Contacts of the helix formed by residues 861 - 888 (chain A) in PDB entry 3KSS
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 GLN 861 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A ILE* 4.3 6.4 - - - +
678A LYS* 2.7 35.0 + - - +
679A SER 3.9 1.7 + - - +
680A PRO* 2.8 37.9 + - + +
829A ARG* 4.7 12.1 + - - +
860A GLY* 1.3 71.4 - - - -
862A PHE* 1.3 57.0 + - - +
864A LEU* 3.8 5.8 + - - +
865A LEU* 3.2 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 862 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A PRO 3.8 4.1 + - - +
681A ILE* 3.6 35.2 - - + -
833A MET* 5.1 12.8 - - + +
834A VAL* 5.0 18.2 - - + -
837A VAL* 3.4 41.7 - - + -
858A PHE* 4.7 20.0 - - + -
859A SER* 4.3 11.7 - - - -
860A GLY* 2.9 2.8 + - - -
861A GLN* 1.3 78.7 - - - +
863A GLU* 1.3 82.3 + - + +
865A LEU* 2.8 12.1 + - + -
866A GLU* 2.5 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A PHE 4.5 5.6 - - - +
859A SER* 4.4 17.5 - - - -
860A GLY 3.4 14.1 + - - +
862A PHE* 1.3 97.4 - - + +
864A LEU* 1.3 59.2 + - + +
866A GLU* 4.0 6.1 - - - +
867A ARG* 3.0 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 864 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A LEU* 6.2 0.2 - - + -
468A GLU* 2.8 45.5 - - + +
469A GLY* 3.7 16.2 - - - -
470A GLN 5.0 0.7 - - - +
860A GLY 4.5 1.5 + - - +
861A GLN 3.8 6.3 + - - +
862A PHE 3.2 0.2 - - - -
863A GLU* 1.3 77.6 - - + +
865A LEU* 1.3 61.2 + - - +
867A ARG* 3.2 35.5 - - + +
868A ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 865 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A LEU* 5.5 7.0 - - + -
471A GLU* 6.0 1.6 - - - +
832A ASP* 4.2 26.9 - - - +
834A VAL* 5.3 6.5 - - + -
861A GLN* 3.2 21.9 + - + +
862A PHE* 2.8 13.5 + - + +
864A LEU* 1.3 73.8 - - - +
866A GLU* 1.3 61.0 + - + +
868A ALA* 2.9 13.3 + - + +
869A ASN* 2.7 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 866 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL* 4.7 23.4 - - + +
862A PHE* 2.5 38.4 + - + +
863A GLU* 4.0 4.7 - - - +
865A LEU* 1.3 79.1 - - + +
867A ARG* 1.3 55.2 + - + +
869A ASN* 3.4 7.2 + - - +
870A HIS* 2.8 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A GLU* 4.5 15.4 + - - -
863A GLU* 3.0 37.7 + - + +
864A LEU* 3.2 37.2 - - + +
865A LEU 3.2 0.4 - - - -
866A GLU* 1.3 80.7 - - + +
868A ALA* 1.3 54.4 + - - +
870A HIS* 3.1 6.6 + - - +
871A LYS* 2.7 66.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A THR* 4.1 9.8 - - - +
467A LEU* 3.8 38.4 - - + -
468A GLU* 4.2 4.3 - - - +
864A LEU* 2.9 17.1 + - + +
865A LEU* 2.9 14.8 + - + +
867A ARG* 1.3 75.8 - - - +
869A ASN* 1.3 57.3 + - - +
871A LYS* 3.9 2.5 - - - +
872A LEU* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A ASP* 5.1 8.1 + - - -
865A LEU* 2.7 29.3 + - + +
866A GLU* 3.6 8.7 + - - +
868A ALA* 1.3 71.4 - - - +
870A HIS* 1.3 65.1 + - - +
872A LEU* 3.3 5.3 + - - +
873A LYS* 3.0 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 870 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A GLU* 2.8 25.1 + - + +
867A ARG* 3.1 6.5 + - - +
869A ASN* 1.3 77.1 - - - +
871A LYS* 1.3 97.0 + - + +
873A LYS* 3.3 12.5 + - - +
874A LEU* 3.3 16.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A THR* 3.3 21.3 - - + +
867A ARG* 2.7 64.1 + - + +
868A ALA* 4.0 1.8 - - - +
870A HIS* 1.3 100.3 + - + +
872A LEU* 1.3 65.4 + - - +
874A LEU* 3.0 18.6 + - + +
875A MET* 3.0 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A PRO* 2.9 50.9 - - + +
464A ILE* 5.1 2.7 - - + -
466A THR* 3.3 10.6 - - + +
467A LEU* 4.3 11.9 - - + +
868A ALA 2.8 18.4 + - - +
869A ASN* 3.5 7.2 - - - +
871A LYS* 1.3 75.5 - - - +
873A LYS* 1.3 73.3 + - - +
875A MET* 2.8 21.3 + - - +
876A VAL* 3.1 18.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A ASN* 3.0 40.2 + - - +
870A HIS* 3.7 6.7 - - - +
871A LYS 3.2 0.4 - - - -
872A LEU* 1.3 90.7 - - + +
874A LEU* 1.3 58.8 + - - +
876A VAL* 3.4 19.3 - - + +
877A PRO* 2.9 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A HIS* 3.3 16.4 + - + +
871A LYS* 3.0 13.8 + - + +
873A LYS* 1.3 75.4 - - - +
875A MET* 1.3 83.7 + - + +
877A PRO* 3.0 20.4 - - + +
878A MET* 3.3 33.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 3.2 30.6 - - + +
463A PRO* 4.3 9.6 - - + -
466A THR* 2.9 38.1 - - + +
871A LYS* 3.1 18.2 - - + +
