
793C GLY 5.8 0.2 + - - -
794C VAL* 3.9 19.3 - - + -
795C GLY* 3.4 37.5 + - - +
798C PHE* 5.0 1.0 - - - -
829C LEU* 6.1 0.2 - - + -
833C PHE* 3.9 20.4 - - + -
863C LYS* 2.6 25.4 + - - +
864C TYR 3.7 3.4 - - - -
866C GLU* 1.3 75.0 - - - +
868C GLN* 1.3 65.7 + - - +
870C LEU* 3.4 2.0 + - - +
871C LEU* 3.0 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 868 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833C PHE* 3.5 43.1 - - + +
864C TYR* 3.0 32.2 + - - +
865C VAL* 3.9 8.5 + - - +
867C THR* 1.3 77.4 - - - +
869C GLN* 1.3 56.8 + - - +
871C LEU* 3.1 5.9 + - + +
872C LEU* 3.0 43.7 + - + +
880C ILE* 3.2 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 869 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865C VAL 3.1 18.8 + - - +
866C GLU* 4.1 3.8 - - - +
868C GLN* 1.3 76.4 - - - +
870C LEU* 1.3 63.1 + - + +
872C LEU* 3.5 19.4 + - - +
873C GLN* 3.0 48.0 + - - +
878C LYS 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 870 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795C GLY* 3.5 29.8 - - - +
798C PHE* 4.1 16.6 - - + -
799C LYS* 4.3 26.2 - - + +
802C ILE* 4.1 25.4 - - + -
866C GLU* 3.2 26.4 + - + +
867C THR 3.9 2.5 - - - +
869C GLN* 1.3 75.2 - - + +
871C LEU* 1.3 65.3 + - - +
873C GLN* 3.1 20.4 + - + +
874C ILE* 3.0 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 871 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794C VAL* 5.9 0.9 - - + -
798C PHE* 4.1 16.7 - - + -
816C TYR* 5.8 0.2 - - + -
826C LEU* 3.7 44.6 - - + +
829C LEU* 4.1 6.5 - - + -
830C GLU* 3.9 27.8 - - + +
833C PHE* 3.5 35.9 - - + -
867C THR* 3.0 19.2 + - + +
868C GLN* 3.1 7.1 + - + +
870C LEU* 1.3 76.0 - - - +
872C LEU* 1.3 66.7 + - + +
874C ILE* 3.3 3.1 + - - +
875C ALA* 3.0 26.2 + - + +
880C ILE* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 872 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830C GLU* 3.9 25.4 - - + +
868C GLN* 3.0 31.5 + - + +
869C GLN* 3.8 22.4 - - - +
871C LEU* 1.3 81.0 - - + +
873C GLN* 1.3 57.0 + - - +
875C ALA* 3.3 3.9 + - - -
876C GLY* 2.8 25.5 + - - -
877C HIS* 3.1 26.9 + - + +
878C LYS 4.3 15.9 - - - +
879C ASP* 4.1 5.8 - - - +
880C ILE* 3.9 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 873 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802C ILE* 6.1 1.0 - - - +
809C PHE* 3.7 36.4 - - + -
813C LYS* 4.1 5.4 - - - +
869C GLN* 3.0 46.9 + - - +
870C LEU* 3.1 24.0 + - + +
872C LEU* 1.3 76.6 - - - +
874C ILE* 1.3 61.4 + - + +
876C GLY* 3.3 11.6 + - - -
877C HIS 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 874 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798C PHE* 3.6 48.9 - - + -
802C ILE* 5.0 4.5 - - + -
809C PHE* 4.2 15.7 - - + -
812C LEU* 3.8 48.0 - - + +
813C LYS* 3.4 25.3 - - - +
816C TYR* 4.0 6.4 - - + +
822C PHE* 4.2 4.0 - - + -
826C LEU* 4.0 19.7 - - + -
870C LEU 3.0 13.4 + - - +
871C LEU 3.9 4.0 - - - +
873C GLN* 1.3 76.2 - - - +
875C ALA* 1.3 62.2 + - - +
876C GLY 3.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 875 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816C TYR* 3.4 49.9 - - + +
817C ASN* 5.3 2.9 + - - -
830C GLU* 4.7 4.3 - - - +
871C LEU* 3.0 20.2 + - + +
872C LEU* 3.9 4.9 - - - +
874C ILE* 1.3 76.0 - - - +
876C GLY* 1.3 60.9 + - - +
877C HIS* 3.6 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 876 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813C LYS* 5.7 4.9 - - - -
872C LEU 2.8 6.4 + - - -
873C GLN* 3.3 7.3 + - - -
874C ILE 3.2 4.6 + - - -
875C ALA* 1.3 79.3 - - - +
877C HIS* 1.3 65.6 + - - +
878C LYS* 4.1 4.2 + - - +
882C GLU* 4.1 5.4 - - - +
----------------------------------------------------------
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