Contacts of the helix formed by residues 826 - 848 (chain B) in PDB entry 6PUO
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 SER 826 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816B VAL* 6.4 0.9 - - - -
820B ASP* 4.6 18.8 - - - -
822B GLN* 5.3 6.5 - - - -
824B VAL 3.2 7.2 + - - -
825B PRO* 1.3 78.2 - - - +
827B TRP* 1.3 66.3 + - - +
828B CYS* 3.3 10.3 - - - -
829B GLU* 3.4 17.7 + - - +
830B CYS* 3.5 9.4 + - - +
886B ARG* 4.0 5.1 - - - +
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Residues in contact with TRP 827 (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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826B SER* 1.3 72.9 - - - +
828B CYS* 1.3 63.9 + - - +
830B CYS* 3.1 10.8 + - - +
831B ALA* 3.0 24.5 + - - +
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Residues in contact with CYS 828 (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* 4.7 8.5 - - + +
815B TYR* 5.5 9.4 - - - -
816B VAL* 3.7 27.1 - - + -
820B ASP* 5.6 5.2 - - + -
826B SER* 3.3 6.8 - - - -
827B TRP* 1.3 76.7 - - - +
829B GLU* 1.3 61.3 + - - +
831B ALA* 3.2 10.6 + - - +
832B ILE* 3.0 33.4 + - - +
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Residues in contact with GLU 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B VAL* 4.8 8.1 - - + +
825B PRO* 5.2 2.2 - - + -
826B SER* 3.4 22.1 + - - +
827B TRP 3.2 0.4 - - - -
828B CYS* 1.3 77.7 - - - +
830B CYS* 1.3 57.3 + - - +
832B ILE* 3.2 16.1 - - + +
833B TYR* 2.9 29.3 + - - +
886B ARG* 4.7 16.4 - - - +
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Residues in contact with CYS 830 (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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826B SER 3.5 6.4 + - - +
827B TRP* 3.1 13.8 + - - +
829B GLU* 1.3 77.7 - - - +
831B ALA* 1.3 57.9 + - - +
833B TYR* 3.3 7.8 + - - +
834B LEU* 2.9 37.5 + - + +
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Residues in contact with ALA 831 (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* 5.2 7.2 - - + -
827B TRP 3.0 12.7 + - - +
828B CYS* 3.2 14.6 + - - +
830B CYS* 1.3 76.0 - - - +
832B ILE* 1.3 58.8 + - + +
834B LEU* 3.3 17.6 - - + +
835B TRP* 3.0 34.4 + - + +
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Residues in contact with ILE 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B PHE* 4.1 23.2 - - + -
812B LEU* 3.7 28.5 - - + +
813B PHE* 3.6 39.7 - - + +
816B VAL* 4.1 18.2 - - + -
828B CYS 3.0 11.8 + - - +
829B GLU* 3.2 22.2 - - + +
831B ALA* 1.3 75.4 - - - +
833B TYR* 1.3 56.4 + - - +
835B TRP* 3.5 8.7 - - + +
836B LEU* 3.0 30.7 + - - +
879B PHE* 5.1 9.9 - - + -
899B LEU* 6.0 2.7 - - + -
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Residues in contact with TYR 833 (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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829B GLU 2.9 19.1 + - - +
830B CYS* 3.5 9.6 - - - +
831B ALA 3.2 0.2 - - - -
832B ILE* 1.3 78.8 - - - +
834B LEU* 1.3 58.8 + - - +
836B LEU* 3.4 2.3 + - - +
837B PHE* 2.9 28.0 + - - +
879B PHE* 4.8 16.4 - - + -
883B LEU* 5.3 9.6 - - + -
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Residues in contact with LEU 834 (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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830B CYS* 2.9 24.5 + - + +
831B ALA* 3.3 18.6 - - - +
833B TYR* 1.3 73.7 - - - +
835B TRP* 1.3 66.8 + - + +
837B PHE* 3.5 17.0 - - + +
838B SER* 2.9 29.0 + - - -
1083B PRO* 5.9 10.1 - - + +
1086B LEU* 5.4 5.0 - - + +
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Residues in contact with TRP 835 (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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805B SER* 3.2 43.5 + - - -
806B TYR* 5.4 1.8 - - - +
808B ALA* 4.7 8.5 - - + -
809B PHE* 3.4 49.5 - + + +
812B LEU* 5.3 14.4 - - + -
831B ALA* 3.0 23.7 + - + +
832B ILE* 3.5 8.1 - - + +
833B TYR 3.2 0.2 - - - -
834B LEU* 1.3 83.8 - - + +
836B LEU* 1.3 57.7 + - - +
838B SER* 2.3 29.2 + - - -
839B LEU* 3.0 18.5 + - + +
1082B PRO* 4.3 8.9 - - + +
1083B PRO* 3.5 31.0 - - + +
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Residues in contact with LEU 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809B PHE* 4.6 14.3 - - + -
832B ILE 3.0 16.5 + - - +
833B TYR 3.9 2.7 - - - +
835B TRP* 1.3 76.5 - - - +
837B PHE* 1.3 56.6 + - - +
839B LEU* 3.3 23.7 + - + -
840B VAL* 3.0 38.1 + - + +
876B ILE* 5.4 5.6 - - + -
879B PHE* 3.6 50.0 - - + -
906B PHE* 3.9 35.9 - - + -
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Residues in contact with PHE 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B TYR 2.9 16.9 + - - +
834B LEU* 3.5 17.3 - - + +
836B LEU* 1.3 77.8 - - - +
838B SER* 1.3 59.2 + - - +
840B VAL* 3.3 14.3 - - + +
841B CYS* 2.9 38.5 + - + +
1086B LEU* 4.2 25.6 - - + -
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Residues in contact with SER 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B LEU 2.9 11.5 + - - -
