Contacts of the helix formed by residues 847 - 868 (chain B) in PDB entry 2IVS
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 847 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821B LYS* 6.3 0.2 - - - -
845B ALA 5.6 1.6 - - - +
846B LEU* 1.3 76.5 - - - +
848B MET* 1.3 65.7 + - - +
849B GLY* 3.4 6.6 + - - -
850B ASP* 2.8 44.2 + - - +
851B LEU* 3.1 15.3 + - - +
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Residues in contact with MET 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847B THR* 1.3 71.3 - - - +
849B GLY* 1.3 62.4 + - - +
851B LEU* 3.2 27.1 + - + +
852B ILE* 2.9 47.4 + - + +
945B VAL* 4.9 16.6 - - + +
975B ASN* 3.2 30.1 - - + +
976B CYS* 4.9 4.7 - - - -
977B SER* 5.4 5.4 - - - +
980B MET* 5.0 7.6 - - + -
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Residues in contact with GLY 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847B THR* 3.0 9.0 + - - -
848B MET* 1.3 77.9 - - - +
850B ASP* 1.3 55.6 + - - +
852B ILE* 3.3 5.8 + - - +
853B SER* 2.9 26.0 + - - -
1009B MET* 3.4 23.9 - - - +
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Residues in contact with ASP 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B ALA 4.1 2.6 - - - +
846B LEU* 3.5 28.2 - - + +
847B THR* 2.8 39.8 + - - +
849B GLY* 1.3 72.2 - - - +
851B LEU* 1.3 58.1 - - - +
853B SER* 3.0 10.5 + - - -
854B PHE* 2.8 43.0 + - + -
886B ARG* 4.1 11.9 + - - -
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Residues in contact with LEU 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816B LEU* 3.8 14.6 - - + -
821B LYS* 5.9 4.0 - - + -
846B LEU* 4.2 11.0 - - + +
847B THR 3.1 12.9 + - - +
848B MET* 3.5 34.5 - - + +
850B ASP* 1.3 79.1 - - - +
852B ILE* 1.3 57.4 + - - +
854B PHE* 3.3 12.8 + - + +
855B ALA* 3.0 27.0 + - - +
944B ILE* 3.7 34.1 - - + +
945B VAL* 4.5 10.3 - - + +
947B LEU* 3.8 33.4 - - + -
980B MET* 5.9 1.6 - - + -
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Residues in contact with ILE 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848B MET* 2.9 39.9 + - + +
849B GLY* 3.8 7.4 - - - +
851B LEU* 1.3 72.2 - - - +
853B SER* 1.3 60.8 + - - +
855B ALA* 3.3 6.4 + - - +
856B TRP* 2.9 28.1 + - + +
980B MET* 3.7 20.4 - - + -
1005B LEU* 3.8 39.6 - - + +
1008B MET* 4.3 26.5 - - + +
1009B MET* 3.8 14.6 - - + -
1012B ARG* 5.9 5.2 - - + -
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Residues in contact with SER 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849B GLY 2.9 14.7 + - - -
850B ASP* 3.1 13.5 - - - -
852B ILE* 1.3 76.3 - - - +
854B PHE* 1.3 65.0 + - - +
856B TRP* 3.3 7.8 + - - +
857B GLN* 3.0 44.7 + - - +
1009B MET* 3.4 15.1 - - - +
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Residues in contact with PHE 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812B LEU* 4.4 10.8 - - + -
815B PHE* 4.0 29.2 - + - -
816B LEU* 4.4 2.5 - - + -
846B LEU* 4.0 28.0 - - + -
850B ASP* 2.8 28.7 + - + -
851B LEU* 3.5 21.5 - - + +
852B ILE 3.2 0.4 - - - -
853B SER* 1.3 79.6 - - - +
855B ALA* 1.3 61.9 - - - +