872A LEU* 2.8 12.0 + - - +
874A LEU* 1.3 94.6 - - + +
876A VAL* 1.3 53.7 + - - +
878A MET* 3.8 6.0 - - - +
879A THR* 2.5 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A PRO* 5.2 4.3 - - + -
872A LEU* 3.1 20.0 + - + +
873A LYS* 3.4 33.0 - - + +
875A MET* 1.3 77.2 - - - +
877A PRO* 1.3 72.1 - - + +
879A THR* 3.1 13.1 - - + +
880A LEU* 2.9 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A LYS 2.9 29.4 - - - +
874A LEU* 3.0 15.7 - - + +
876A VAL* 1.3 90.5 - - + +
878A MET* 1.3 60.3 + - + +
880A LEU* 3.3 4.0 + - + +
881A MET* 2.9 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 878 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ILE* 6.3 0.4 - - + -
874A LEU* 3.3 37.3 + - + +
875A MET* 3.2 9.5 + - - +
877A PRO* 1.3 81.2 - - + +
879A THR* 1.3 59.5 + - - +
881A MET* 3.5 13.6 + - + +
882A ILE* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A LEU 4.2 4.9 + - - -
460A SER* 3.9 25.5 + - - +
462A ILE* 4.3 9.1 - - - +
463A PRO* 4.7 12.1 - - + -
875A MET 2.5 28.3 + - - +
876A VAL* 3.1 22.9 - - + +
878A MET* 1.3 70.5 - - - +
880A LEU* 1.3 71.1 + - + +
882A ILE* 2.9 23.7 - - - +
883A ILE* 2.9 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A VAL* 2.9 23.9 + - + +
877A PRO* 3.8 5.4 - - + +
879A THR* 1.3 83.2 - - + +
881A MET* 1.3 62.1 + - + +
883A ILE* 3.1 20.9 + - + +
884A PHE* 2.6 37.7 + - - +
901A ILE* 5.2 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 881 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A PRO* 2.9 39.4 + - + +
878A MET* 3.8 17.0 - - + +
880A LEU* 1.3 81.4 - - + +
882A ILE* 1.3 59.9 + - - +
884A PHE* 3.4 14.6 + - + +
885A VAL* 3.1 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 882 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A LEU* 3.4 33.0 - - + -
878A MET 3.0 14.8 + - - +
879A THR* 2.9 28.3 - - - +
881A MET* 1.3 73.8 - - - +
883A ILE* 1.3 68.6 + - + +
885A VAL* 3.2 9.8 + - + +
886A LEU* 2.9 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 883 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ILE* 3.6 38.3 - - + +
459A LEU* 4.7 10.5 - - + -
460A SER* 4.7 10.5 - - - +
879A THR* 2.9 29.5 + - - +
880A LEU* 3.4 24.0 - - + +
882A ILE* 1.3 84.7 - - + +
884A PHE* 1.3 58.5 + - - +
886A LEU* 3.1 5.2 + - + +
887A LEU* 2.8 50.1 + - + +
900A ILE* 5.3 2.0 - - + -
901A ILE* 4.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 884 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A LEU 2.6 19.9 + - - +
881A MET* 3.6 19.5 - - + +
883A ILE* 1.3 76.8 - - - +
885A VAL* 1.3 75.5 + - + +
887A LEU* 3.7 7.7 - - - +
888A TYR* 2.9 63.3 + + + +
894A VAL* 5.2 14.4 - - + -
897A ALA* 5.3 6.7 - - + -
898A LEU* 5.7 4.3 - - + -
901A ILE* 4.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 885 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A MET 3.1 18.1 + - - +
882A ILE* 3.6 12.3 - - + +
884A PHE* 1.3 93.1 - - + +
886A LEU* 1.3 65.4 + - + +
887A LEU 3.4 0.2 - - - -
888A TYR* 2.8 33.9 - - + +
889A LEU* 3.6 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 886 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ILE* 3.8 15.6 - - + +
455A LEU* 4.9 14.6 - - + -
456A ILE* 4.1 39.1 - - + +
459A LEU* 4.2 15.7 - - + -
882A ILE* 2.9 41.0 + - + +
883A ILE* 3.1 5.1 + - + +
885A VAL* 1.3 89.2 - - + +
887A LEU* 1.3 59.9 + - - +
889A LEU* 2.9 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 887 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ILE* 4.0 17.0 - - + -
883A ILE* 2.8 34.8 + - + +
884A PHE* 3.1 5.4 + - - +
886A LEU* 1.3 80.4 - - - +
888A TYR* 1.3 59.0 + - - +
889A LEU* 3.3 9.4 + - - +
890A ALA* 4.1 6.8 + - - +
891A PHE* 5.2 1.9 - - - -
896A GLU* 4.7 9.0 - - - +
897A ALA* 3.9 22.0 - - + +
900A ILE* 3.3 48.5 - - + -
901A ILE* 3.7 17.3 - - + -
938A ALA* 5.6 1.6 - - + -
942A VAL* 4.8 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 888 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A PHE* 2.9 46.9 + + + +
885A VAL* 2.8 24.9 - - + +
887A LEU* 1.3 75.1 - - - +
889A LEU* 1.3 70.0 + - - +
892A ARG* 3.1 40.8 - - + +
893A ARG 4.8 1.6 - - - +
894A VAL* 5.9 1.3 - - + -
896A GLU* 5.8 0.2 - - - -
897A ALA* 4.4 10.7 - - + +
----------------------------------------------------------
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