835B TRP* 2.3 35.0 + - - -
837B PHE* 1.3 80.5 - - - +
839B LEU* 1.3 61.2 + - - +
841B CYS* 3.2 8.2 + - - +
842B GLU* 3.0 23.9 + - - +
1082B PRO* 3.3 30.9 + - - +
1083B PRO* 4.9 0.6 - - - +
1085B ILE* 4.5 6.6 - - - +
1086B LEU* 3.6 23.1 - - - -
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Residues in contact with LEU 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806B TYR* 4.4 26.9 - - + -
809B PHE* 5.3 7.2 - - + -
835B TRP* 3.0 17.3 + - + +
836B LEU* 3.6 27.8 - - + +
837B PHE 3.3 0.2 - - - -
838B SER* 1.3 81.7 + - - +
840B VAL* 1.3 64.6 + - + +
842B GLU* 3.3 7.2 + - - +
843B GLU* 3.0 31.5 + - + +
872B ASP* 6.1 4.5 - - + -
876B ILE* 5.7 4.9 - - + -
906B PHE* 5.3 7.2 - - + -
1082B PRO* 5.4 11.0 - - + -
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Residues in contact with VAL 840 (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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836B LEU* 3.0 26.2 + - + +
837B PHE* 3.3 24.7 - - + +
839B LEU* 1.3 77.2 - - + +
841B CYS* 1.3 59.9 + - - +
843B GLU* 3.7 7.5 - - + +
844B MET* 2.9 29.6 + - - +
876B ILE* 3.7 43.1 - - + -
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Residues in contact with CYS 841 (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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837B PHE* 2.9 31.6 + - + +
838B SER* 3.5 8.7 - - - +
840B VAL* 1.3 76.7 - - - +
842B GLU* 1.3 59.4 + - - +
844B MET* 3.3 19.2 + - + +
845B ARG* 2.9 26.7 + - - +
1086B LEU* 4.4 9.2 - - + -
1089B HIS* 3.5 34.8 - - - -
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Residues in contact with GLU 842 (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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838B SER 3.0 13.9 + - - +
839B LEU* 3.7 8.5 - - - +
841B CYS* 1.3 75.4 - - - +
843B GLU* 1.3 58.1 + - - +
845B ARG* 3.2 20.9 + - - +
846B GLN* 3.0 40.4 + - - +
1077B ARG* 4.4 28.3 + - - +
1078B PRO* 4.4 10.5 - - - +
1085B ILE* 3.7 21.0 - - + +
1089B HIS* 3.4 26.2 + - - +
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Residues in contact with GLU 843 (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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839B LEU* 3.0 21.3 + - + +
840B VAL* 3.7 10.3 - - + +
842B GLU* 1.3 76.4 - - - +
844B MET* 1.3 62.2 + - - +
846B GLN* 3.4 32.3 + - - +
847B LEU* 3.7 23.0 + - + +
863B TYR* 5.9 1.2 - - - +
869B ASN* 5.1 11.2 - - - +
872B ASP* 5.8 9.9 - - + -
873B VAL* 6.1 4.7 - - + -
876B ILE* 5.7 8.1 - - + -
909B ARG* 5.9 1.4 + - - -
1077B ARG* 6.0 0.2 + - - -
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Residues in contact with MET 844 (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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840B VAL 2.9 18.5 + - - +
841B CYS* 3.7 20.0 - - - +
842B GLU 3.3 0.2 - - - -
843B GLU* 1.3 72.8 - - - +
845B ARG* 1.3 68.8 + - - +
847B LEU* 3.2 17.2 + - + +
848B PHE* 3.7 41.2 + - + -
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Residues in contact with ARG 845 (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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841B CYS* 2.9 17.2 + - - +
842B GLU* 3.2 24.3 + - - +
844B MET* 1.3 82.1 - - - +
846B GLN* 1.3 68.6 + - - +
847B LEU 3.3 0.5 + - - -
848B PHE* 3.4 14.7 + - - +
849B TYR* 4.0 36.2 + - - +
1076B GLY 3.9 16.8 + - - -
1077B ARG* 4.6 2.4 - - - +
1078B PRO* 3.8 26.7 - - - +
1089B HIS* 3.9 19.1 - - + +
1092B LEU* 3.8 38.0 - - + +
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Residues in contact with GLN 846 (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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842B GLU* 3.0 25.7 + - - +
843B GLU* 3.6 26.7 + - - +
844B MET 3.2 0.6 - - - -
845B ARG* 1.3 86.2 - - - +
847B LEU* 1.3 64.6 + - + +
849B TYR* 4.0 14.0 - - - +
859B LYS* 4.3 6.6 + - - -
1073B GLU* 2.5 44.4 + - + +
1077B ARG* 3.3 20.2 - - - +
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Residues in contact with LEU 847 (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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843B GLU* 3.7 25.8 - - + +
844B MET* 3.2 11.7 + - - +
845B ARG 3.2 1.0 - - - -
846B GLN* 1.3 83.0 - - + +
848B PHE* 1.3 72.3 + - + +
849B TYR 3.2 5.3 + - - -
850B ASP* 4.6 0.7 + - - +
856B LEU* 5.0 5.2 - - - +
859B LYS* 3.3 49.5 + - + +
860B ALA* 4.3 7.6 - - + +
863B TYR* 3.8 32.3 - - + -
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Residues in contact with PHE 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844B MET* 3.7 42.4 + - + -
845B ARG* 3.4 11.2 + - - +
847B LEU* 1.3 89.2 - - + +
849B TYR* 1.3 59.7 + - - +
850B ASP 3.6 1.6 - - - -
856B LEU* 4.7 19.3 - - + -
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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
------------------------------------------------------------
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