857B GLN* 3.3 8.6 + - - +
858B ILE* 3.2 28.6 + - - +
886B ARG* 3.9 29.6 - - + -
888B MET* 3.5 34.7 - - + +
944B ILE* 4.6 10.1 - - + -
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Residues in contact with ALA 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851B LEU 3.0 14.0 + - - +
852B ILE* 3.7 8.3 - - - +
854B PHE* 1.3 76.1 - - - +
856B TRP* 1.3 56.0 + - - +
858B ILE* 3.5 3.4 + - - +
859B SER* 3.0 28.8 + - - -
937B PHE* 3.6 9.9 - - + -
941B LEU* 3.7 30.3 - - + -
944B ILE* 4.2 13.8 - - + +
980B MET* 5.5 0.7 - - + -
1005B LEU* 3.7 16.8 - - + -
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Residues in contact with TRP 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786B HIS* 4.7 8.5 - + - -
852B ILE* 2.9 17.7 + - + +
853B SER* 3.7 9.0 - - - +
855B ALA* 1.3 73.2 - - - +
857B GLN* 1.3 90.5 + - + +
859B SER* 3.3 2.4 + - - -
860B GLN* 2.8 61.0 + - + +
1002B SER* 3.7 17.0 - - - -
1005B LEU* 3.7 16.6 - - + +
1006B GLU* 2.7 47.8 + - + +
1009B MET* 5.7 2.2 - - + -
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Residues in contact with GLN 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786B HIS* 2.7 53.2 - - + +
853B SER* 3.0 39.7 + - - +
854B PHE* 3.3 13.3 + - - +
856B TRP* 1.3 94.9 - - + +
858B ILE* 1.3 61.2 + - - +
860B GLN* 3.3 4.8 + - - +
861B GLY 3.1 17.2 + - - -
886B ARG 3.7 16.0 + - - -
887B LYS* 3.5 10.3 - - - +
888B MET* 3.0 23.3 + - + -
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Residues in contact with ILE 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786B HIS* 5.3 0.7 - - - -
812B LEU* 3.9 27.6 - - + -
854B PHE 3.2 15.1 + - - +
855B ALA* 3.7 6.3 - - - +
857B GLN* 1.3 74.8 - - - +
859B SER* 1.3 58.5 + - - +
861B GLY* 3.1 3.5 + - - -
862B MET* 2.8 32.2 + - + +
875B LEU* 4.8 1.3 - - + -
880B ILE* 3.9 27.6 - - + -
888B MET* 3.8 17.3 - - + -
890B ILE* 3.6 15.6 - - + +
937B PHE* 3.8 18.4 - - + -
940B LEU* 3.9 16.6 - - + -
944B ILE* 4.1 15.0 - - + -
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Residues in contact with SER 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855B ALA 3.0 17.8 + - - -
856B TRP* 3.7 6.7 - - - -
858B ILE* 1.3 75.5 - - - +
860B GLN* 1.3 57.2 + - - +
862B MET* 3.7 6.3 - - - +
863B GLN* 2.9 29.5 + - - +
937B PHE* 3.9 8.9 - - - -
998B PHE* 3.1 17.0 + - - +
1001B ILE* 3.5 22.0 - - - +
1002B SER* 2.7 29.6 + - - -
1005B LEU* 4.3 0.2 - - - -
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Residues in contact with GLN 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784B HIS* 3.8 17.9 + - + +
786B HIS* 4.6 3.1 - - + -
856B TRP* 2.8 61.0 + - + +
857B GLN* 3.5 8.5 - - - +
858B ILE 3.2 0.2 - - - -
859B SER* 1.3 71.1 - - - +
861B GLY* 1.3 65.6 + - - +
863B GLN* 3.4 16.9 + - - +
864B TYR* 3.1 22.2 + - - +
1002B SER* 2.9 36.6 + - - -
1006B GLU* 3.8 4.0 + - - -
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Residues in contact with GLY 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784B HIS* 3.7 21.1 - - - -
786B HIS* 4.4 2.7 - - - -
