Contacts of the helix formed by residues 873 - 889 (chain C) in PDB entry 1X86
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 SER 873 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869C LEU* 2.9 37.2 + - - +
870C THR* 4.3 1.6 - - - +
872C PHE* 1.3 79.6 - - - +
874C GLY* 1.3 70.6 + - - +
875C PRO* 3.1 3.5 - - - +
876C GLY* 2.9 13.0 + - - -
877C GLU* 3.6 5.4 - - - -
962C LYS* 4.5 7.8 + - - -
966C HIS* 3.7 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 874 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873C SER* 1.3 75.3 + - - +
875C PRO* 1.4 67.3 - - - +
877C GLU* 3.2 10.2 + - - +
878C GLU* 2.9 42.0 + - - +
966C HIS* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 875 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870C THR 5.8 0.2 - - - +
873C SER 3.6 4.7 - - - +
874C GLY* 1.4 82.8 - - - +
876C GLY* 1.3 56.4 + - - +
878C GLU* 4.1 4.3 - - + +
879C LYS* 3.1 42.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
841C LEU* 5.6 2.1 - - - +
870C THR 3.9 11.6 + - - -
871C TRP* 3.7 20.8 - - - +
873C SER 2.9 11.6 + - - -
875C PRO* 1.3 73.8 - - - +
877C GLU* 1.3 67.9 + - - +
879C LYS* 3.8 5.9 - - - +
880C LEU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 877 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872C PHE* 3.2 19.6 - - - +
873C SER* 3.4 13.7 + - - +
874C GLY* 3.2 12.8 + - - +
876C GLY* 1.3 74.6 - - - +
878C GLU* 1.3 67.3 + - + +
880C LEU* 3.8 1.2 - - - +
881C LYS* 2.8 45.7 + - + +
966C HIS* 2.4 40.1 + - - -
969C GLN* 3.4 26.0 - - - +
970C ILE* 4.0 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 878 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C GLY* 2.9 27.0 + - - +
875C PRO* 4.1 4.3 - - + +
877C GLU* 1.3 84.8 - - + +
879C LYS* 1.3 67.1 + - - +
881C LYS* 3.3 31.2 + - - -
882C HIS* 3.2 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 879 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841C LEU* 4.6 19.5 - - + +
875C PRO* 3.1 26.1 + - + +
876C GLY* 3.8 6.3 - - - +
878C GLU* 1.3 79.1 - - - +
880C LEU* 1.3 62.3 + - - +
882C HIS* 4.4 1.7 - - - +
883C ALA* 3.4 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 880 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841C LEU* 3.2 33.0 - - + +
842C HIS* 4.2 13.9 - - + +
845C LEU* 4.8 7.2 - - + -
871C TRP 4.9 1.6 - - - +
872C PHE* 4.2 22.4 - - + -
876C GLY 3.0 17.8 + - - +
877C GLU 3.9 2.0 - - - +
879C LYS* 1.3 73.0 - - - +
881C LYS* 1.3 58.7 + - - +
882C HIS 3.0 2.1 + - - -
883C ALA* 3.2 1.2 + - - -
884C ALA* 2.7 40.4 + - + +
933C GLN* 4.3 4.0 - - - +
937C LEU* 3.8 28.7 - - + -
940C TYR* 4.5 8.5 - - + -
970C ILE* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 881 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877C GLU* 2.8 35.0 + - + +
878C GLU* 3.3 36.7 + - - +
880C LEU* 1.3 73.1 - - - +
882C HIS* 1.3 70.8 + - + +
884C ALA* 3.6 1.9 - - - +
885C ALA* 2.9 29.8 + - - +
969C GLN 5.1 1.8 - - - +
970C ILE* 3.7 32.3 - - + +
973C PHE* 3.4 51.1 - - + -
974C VAL* 4.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 882 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878C GLU* 3.2 45.4 + - + +
