Contacts of the helix formed by residues 902 - 923 (chain C) in PDB entry 6CIM
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 CYS 902 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891C PRO* 3.7 42.0 - - + -
892C VAL* 3.9 4.0 - - - -
895C SER* 4.2 5.2 - - - -
898C PRO* 3.2 29.6 + - - +
901C GLU* 1.3 80.3 - - - +
903C PRO* 1.3 65.9 - - - +
904C GLU* 3.3 3.4 - - - -
905C SER* 3.2 17.2 + - - +
906C LEU* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 903 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898C PRO 3.7 5.4 - - - +
899C ALA* 3.7 24.7 - - - +
900C LYS* 3.5 15.9 - - - +
901C GLU 3.7 1.6 - - - +
902C CYS* 1.3 88.2 - - - +
904C GLU* 1.3 63.9 + - - +
906C LEU* 3.4 5.9 + - + +
907C CYS* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 904 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902C CYS* 3.3 0.8 - - - -
903C PRO* 1.3 80.7 - - + +
905C SER* 1.3 58.8 + - - +
907C CYS* 3.3 4.3 + - - +
908C GLN* 2.9 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 905 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888C LYS* 3.7 18.6 + - - +
891C PRO* 4.5 8.1 - - - +
892C VAL* 3.6 19.0 - - - +
902C CYS* 3.2 21.5 + - - +
904C GLU* 1.3 76.0 - - - +
906C LEU* 1.3 60.9 + - - +
908C GLN* 3.6 4.3 - - - +
909C TYR* 2.9 31.5 + - - +
912C ASN* 4.8 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 906 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892C VAL* 3.5 30.9 - - + +
898C PRO* 4.1 11.0 - - + +
899C ALA* 4.0 32.8 - - + +
902C CYS 3.0 15.6 + - - +
903C PRO* 3.7 7.0 - - + +
904C GLU 3.4 0.2 - - - -
905C SER* 1.3 76.3 - - - +
907C CYS* 1.3 66.0 + - - +
909C TYR* 3.4 11.3 + - + +
910C SER* 4.9 0.3 + - - -
944C PRO* 5.3 9.2 - - + +
947C ILE* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 907 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903C PRO* 2.9 18.3 + - - +
904C GLU* 3.6 6.1 - - - +
906C LEU* 1.3 79.9 - - - +
908C GLN* 1.3 67.3 + - + +
909C TYR 2.9 6.6 + - - -
910C SER* 3.9 8.3 + - - -
911C PHE 5.0 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 908 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904C GLU* 2.9 29.0 + - + +
905C SER* 3.6 3.6 - - - +
907C CYS* 1.3 79.1 - - - +
909C TYR* 1.3 63.9 + - - +
910C SER 3.3 0.9 - - - -
911C PHE* 3.3 26.0 + - + +
912C ASN* 2.9 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 909 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889C MET* 3.3 54.6 - - + +
892C VAL* 3.5 30.5 - - + -
893C TRP* 3.6 9.6 - + - -
905C SER 2.9 12.2 + - - +
906C LEU* 3.4 14.1 - - + +
907C CYS 2.9 2.6 + - - -
908C GLN* 1.3 76.8 - - - +
910C SER* 1.3 59.7 + - - +
912C ASN* 3.3 6.8 + - - +
913C SER* 2.8 33.0 + - - -
939C THR 2.9 25.0 + - - -
940C LEU 5.0 1.6 - - - -
943C VAL* 3.5 18.2 - - + +
944C PRO* 3.4 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 910 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906C LEU 5.6 0.3 + - - -
907C CYS 3.9 6.4 + - - -
908C GLN 3.3 0.6 - - - -
909C TYR* 1.3 79.7 - - - +
911C PHE* 1.3 64.3 + - - +
913C SER* 3.3 4.8 + - - -
914C GLN* 2.9 42.9 + - - +
944C PRO* 4.2 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 911 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907C CYS 5.0 0.4 + - - -
908C GLN* 3.3 28.5 + - - +
910C SER* 1.3 78.6 - - - +
912C ASN* 1.3 71.0 + - - +
914C GLN* 3.3 9.8 + - + +
915C ARG* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 912 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C LEU* 3.8 25.2 - - + +
888C LYS* 3.7 36.9 + - + +
889C MET* 4.0 16.4 - - + +
905C SER* 4.8 3.4 + - - +
908C GLN* 2.9 36.5 + - - +
909C TYR* 3.7 5.8 - - - +
911C PHE* 1.3 88.5 - - - +
913C SER* 1.3 61.2 + - - +
915C ARG* 3.3 2.2 + - - +
916C PHE* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 913 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742C VAL* 3.7 13.9 - - - +