787B VAL* 4.3 5.3 - - - +
857B GLN 3.1 6.5 + - - -
858B ILE 3.1 6.5 + - - -
860B GLN* 1.3 78.0 - - - +
862B MET* 1.3 56.2 + - - +
864B TYR* 3.2 5.2 + - - +
865B LEU* 2.9 31.6 + - - +
890B ILE* 3.7 16.4 - - - -
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Residues in contact with MET 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858B ILE* 2.8 23.1 + - + +
859B SER 3.7 0.9 - - - +
861B GLY* 1.3 73.3 - - - +
863B GLN* 1.3 56.1 + - - +
865B LEU* 3.1 27.4 + - + +
866B ALA* 2.7 38.9 + - + +
870B LEU 5.2 1.3 - - - +
872B HIS* 4.3 9.4 - - + +
875B LEU* 3.9 25.6 - - + -
890B ILE* 3.8 11.7 - - + -
930B THR* 5.8 0.4 - - + -
933B ASP* 3.5 28.0 - - + +
998B PHE* 3.5 49.6 - - + -
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Residues in contact with GLN 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859B SER 2.9 10.1 + - - +
860B GLN* 3.4 23.1 + - - +
862B MET* 1.3 73.2 - - - +
864B TYR* 1.3 58.1 + - - +
866B ALA* 3.8 4.1 - - - +
867B GLU* 2.9 30.7 + - - +
998B PHE* 3.7 11.9 - - + +
999B ALA* 3.5 40.0 - - + +
1002B SER* 3.3 22.9 + - - -
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Residues in contact with TYR 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781B GLN 4.0 3.3 + - - -
782B VAL* 3.7 21.0 - - + -
783B ASN* 3.1 33.4 + - - +
784B HIS* 3.5 39.3 - + + -
787B VAL* 4.5 0.7 - - + -
860B GLN 3.1 5.7 + - - +
861B GLY 3.3 8.5 - - - +
862B MET 3.2 0.2 - - - -
863B GLN* 1.3 80.0 - - - +
865B LEU* 1.3 70.7 + - + +
867B GLU* 3.3 8.8 + - + +
868B MET* 3.1 53.1 + - + +
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Residues in contact with LEU 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782B VAL* 4.1 8.3 - - + -
787B VAL* 4.1 11.2 - - + -
861B GLY 2.9 16.4 + - - +
862B MET* 3.1 35.2 + - + +
864B TYR* 1.3 90.1 - - + +
866B ALA* 1.3 61.9 + - - +
868B MET* 3.0 14.4 + - - +
870B LEU* 3.1 51.9 + - + +
872B HIS* 4.7 4.9 - - + -
890B ILE* 4.2 10.3 - - + -
893B PHE* 3.8 33.2 - - + -
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Residues in contact with ALA 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862B MET* 2.7 22.5 + - + +
863B GLN* 3.8 5.8 - - - +
865B LEU* 1.3 72.5 - - - +
867B GLU* 1.3 57.9 + - - +
869B LYS* 3.0 18.8 + - - +
870B LEU 4.0 5.1 + - - +
930B THR* 3.6 40.2 + - + +
998B PHE* 4.5 4.5 - - + -
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Residues in contact with GLU 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863B GLN 2.9 18.3 + - - +
864B TYR* 3.6 8.7 - - + +
865B LEU 3.2 0.2 - - - -
866B ALA* 1.3 76.7 - - - +
868B MET* 1.3 58.5 + - + +
869B LYS* 3.3 4.5 + - - +
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Residues in contact with MET 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781B GLN* 3.9 40.4 - - + +
782B VAL* 4.0 2.5 - - - -
864B TYR* 3.1 49.7 + - + +
865B LEU 3.0 9.9 + - - +
867B GLU* 1.3 76.1 - - + +
869B LYS* 1.3 67.6 + - - +
870B LEU* 3.4 31.6 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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