Contacts of the helix formed by residues 834 - 845 (chain B) in PDB entry 4RIB
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 GLU 834 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B GLU* 4.7 1.2 - - - +
832B HIS* 3.7 18.3 - - + -
833B GLY* 1.3 78.7 - - - +
835B GLY* 1.3 64.4 + - - +
837B THR* 3.8 7.0 + - - -
838B PHE* 3.9 14.7 - - - -
958B LEU* 4.3 10.6 - - - +
959B PRO 3.4 23.8 - - - +
960B ASP* 2.6 39.8 + - - +
962B VAL* 5.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 835 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B GLU* 1.3 80.3 - - - +
836B SER* 1.3 64.4 + - - +
837B THR 3.3 0.3 + - - -
838B PHE* 3.3 5.7 + - - +
839B SER* 3.0 22.1 + - - -
955B ARG 4.6 8.5 - - - -
957B GLY 6.2 0.2 - - - -
958B LEU* 3.5 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 836 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B GLY 2.9 12.8 + - - -
835B GLY* 1.3 76.0 - - - +
837B THR* 1.3 63.5 + - - +
839B SER* 3.1 7.2 + - - -
840B THR* 2.8 31.1 + - - +
918B SER* 4.2 15.3 - - - -
921B ARG* 2.6 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 837 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831B ILE* 3.4 12.1 + - + +
833B GLY* 3.3 24.2 + - - -
834B GLU 4.0 7.6 - - - -
835B GLY 3.2 0.2 - - - -
836B SER* 1.3 81.5 + - - +
838B PHE* 1.3 67.3 + - + +
840B THR* 3.3 10.0 + - - -
841B LEU* 3.3 17.2 + - + +
921B ARG* 3.4 15.6 - - - +
922B PHE* 4.0 21.4 - - + -
931B LEU* 4.1 16.8 - - + -
962B VAL* 4.3 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 838 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B GLU 3.9 17.3 - - - -
835B GLY 3.3 5.3 + - - +
837B THR* 1.3 81.5 - - + +
839B SER* 1.3 62.8 + - - +
841B LEU* 3.4 13.3 + - + +
842B TYR* 3.2 22.0 + - - +
935B LEU* 4.9 15.5 - - + -
939B VAL* 5.9 1.8 - - + -
940B LEU* 6.1 3.8 - - + -
943B VAL* 4.2 38.2 - - + +
947B LEU* 4.2 5.0 - - + +
958B LEU* 4.0 33.2 - - + -
959B PRO* 4.8 8.7 - - + -
962B VAL* 3.9 21.1 - - + -
973B LEU* 3.6 36.3 - - + -
994B LEU* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 839 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835B GLY 3.0 15.4 + - - -
836B SER* 3.4 12.8 - - - -
838B PHE* 1.3 75.9 - - - +
840B THR* 1.3 58.4 + - - +
841B LEU 3.1 0.5 + - - -
842B TYR* 3.2 6.1 + - - +
843B GLY* 2.8 25.8 + - - -
916B LEU* 3.2 34.7 + - - +
947B LEU* 4.5 10.5 - - - +
951B PHE* 4.1 15.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 840 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836B SER* 2.8 22.6 + - - +
837B THR 3.3 1.4 + - - -
839B SER* 1.3 71.6 - - - +
841B LEU* 1.3 57.7 + - - +
843B GLY 3.7 1.7 - - - +
844B LEU* 3.1 33.4 + - - +
916B LEU 3.3 12.6 - - - +
917B VAL* 3.7 9.3 - - - +
918B SER* 3.1 47.4 + - - +
921B ARG* 4.3 5.9 - - + +
922B PHE* 3.3 28.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 841 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837B THR* 3.3 14.2 + - + +
838B PHE* 3.7 13.0 - - + +
839B SER 3.1 0.8 - - - -
840B THR* 1.3 74.5 - - - +
842B TYR* 1.3 52.6 + - - +
843B GLY 2.8 3.5 + - - -
844B LEU* 2.7 33.5 + - + +
845B LEU* 2.7 25.4 + - + +
902B VAL* 5.6 3.1 - - + -
922B PHE* 3.6 29.4 - - + -
928B ALA* 4.9 8.3 - - + +
931B LEU* 4.7 9.0 - - + -
932B VAL* 4.0 18.6 - - + -
935B LEU* 3.8 28.7 - - + -
940B LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 842 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B PHE 3.2 10.5 + - - +
839B SER 3.4 7.6 - - - +
841B LEU* 1.3 76.5 - - - +
843B GLY* 1.3 59.7 + - - +
845B LEU* 3.9 2.2 - - - +
846B LEU* 3.3 41.9 + - + +
850B ILE* 4.4 9.8 - - + +
870B LEU* 4.3 5.2 - - + +
875B PHE* 3.6 18.7 - - - -
916B LEU* 3.5 33.9 - - + -
943B VAL* 5.7 0.4 - - + -
944B CYS* 3.7 51.9 - - + -
947B LEU* 3.7 36.2 + - + -
948B ALA* 3.4 22.4 - - + +
951B PHE* 4.8 1.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 843 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B SER 2.8 14.6 + - - -
841B LEU 2.9 0.4 - - - -
842B TYR* 1.3 77.8 - - - +
844B LEU* 1.3 58.9 + - - +
845B LEU 3.2 0.4 - - - -
847B TRP* 3.2 35.3 + - - +
850B ILE* 4.4 11.1 - - - +
916B LEU* 4.5 8.3 - - - -
917B VAL* 3.8 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 844 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840B THR* 3.1 30.3 + - - +
841B LEU* 2.7 19.8 + - + +
843B GLY* 1.3 74.8 - - - +
845B LEU* 1.3 65.0 + - - +
846B LEU 3.3 0.7 + - - -
847B TRP* 4.4 1.4 + - + -
901B TRP 4.4 0.9 - - - +
902B VAL* 4.5 24.9 - - + +
905B THR* 2.7 46.3 + - + +
906B TRP* 4.2 25.8 - - + +
917B VAL* 4.4 9.9 - - + -
919B TRP* 3.7 33.4 - - + -
922B PHE* 5.2 3.6 - - + -
928B ALA* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 845 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B LEU* 2.7 21.7 + - + +
842B TYR* 4.4 1.1 - - - +
843B GLY 3.2 0.2 - - - -
844B LEU* 1.3 82.5 - - - +
846B LEU* 1.3 79.5 + - + +
847B TRP 3.8 0.4 - - - -
848B ASP* 5.3 0.2 - - - -
886B ARG* 3.4 19.6 + - - +
890B ILE* 4.2 22.4 - - + -
898B LEU* 5.0 7.0 - - + +
901B TRP* 4.3 24.2 - - + -
902B VAL* 3.8 28.9 - - + +
932B VAL* 5.1 4.5 - - + -
940B LEU* 4.4 32.8 - - + -
944B CYS* 5.0 5.6 - - - -
----------------------------------------------------------
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