889C MET* 3.6 25.5 - - - +
909C TYR* 2.8 27.6 + - - -
910C SER* 3.8 4.9 - - - -
912C ASN* 1.3 72.3 - - - +
914C GLN* 1.3 58.8 + - - +
916C PHE* 3.6 3.6 - - - +
917C ALA* 2.9 30.7 + - - +
940C LEU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 914 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742C VAL* 4.3 15.0 - - + -
743C PHE* 3.2 40.1 - - + -
910C SER* 2.9 34.8 + - - +
911C PHE* 3.7 8.5 - - + +
913C SER* 1.3 76.4 - - - +
915C ARG* 1.3 57.4 + - - +
917C ALA* 3.3 5.0 + - - +
918C GLU* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 915 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C GLU* 3.0 35.3 + - - +
885C LEU* 3.8 23.1 - - + -
911C PHE* 3.0 32.4 + - + +
912C ASN* 3.8 3.6 - - - +
914C GLN* 1.3 76.5 - - - +
916C PHE* 1.3 57.9 + - - +
918C GLU* 3.3 29.7 + - - +
919C LEU* 2.9 57.7 + - - +
922C THR* 5.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 916 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800C ASN* 4.2 6.7 - - - -
803C GLU* 5.8 1.8 - - + -
804C PHE* 3.9 21.8 - + - -
882C LEU* 3.6 32.7 - - + +
885C LEU* 3.6 28.2 - - + +
886C TYR* 4.5 8.3 - - + -
889C MET* 4.4 9.0 - - - -
912C ASN 2.8 18.8 + - - +
913C SER* 3.6 7.0 - - - +
914C GLN 3.3 0.2 - - - -
915C ARG* 1.3 77.2 - - - +
917C ALA* 1.3 64.5 + - - +
919C LEU* 3.3 4.6 + - - +
920C LEU* 3.0 52.0 + - + +
936C PHE* 3.8 22.9 - + - -
940C LEU* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 917 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C LEU* 3.8 21.7 - - + +
742C VAL* 3.4 34.1 - - + -
913C SER 2.9 9.3 + - - +
914C GLN* 3.9 4.3 - - - +
916C PHE* 1.3 81.5 - - + +
918C GLU* 1.3 57.4 + - - +
920C LEU* 3.3 4.8 + - - +
921C SER* 2.9 34.6 + - - +
940C LEU* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 918 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914C GLN 2.9 16.4 + - - +
915C ARG* 3.6 32.8 + - - +
917C ALA* 1.3 78.2 - - - +
919C LEU* 1.3 57.6 + - - +
921C SER* 3.0 7.4 + - - -
922C THR* 2.9 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 919 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878C ALA* 3.6 28.0 - - + +
881C GLU* 3.6 28.0 - - + +
882C LEU* 4.0 17.7 - - + +
885C LEU* 5.0 1.6 - - + -
915C ARG* 2.9 43.2 + - - +
916C PHE* 3.8 4.7 - - - +
918C GLU* 1.3 75.9 - - - +
920C LEU* 1.3 62.4 + - - +
922C THR* 4.5 3.8 - - - +
923C LYS* 3.0 46.8 + - + -
924C PHE* 3.4 18.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 920 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741C LEU* 4.4 19.3 - - + -
803C GLU* 4.7 11.0 - - + +
807C ILE* 3.8 28.3 - - + -
882C LEU* 4.4 11.4 - - + -
916C PHE* 3.0 46.0 + - + +
917C ALA* 3.5 8.1 - - - +
919C LEU* 1.3 77.7 - - - +
921C SER* 1.3 57.8 + - - +
924C PHE* 3.1 44.7 + - + +
925C LYS* 3.5 1.0 + - - -
927C ARG* 6.3 0.9 - - + -
936C PHE* 4.6 13.7 - - + -
940C LEU* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 921 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739C GLN 5.4 3.5 + - - -
741C LEU* 4.6 9.9 - - - +
917C ALA* 2.9 18.9 + - - +
918C GLU* 3.0 7.8 + - - -
920C LEU* 1.3 76.3 - - - +
922C THR* 1.3 60.2 + - - +
925C LYS* 4.4 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 922 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915C ARG* 5.8 0.4 + - - -
918C GLU* 2.9 24.6 + - - +
919C LEU* 4.2 4.0 - - + -
921C SER* 1.3 80.7 - - - +
923C LYS* 1.3 88.1 + - + +
924C PHE 3.3 1.4 + - - -
925C LYS* 3.9 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 923 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816C TYR* 5.9 0.7 - - - -
874C GLU* 5.6 7.1 + - - +
875C ARG* 2.7 45.0 + - - +
878C ALA* 4.2 12.1 - - + -
919C LEU* 3.0 32.8 + - + +
922C THR* 1.3 91.9 - - + +
924C PHE* 1.3 67.3 + - + +
925C LYS 3.5 2.0 + - - -
----------------------------------------------------------
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