Contacts of the helix formed by residues 830 - 861 (chain B) in PDB entry 3QCF
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 VAL 830 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B ILE 3.7 0.4 + - - -
829B PRO* 1.3 71.6 - - - +
831B LYS* 1.3 64.8 + - - +
833B PHE* 3.6 7.2 - - - +
834B VAL* 3.0 24.3 + - + +
1080B ILE* 4.2 26.0 - - + -
1084B SER* 3.1 35.3 + - - +
1085B THR* 4.4 2.0 - - - +
1086B VAL* 5.0 1.8 - - + -
1120B ILE* 3.3 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 831 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829B PRO* 3.2 6.3 - - + +
830B VAL* 1.3 81.3 - - - +
832B GLN* 1.3 61.9 + - - +
834B VAL* 3.7 6.7 + - - +
835B LYS* 3.3 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 832 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B ILE* 3.6 26.1 - - + +
829B PRO* 3.0 36.5 + - + +
831B LYS* 1.3 76.4 - - - +
833B PHE* 1.3 60.7 + - - +
835B LYS* 3.3 16.8 + - + +
836B HIS* 2.9 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 833 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B ILE* 3.3 15.6 - - + +
829B PRO 2.9 12.2 + - - +
830B VAL 3.6 4.3 - - - +
832B GLN* 1.3 78.2 - - - +
834B VAL* 1.3 57.4 + - - +
836B HIS* 3.0 26.3 + + + +
837B ILE* 3.0 40.6 + - + +
1086B VAL* 3.1 38.6 - - + -
1088B VAL* 4.0 23.1 - - + -
1113B HIS* 3.7 27.1 - + - -
1116B LEU* 4.1 22.7 - - + -
1120B ILE* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 834 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B VAL* 3.0 19.8 + - + +
831B LYS* 3.9 6.5 - - - +
833B PHE* 1.3 74.6 - - + +
835B LYS* 1.3 67.9 + - - +
836B HIS 3.4 0.2 + - - -
837B ILE* 3.4 16.1 + - - +
838B GLY* 3.5 7.6 + - - -
1117B LEU* 3.5 30.1 - - + +
1120B ILE* 4.1 29.4 - - + -
1121B LEU* 5.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 835 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B LYS* 3.3 36.8 + - - +
832B GLN* 3.3 18.3 + - + +
833B PHE 3.2 0.2 - - - -
834B VAL* 1.3 82.1 - - + +
836B HIS* 1.3 61.1 + - - +
838B GLY* 3.2 11.3 + - - -
839B GLU* 3.3 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 836 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B ILE* 4.5 8.7 - - + -
832B GLN* 2.9 15.0 + - + +
833B PHE* 3.0 26.9 + + - +
835B LYS* 1.3 75.8 - - - +
837B ILE* 1.3 58.3 + - - +
839B GLU* 3.1 24.3 + - - +
840B LEU* 3.0 68.4 + - + +
851B ASP* 4.6 6.8 + - - -
1113B HIS* 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 837 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B PHE* 3.0 51.1 + - + +
834B VAL* 3.8 12.1 - - - +
835B LYS 3.3 0.4 - - - -
836B HIS* 1.3 76.5 - - - +
838B GLY* 1.3 61.9 + - - +
840B LEU* 3.4 9.3 + - + +
841B TYR* 3.2 47.8 + - + -
848B PHE* 4.3 2.7 - - + -
1113B HIS* 3.7 39.0 - - + +
1114B ASP* 5.8 0.2 - - - -
1117B LEU* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 838 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B VAL 3.5 6.0 + - - -
835B LYS 3.2 8.9 + - - -
836B HIS 3.1 0.6 - - - -
837B ILE* 1.3 81.2 - - - +
839B GLU* 1.3 61.5 + - - +
841B TYR* 3.5 8.5 + - - +
842B SER* 3.4 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 839 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B LYS 3.3 10.3 + - - +
836B HIS* 3.1 28.9 + - + +
838B GLY* 1.3 76.8 - - - +
840B LEU* 1.3 65.2 + - + +
842B SER* 2.7 30.3 + - - +
847B GLY* 5.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 840 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836B HIS* 3.0 55.7 + - + +
837B ILE* 3.4 4.7 + - - +
839B GLU* 1.3 77.0 - - + +
841B TYR* 1.3 60.3 + - - +
845B GLN* 3.3 21.7 - - - -
847B GLY* 3.5 35.6 + - - +
