Contacts of the helix formed by residues 881 - 889 (chain C) in PDB entry 6DBV
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 THR 881 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863C MET* 4.5 7.5 - - - -
877C ARG 3.6 11.0 - - - +
878C ARG* 3.3 24.9 + - - +
879C LEU 2.9 4.9 + - - -
880C MET* 1.3 77.9 - - - +
882C ARG* 1.3 64.0 + - - +
883C GLU* 2.9 21.4 - - - +
884C ALA* 2.9 32.4 + - - +
885C VAL* 3.1 15.2 + - - +
905C MET* 4.2 0.6 - - - +
909C LEU* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 882 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C MET 4.2 0.8 + - - -
881C THR* 1.3 71.3 - - - +
883C GLU* 1.3 64.2 + - - +
885C VAL* 3.6 8.7 - - + +
886C GLU* 2.4 67.5 + - + +
902C LEU* 4.0 22.2 - - + +
905C MET* 4.3 12.9 - - + +
906C ASP* 5.2 14.6 + - + -
909C LEU* 4.7 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 883 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863C MET* 4.2 17.7 - - + +
881C THR* 3.2 16.5 - - - +
882C ARG* 1.3 84.7 + - + +
884C ALA* 1.3 60.6 + - - +
886C GLU* 3.9 5.1 - - - +
887C ALA* 2.9 33.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
830C PHE* 4.5 3.8 - - + -
859C LEU* 4.2 27.0 - - + +
863C MET* 4.8 6.8 - - + -
878C ARG 4.8 2.2 - - - +
879C LEU* 3.9 21.8 - - + +
881C THR* 2.9 27.4 + - - +
883C GLU* 1.3 73.3 - - - +
885C VAL* 1.3 57.8 + - + +
887C ALA* 3.8 4.3 - - - +
888C VAL* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 885 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830C PHE* 4.1 15.5 - - + -
879C LEU 5.1 0.9 - - - +
881C THR 3.1 14.3 + - - +
882C ARG* 3.6 8.1 - - + +
884C ALA* 1.3 76.4 - - + +
886C GLU* 1.3 59.6 + - + +
888C VAL* 3.1 11.1 - - - +
889C CYS* 2.9 30.2 + - - -
901C LEU* 3.6 30.9 - - + +
902C LEU* 4.2 22.2 - - + -
905C MET* 3.5 37.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
882C ARG* 2.4 67.4 + - + +
883C GLU* 4.3 4.0 - - - +
885C VAL* 1.3 74.3 - - + +
887C ALA* 1.3 61.4 + - - +
889C CYS* 3.3 21.9 - - - +
890C GLU* 4.2 2.4 + - - +
902C LEU* 3.6 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 887 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858C GLN* 4.2 0.2 + - - -
859C LEU* 6.3 1.1 - - + -
862C LYS* 3.2 49.9 - - + +
863C MET* 5.7 1.8 - - + +
883C GLU 2.9 19.6 + - - +
884C ALA* 3.8 5.4 - - - +
886C GLU* 1.3 77.6 - - - +
888C VAL* 1.3 61.1 + - - +
890C GLU* 3.3 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 888 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830C PHE* 3.5 37.9 - - + -
834C ILE* 4.8 12.1 - - + -
855C LEU* 3.5 31.2 - - + -
858C GLN* 4.7 12.8 - - + -
859C LEU* 6.1 3.4 - - + -
862C LYS* 4.3 4.7 - - - +
884C ALA 2.9 18.3 + - - +
885C VAL* 3.1 15.0 - - + +
887C ALA* 1.3 70.8 - - - +
889C CYS* 1.3 62.3 + - - +
890C GLU 3.0 5.6 - - - -
891C LEU* 3.0 16.8 + - + +
892C VAL* 3.9 5.8 + - + +
901C LEU* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 889 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885C VAL* 2.9 25.5 + - - -
886C GLU* 3.3 20.9 - - - +
887C ALA 3.2 0.2 - - - -
888C VAL* 1.3 76.8 - - - +
890C GLU* 1.3 61.3 + - - +
891C LEU 3.1 1.5 + - - -
892C VAL* 3.2 28.6 - - - +
898C ARG* 3.5 35.8 + - - +
901C LEU* 3.9 22.7 - - - -
902C LEU* 4.6 9.6 - - - -
----------------------------------------------------------
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