Contacts of the helix formed by residues 875 - 892 (chain B) in PDB entry 1SO2
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 ASP 875 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873B HIS 4.1 0.8 + - - -
874B LEU* 1.3 75.4 - - - +
876B HIS* 1.3 68.3 + - - +
877B VAL* 2.9 15.2 + - + +
878B GLU* 2.8 60.6 + - - +
879B PHE* 2.8 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 876 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B ASP* 1.3 75.9 - - - +
877B VAL* 1.3 78.2 + - + +
879B PHE* 4.0 8.4 - - - +
880B LYS* 3.0 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 877 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B ASP* 3.0 11.8 - - + +
876B HIS* 1.3 101.8 - - + +
878B GLU* 1.3 66.8 + - + +
880B LYS* 3.5 7.7 + - + +
881B ARG* 3.1 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 878 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B PHE* 5.1 5.6 - - - -
809B LEU* 4.2 18.3 - - + +
873B HIS 4.4 2.1 - - - +
874B LEU* 3.3 32.6 - - + +
875B ASP* 2.8 49.2 + - - +
877B VAL* 1.3 74.9 - - + +
879B PHE* 1.3 57.6 + - - +
881B ARG* 3.2 5.1 + - - +
882B PHE* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 879 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A ASN* 5.8 6.1 - - - -
859B TRP* 3.8 18.8 - + - -
862B TYR* 3.8 28.9 - + - -
863B LEU* 4.6 12.3 - - + -
869B ASN* 5.2 2.9 - - - -
871B LEU* 3.8 39.9 - - + +
874B LEU* 4.2 12.7 - - + +
875B ASP 2.8 15.7 + - - +
876B HIS* 4.1 7.6 - - - +
878B GLU* 1.3 74.7 - - - +
880B LYS* 1.3 69.9 + - - +
882B PHE* 3.1 6.9 + - + +
883B ARG* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 880 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A VAL* 5.2 16.8 - - + +
876B HIS* 3.0 26.3 + - + +
877B VAL* 3.8 6.5 - - + +
879B PHE* 1.3 79.8 - - - +
881B ARG* 1.3 62.1 + - - +
883B ARG* 3.5 10.9 + - - +
884B PHE* 3.2 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 881 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B LEU* 4.6 13.3 - - + +
810B GLU* 2.9 35.2 + - - +
877B VAL* 3.1 19.0 + - + +
878B GLU* 3.7 5.8 - - - +
880B LYS* 1.3 73.9 - - - +
882B PHE* 1.3 67.0 + - - +
884B PHE* 3.2 18.7 + - + +
885B LEU* 2.9 49.5 + - + +
922B GLU* 3.4 45.1 + - - +
925B ARG* 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 882 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B LEU* 3.8 30.0 - - + +
812B MET* 3.5 23.6 - - + -
813B ALA* 3.4 30.3 - - + -
816B VAL* 3.7 31.6 - - + -
859B TRP* 3.9 16.6 - + - -
871B LEU* 3.9 24.0 - - + -
874B LEU* 4.5 4.7 - - + -
878B GLU 2.8 18.2 + - - +
879B PHE* 3.4 10.5 - + - +
881B ARG* 1.3 76.8 - - - +
883B ARG* 1.3 65.6 + - - +
885B LEU* 3.1 10.3 + - - +
886B VAL* 3.0 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 883 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A ASN* 5.2 9.5 + - - -
841A ALA 3.7 1.8 + - - -
842A VAL* 3.7 30.2 + - - +
845A ASN* 3.9 10.5 + - - +
846A ASP* 2.9 43.5 + - - +
859B TRP* 3.3 62.4 + - + +
863B LEU* 5.3 3.8 - - - +
879B PHE* 2.9 29.1 + - + +
880B LYS* 3.6 9.2 - - - +
882B PHE* 1.3 77.4 - - - +
884B PHE* 1.3 64.0 + - - +
886B VAL* 3.3 2.3 + - - +
887B ILE* 3.0 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 884 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B LYS* 3.2 13.0 + - - +
881B ARG* 3.2 23.5 + - + +
883B ARG* 1.3 80.0 - - - +
885B LEU* 1.3 74.8 + - + +
887B ILE* 3.3 10.2 + - + +