848B PHE* 3.3 42.3 - - + +
851B ASP* 3.9 16.8 - - - +
1113B HIS* 3.9 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 841 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B ILE* 3.2 45.3 + - + +
838B GLY* 3.8 8.1 - - - +
839B GLU 3.1 0.8 - - - -
840B LEU* 1.3 76.6 - - - +
842B SER* 1.3 59.3 + - - +
844B ASN* 3.9 2.3 + - - -
845B GLN* 2.8 51.2 + - + +
848B PHE* 3.6 20.6 - + - -
1110B ILE* 3.7 18.8 + - + +
1114B ASP* 4.0 25.9 + - - +
1117B LEU* 5.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 842 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B GLY 3.4 9.7 + - - -
839B GLU* 2.7 27.6 + - - +
840B LEU 4.0 1.6 - - - +
841B TYR* 1.3 78.5 - - - +
843B ASN* 1.3 75.5 + - - +
844B ASN 4.2 0.2 - - - +
845B GLN 3.2 0.2 + - - -
846B HIS* 3.2 17.2 + - - +
847B GLY 4.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 843 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B SER* 1.3 81.5 - - - +
844B ASN* 1.3 79.0 + - - +
846B HIS* 3.3 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 844 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B TYR 3.9 2.1 + - - -
842B SER 3.1 0.6 - - - -
843B ASN* 1.3 88.7 + - - +
845B GLN* 1.3 71.6 + - - +
846B HIS* 3.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 845 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B LEU 3.3 9.9 - - - -
841B TYR* 2.8 55.0 + - + +
842B SER 3.2 0.4 + - - -
844B ASN* 1.3 76.2 - - - +
846B HIS* 1.3 66.1 + - - +
847B GLY 3.2 3.2 + - - -
848B PHE* 3.3 16.1 + - + +
849B SER* 3.3 13.2 + - - -
1106B GLU* 4.3 7.4 + - - +
1107B GLU* 5.9 0.2 + - - -
1110B ILE* 3.4 27.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 846 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842B SER 3.2 3.7 + - - +
843B ASN* 3.3 43.2 + - + +
844B ASN 3.0 4.3 + - - -
845B GLN* 1.3 77.6 - - - +
847B GLY* 1.3 60.5 + - - +
849B SER* 3.2 9.7 + - - -
850B GLU* 3.0 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 847 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B GLU* 5.0 1.7 + - - -
840B LEU* 3.5 26.3 + - - +
842B SER 4.5 0.8 + - - -
845B GLN 3.2 1.0 - - - -
846B HIS* 1.3 80.9 - - - +
848B PHE* 1.3 60.5 + - - +
850B GLU* 3.6 9.4 - - - +
851B ASP* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 848 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B ILE* 4.3 2.2 - - + -
840B LEU* 3.3 49.6 + - + +
841B TYR* 3.6 48.9 - + - -
845B GLN* 3.3 12.6 + - + +
847B GLY* 1.3 75.2 - - - +
849B SER* 1.3 58.2 + - - +
851B ASP* 3.2 5.4 + - - +
852B PHE* 2.8 32.1 + - - +
1106B GLU* 4.4 5.6 - - + +
1109B TYR* 3.9 19.4 - + + -
1110B ILE* 3.6 40.2 - - + -
1113B HIS* 3.7 30.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 849 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B GLN* 3.3 6.9 + - - +
846B HIS* 3.2 12.4 + - - -
848B PHE* 1.3 74.6 - - - +
850B GLU* 1.3 64.7 + - - +
852B PHE* 4.0 0.7 - - - +
853B GLU* 3.0 27.0 + - - +
1106B GLU* 2.9 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 850 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B HIS* 3.0 41.4 + - + +
847B GLY* 3.6 9.8 - - - +
849B SER* 1.3 76.2 - - - +
851B ASP* 1.3 66.1 + - - +
853B GLU* 3.6 8.6 + - + +
854B GLU* 3.2 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 851 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836B HIS* 4.6 6.3 + - - -
840B LEU* 3.9 21.3 - - - +
847B GLY 2.7 22.3 + - - +
848B PHE* 3.5 4.9 - - - +
850B GLU* 1.3 76.3 - - - +
852B PHE* 1.3 57.4 + - - +
854B GLU* 2.8 34.0 + - - +
855B VAL* 3.1 11.4 + - - +
1089B LEU* 3.9 22.4 - - + +
1109B TYR* 2.8 32.8 + - + +
