Contacts of the helix formed by residues 884 - 896 (chain C) in PDB entry 2OO9
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 ASN 884 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C ALA* 2.7 32.5 + - + +
882C GLN 3.1 2.4 + - - +
883C ASN* 1.3 68.1 - - - +
885C ILE* 1.3 54.3 + - - +
886C GLU* 3.7 15.1 + - - +
887C MSE 3.3 24.9 + - + +
888C ALA* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 885 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C GLU* 3.5 44.6 - - + +
864C LEU* 6.3 0.9 - - + -
878C LEU* 4.8 6.7 - - + -
883C ASN 3.4 8.7 + - - +
884C ASN* 1.3 72.4 - - - +
886C GLU* 1.3 58.3 + - - +
888C ALA* 3.4 7.0 - - - +
889C LYS* 2.9 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 886 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884C ASN* 3.5 11.6 + - - +
885C ILE* 1.3 79.3 - - - +
887C MSE 1.4 58.4 + - - +
889C LYS* 4.1 7.2 - - - +
890C ASN* 3.4 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 887 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C ILE* 3.6 15.3 - - + +
881C ALA* 3.4 30.7 - - + +
884C ASN* 3.3 21.7 + - + +
885C ILE 3.2 0.4 - - - -
886C GLU* 1.4 77.9 + - - +
888C ALA* 1.3 65.3 + - - +
889C LYS 3.3 1.3 - - - -
890C ASN* 3.1 8.0 + - + +
891C ILE* 2.9 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 888 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864C LEU* 5.5 4.5 - - + -
874C ILE* 5.3 0.4 - - + +
877C ALA* 3.8 15.4 - - + +
878C LEU* 3.6 30.7 - - + -
881C ALA* 3.6 6.9 - - - +
884C ASN 2.8 20.9 + - - +
885C ILE* 3.4 7.0 - - - +
887C MSE 1.3 74.0 - - - +
889C LYS* 1.3 64.9 + - + +
890C ASN 3.0 1.0 + - - -
891C ILE* 3.2 3.7 + - - +
892C LEU* 3.1 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 889 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C GLU* 3.4 32.9 + - - -
863C ASN* 4.9 10.0 - - - +
864C LEU* 4.0 35.4 - - + -
867C GLN* 5.5 2.0 - - - +
869C TYR* 5.2 0.9 + - - -
885C ILE* 2.9 29.4 + - + +
886C GLU* 4.1 7.4 - - - +
888C ALA* 1.3 74.7 - - - +
890C ASN* 1.3 58.0 + - - +
892C LEU* 3.3 10.4 + - - +
893C ARG* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 890 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886C GLU 3.4 14.8 + - - +
887C MSE 3.1 14.3 + - + +
888C ALA 3.0 0.6 - - - -
889C LYS* 1.3 78.5 - - - +
891C ILE* 1.3 66.5 + - + +
893C ARG* 3.2 10.1 + - - +
894C GLU* 3.0 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 891 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877C ALA* 3.9 24.7 - - + +
880C ILE* 3.7 33.2 - - + -
887C MSE 2.9 49.8 + - + +
888C ALA 3.5 7.2 - - - +
890C ASN* 1.3 71.6 - - + +
892C LEU* 1.3 60.0 + - + +
894C GLU* 3.3 3.9 + - - -
895C PHE* 2.8 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 892 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864C LEU* 3.9 24.9 - - + -
869C TYR* 3.3 30.8 + - + -
873C ASP* 3.5 30.7 - - + +
874C ILE* 3.9 28.5 - - + +
877C ALA* 3.8 9.6 - - + -
888C ALA* 3.1 20.3 + - + +
889C LYS* 3.6 6.5 - - - +
891C ILE* 1.3 75.9 - - + +
893C ARG* 1.3 66.7 - - - +
896C ALA* 3.0 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 893 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869C TYR* 3.6 13.6 + - - +
889C LYS 2.8 19.0 + - - +
890C ASN* 3.2 11.2 + - - +
892C LEU* 1.3 78.3 - - - +
894C GLU* 1.3 77.3 + - - +
896C ALA 5.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 894 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890C ASN* 3.0 36.6 + - - +
891C ILE* 3.9 4.3 - - - +
893C ARG* 1.3 103.2 + - - +
895C PHE* 1.3 79.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 895 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891C ILE* 2.8 36.7 + - + +
894C GLU* 1.3 90.4 - - + +
896C ALA* 1.3 60.2 + - + +
897C ALA 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 896 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869C TYR* 3.8 12.7 - - + -
873C ASP* 3.9 16.8 - - + +
891C ILE* 6.3 0.2 - - + -
892C LEU* 3.0 48.7 + - + +
893C ARG 5.3 1.6 - - - +
894C GLU 5.7 0.2 - - - -
895C PHE* 1.3 80.8 - - + +
897C ALA* 1.3 64.1 + - - +
898C ALA* 3.9 1.2 + - - +
----------------------------------------------------------
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