888B GLU* 2.8 68.1 + - + +
926B LEU* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 885 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B LEU* 4.8 5.2 - - + +
810B GLU* 3.5 39.5 - - + +
813B ALA* 3.6 19.5 - - + -
881B ARG* 2.9 47.9 + - + +
882B PHE* 3.6 4.9 - - - +
884B PHE* 1.3 92.8 - - + +
886B VAL* 1.3 57.5 + - - +
888B GLU* 3.3 4.4 + - - +
889B ALA* 2.9 30.9 + - - +
926B LEU* 4.0 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 886 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813B ALA* 3.6 20.2 - - - +
816B VAL* 4.5 3.6 - - + -
817B ALA* 3.8 14.2 - - + +
820B MET* 3.7 28.9 - - - -
859B TRP* 3.8 14.6 - - + +
882B PHE* 3.0 45.1 + - + +
883B ARG 3.6 7.0 - - - +
885B LEU* 1.3 75.3 - - - +
887B ILE* 1.3 59.2 + - - +
889B ALA 3.3 0.7 + - - -
890B ILE* 3.0 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 887 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A ASN* 3.5 53.2 - - + +
846A ASP* 5.1 1.3 - - - +
847A ARG* 4.4 7.4 - - + +
855B ALA* 4.5 5.6 - - + -
859B TRP* 4.0 12.6 - - + +
883B ARG* 3.0 38.7 + - + +
884B PHE* 3.6 11.4 - - + +
886B VAL* 1.3 73.2 - - - +
888B GLU* 1.3 69.8 + - - +
890B ILE* 4.0 4.5 - - - +
891B LEU* 3.0 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 888 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A ARG* 3.1 30.8 + - - +
884B PHE* 2.8 58.6 + - + +
885B LEU 3.3 5.8 + - - +
887B ILE* 1.3 79.4 - - - +
889B ALA* 1.3 60.9 + - - +
891B LEU* 4.0 1.6 - - - +
892B ALA* 3.1 17.0 + - - +
926B LEU* 3.9 26.4 - - + +
930B GLN* 3.3 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 889 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814B LEU* 4.6 13.7 - - + -
817B ALA* 3.7 21.3 - - + -
885B LEU 2.9 17.0 + - - +
886B VAL* 4.6 0.2 - - - -
887B ILE 3.3 0.2 - - - -
888B GLU* 1.3 75.2 - - - +
890B ILE* 1.3 64.8 + - - +
892B ALA* 3.3 18.7 + - - +
893B THR* 3.8 3.6 + - - +
926B LEU* 5.1 1.7 - - + +
929B CYS* 5.4 3.6 - - + +
930B GLN* 4.7 7.4 - - + -
933B ILE* 3.7 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 890 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B ALA* 3.7 20.0 - - + +
820B MET* 4.2 13.7 - - + +
821B HIS* 3.8 40.2 - - - +
851B GLU* 3.8 25.7 - - - +
854B HIS* 4.3 2.2 - - + -
855B ALA* 4.0 25.4 - - + -
886B VAL* 3.0 33.9 + - + +
887B ILE 4.0 2.2 - - - +
889B ALA* 1.3 76.2 - - - +
891B LEU* 1.3 61.3 + - - +
893B THR* 2.6 28.9 + - - +
933B ILE* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 891 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A ASN* 4.9 2.7 - - - +
847A ARG* 3.0 52.0 - - - +
848B SER* 3.8 30.8 + - - +
851B GLU* 4.0 15.3 - - + +
852B ASN* 3.9 25.1 - - - +
855B ALA* 5.6 1.6 - - + -
887B ILE* 3.0 31.1 + - + +
888B GLU 4.1 2.0 - - - +
890B ILE* 1.3 72.4 - - + +
892B ALA* 1.3 61.8 + - - +
893B THR 3.0 6.6 + - - -
894B ASP* 3.3 19.8 + - - +
897B LYS* 5.0 5.1 - - + +
901B PHE* 4.9 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 892 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B GLU 3.1 19.1 + - - +
889B ALA 3.4 8.5 - - - +
890B ILE 3.1 1.0 - - - -
891B LEU* 1.3 77.7 - - - +
893B THR* 1.3 58.6 + - - +
894B ASP 3.2 3.7 + - - +
901B PHE* 3.7 34.0 - - + -
930B GLN* 3.7 28.9 - - + +
933B ILE* 4.9 0.2 - - + -
934B LYS* 3.4 24.7 + - + +
----------------------------------------------------------
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