1113B HIS* 5.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 852 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B PHE 2.8 19.9 + - - +
849B SER 4.0 2.9 - - - +
851B ASP* 1.3 73.2 - - - +
853B GLU* 1.3 63.3 + - - +
855B VAL* 3.1 22.0 + - + +
856B GLN* 3.1 47.1 + - + +
1092B LEU* 5.7 0.7 - - + -
1096B ARG* 4.1 6.1 - - - -
1103B VAL* 3.8 17.3 - - + -
1104B GLN 3.5 15.5 - - - -
1105B THR* 3.4 26.7 - - - -
1106B GLU* 3.5 34.8 - - + +
1109B TYR* 4.0 28.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 853 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849B SER 3.0 18.1 + - - +
850B GLU* 3.7 8.7 - - + +
852B PHE* 1.3 77.4 - - - +
854B GLU* 1.3 58.7 - - - +
856B GLN* 3.4 11.7 + - - +
857B ARG* 2.7 63.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 854 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850B GLU* 3.2 13.7 + - - +
851B ASP* 2.8 19.3 + - - +
853B GLU* 1.3 78.6 - - - +
855B VAL* 1.3 57.8 + - - +
857B ARG* 3.1 5.9 + - + +
858B CYS* 2.8 33.6 + - - +
1089B LEU* 4.0 17.2 - - + +
1093B LYS* 2.6 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 855 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851B ASP 3.1 7.0 + - - +
852B PHE* 3.1 16.5 + - + +
854B GLU* 1.3 76.1 - - - +
856B GLN* 1.3 62.7 + - - +
857B ARG 3.2 0.3 + - - -
858B CYS* 3.3 8.7 + - - +
859B THR* 3.2 15.1 + - - -
1089B LEU* 3.7 27.4 - - + -
1092B LEU* 4.1 26.9 - - + -
1093B LYS* 4.4 13.6 - - + -
1096B ARG* 3.5 45.6 - - + +
1109B TYR* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 856 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B PHE* 3.1 45.5 + - + +
853B GLU* 3.7 13.7 - - - +
855B VAL* 1.3 74.8 - - - +
857B ARG* 1.3 62.4 + - - +
859B THR* 3.4 16.3 - - - -
860B ALA* 3.6 8.0 + - - +
1096B ARG* 3.0 35.7 + - - +
1101B TYR* 5.0 8.3 - - - -
1104B GLN 4.7 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 857 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959A ARG* 6.3 1.2 - - - +
853B GLU* 2.7 55.0 + - - +
854B GLU* 3.6 7.2 - - - +
856B GLN* 1.3 78.4 - - - +
858B CYS* 1.3 60.6 + - - +
859B THR 3.0 5.2 - - - -
860B ALA* 3.2 17.7 + - - +
861B ASP* 2.8 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B GLU* 2.8 19.4 + - - +
855B VAL 3.3 4.0 + - - +
857B ARG* 1.3 76.5 - - - +
859B THR* 1.3 61.1 + - - +
861B ASP* 3.9 12.9 + - - +
862B MET* 3.8 16.5 - - - +
1093B LYS* 3.4 47.6 - - + -
1096B ARG* 6.4 0.4 - - - -
1097B THR* 5.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 859 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855B VAL 3.2 13.8 + - - -
856B GLN 3.4 9.6 - - - -
857B ARG 3.0 0.8 - - - -
858B CYS* 1.3 77.2 - - - +
860B ALA* 1.3 59.9 + - - +
861B ASP 3.1 2.0 - - - -
862B MET* 2.8 36.3 + - + +
864B ILE* 5.9 2.5 - - + -
886B TYR* 4.1 20.6 - - - +
1096B ARG* 3.6 36.5 + - - +
1100B ASN* 6.0 1.8 - - + -
1101B TYR 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 860 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A ARG 5.0 0.2 - - - +
880A TYR* 3.4 20.8 - - - -
856B GLN 3.6 8.0 + - - +
857B ARG* 3.2 22.2 + - - +
859B THR* 1.3 80.9 - - - +
861B ASP* 1.3 64.9 + - - +
862B MET 3.1 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 861 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A ARG 4.0 15.1 - - - +
880A TYR* 3.2 6.3 - - - -
881A ILE* 3.0 42.1 + - + +
857B ARG* 2.8 28.1 - - - +
858B CYS* 3.9 12.6 - - - +
859B THR 3.1 1.2 - - - -
860B ALA* 1.3 83.9 - - - +
862B MET* 1.3 57.4 + - - +
----------------------------------------------------------
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