879C LYS* 4.4 1.8 - - - +
880C LEU 3.1 0.8 - - - -
881C LYS* 1.3 92.4 + - + +
883C ALA* 1.3 63.6 + - - +
885C ALA* 3.3 5.7 + - - +
886C THR* 2.8 30.3 + - - +
973C PHE* 4.2 23.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 883 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834C ASN* 3.4 26.8 + - - +
837C ASP* 3.8 13.9 - - - +
838C ILE* 3.6 17.1 - - + +
841C LEU* 5.1 5.4 - - + -
879C LYS 3.4 16.6 + - - +
880C LEU* 3.2 3.7 + - - +
882C HIS* 1.3 77.1 - - - +
884C ALA* 1.3 65.6 + - - +
886C THR* 3.6 1.5 + - - -
887C PHE* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 884 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838C ILE* 4.2 1.7 - - - +
880C LEU* 2.7 25.5 + - + +
881C LYS* 3.6 4.5 - - - +
883C ALA* 1.3 70.1 - - - +
885C ALA* 1.3 69.9 + - - +
887C PHE* 3.3 2.3 + - - +
888C CYS* 3.0 25.5 + - - -
933C GLN* 4.3 12.3 - - - +
937C LEU* 3.5 39.0 - - + -
974C VAL* 3.9 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 885 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C LYS 2.9 19.3 + - - +
882C HIS* 3.5 5.2 - - - +
884C ALA* 1.3 76.9 - - - +
886C THR* 1.3 65.6 + - - +
889C SER* 2.8 30.0 + - - -
973C PHE* 4.1 16.8 - - + -
974C VAL* 3.9 15.1 - - - +
977C ALA* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 886 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833C SER* 4.5 3.7 + - - -
834C ASN* 3.8 25.5 - - + +
882C HIS* 2.8 17.0 + - - +
883C ALA* 3.8 3.7 - - - -
884C ALA 3.5 0.2 - - - -
885C ALA* 1.3 78.4 - - - +
887C PHE* 1.3 59.2 + - - +
889C SER* 4.2 5.6 + - - -
890C ASN* 3.5 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 887 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C LEU* 5.7 0.7 - - + -
809C LEU* 4.4 17.0 - - + -
831C ILE 5.5 1.6 - - - -
832C PHE* 3.5 19.3 - + - -
833C SER* 3.1 20.6 - - - -
834C ASN* 3.2 13.5 - - - +
835C LEU* 4.2 11.9 - - + -
838C ILE* 3.5 25.4 - - + -
883C ALA 3.3 11.4 + - - +
884C ALA 3.9 2.0 - - - +
885C ALA 2.9 1.6 + - - -
886C THR* 1.3 78.0 - - - +
888C CYS* 1.3 68.8 + - - +
890C ASN* 3.1 15.8 + - - +
891C GLN* 3.3 8.5 + - - -
930C ILE* 3.6 45.2 - - + +
933C GLN* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 888 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884C ALA 3.0 24.3 + - - +
887C PHE* 1.3 70.2 - - - +
889C SER* 1.3 60.0 + - - +
891C GLN* 2.6 36.8 + - - +
892C PRO* 3.7 3.1 - - - +
933C GLN* 4.3 13.5 - - - -
934C MET* 3.9 35.2 - - + -
937C LEU* 4.4 2.5 - - - -
974C VAL* 4.0 20.9 - - + -
978C VAL* 4.2 11.4 - - + +
69D LEU* 5.0 0.2 - - + -
72D LEU* 4.4 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 889 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C ALA 2.8 22.8 + - - -
886C THR* 4.2 5.7 + - - -
888C CYS* 1.3 77.3 - - - +
890C ASN* 1.3 60.9 + - - +
891C GLN 3.4 0.5 + - - -
892C PRO* 3.5 9.7 - - - +
893C PHE* 4.0 5.7 - - - -
977C ALA* 4.1 19.6 + - - -
978C VAL* 4.1 16.3 - - - +
981C ALA* 3.4 29.7 - - - +
982C GLU 5.5 0.2 + - - -
----------------------------------------------------------
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