Contacts of the helix formed by residues 829 - 849 (chain B) in PDB entry 5PYC
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 ARG 829 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LYS* 6.2 0.4 - - - +
790A SER* 4.8 7.3 + - - -
793A CYS* 3.4 29.1 - - - +
767B LEU 3.8 8.5 - - - +
768B MET* 3.7 47.4 + - - +
769B ARG 3.3 9.0 - - - +
770B GLN* 4.5 12.2 - - + +
771B MET* 3.6 10.8 - - - +
827B TYR* 4.0 4.5 - - - +
828B THR* 1.3 102.5 + - - +
830B VAL* 1.3 66.1 + - - +
831B GLU* 3.1 16.6 - - + +
832B GLY* 3.1 15.8 + - - +
833B PHE 3.9 3.1 + - - -
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Residues in contact with VAL 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B VAL* 3.5 33.9 - - + +
767B LEU* 3.6 6.9 + - + -
769B ARG* 3.0 24.9 + - + +
771B MET* 3.9 20.8 - - - +
775B GLU* 4.2 7.0 - - + -
779B CYS* 4.2 8.7 - - - -
829B ARG* 1.3 69.6 - - - +
831B GLU* 1.3 63.4 + - - +
833B PHE* 3.1 7.0 + - - +
834B VAL* 3.1 36.1 + - + +
868B PHE* 4.4 1.3 - - + -
872B PHE* 4.2 26.7 - - + -
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Residues in contact with GLU 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A LYS* 5.4 7.4 + - - -
767B LEU* 2.8 45.7 + - + +
768B MET* 4.7 14.1 - - - +
829B ARG* 4.3 17.1 - - + +
830B VAL* 1.3 74.7 - - - +
832B GLY* 1.3 57.4 + - - +
834B VAL* 3.5 1.0 + - - +
835B GLN* 2.9 62.5 + - + +
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Residues in contact with GLY 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B TYR* 3.4 23.3 - - - -
828B THR 6.1 0.2 - - - -
829B ARG* 3.1 11.3 + - - +
831B GLU* 1.3 77.9 + - - +
833B PHE* 1.3 65.4 + - - +
835B GLN* 3.5 10.9 + - - +
836B ASP* 3.2 19.1 + - - +
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Residues in contact with PHE 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B MET* 4.8 1.8 - - + -
779B CYS* 3.3 53.2 - - + -
782B LEU* 3.7 27.4 - - + -
783B LEU* 4.1 15.7 - - + -
818B VAL* 3.6 31.2 - - + -
822B LEU* 3.9 12.1 - - + -
827B TYR* 3.5 32.1 - + + -
829B ARG 3.9 1.0 + - - -
830B VAL 3.1 7.7 + - - +
832B GLY* 1.3 74.0 - - - +
834B VAL* 1.3 74.6 + - + +
836B ASP* 3.2 4.0 + - - +
837B MET* 3.0 40.9 + - + +
864B PHE* 4.2 2.0 - + - -
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Residues in contact with VAL 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B LEU* 3.7 26.9 - - + -
830B VAL* 3.1 17.5 + - + +
831B GLU 4.0 0.9 - - - +
833B PHE* 1.3 88.1 - - + +
835B GLN* 1.3 59.2 + - + +
837B MET* 3.7 0.7 - - - +
838B ARG* 2.9 70.8 + - + +
864B PHE* 4.3 13.5 - - + -
868B PHE* 3.8 23.8 - - + -
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Residues in contact with GLN 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B LEU* 6.2 2.4 - - + +
831B GLU* 2.9 50.7 + - + +
832B GLY* 3.8 9.0 - - - +
834B VAL* 1.3 79.0 - - + +
836B ASP* 1.3 64.8 + - - +
838B ARG* 3.5 6.5 + - - +
839B LEU* 3.0 24.3 + - - +
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Residues in contact with ASP 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B LYS* 3.2 26.1 + - - -
813B MET* 3.3 36.3 - - - +
818B VAL* 4.0 10.8 - - + -
821B SER* 4.9 2.3 + - - -
827B TYR* 2.6 34.7 + - - +
832B GLY 3.2 9.4 + - - +
833B PHE 3.2 7.2 + - - +
835B GLN* 1.3 81.2 - - - +
837B MET* 1.3 64.7 + - - +
839B LEU* 3.3 7.1 + - - +
840B ILE* 3.3 16.6 + - - +
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Residues in contact with MET 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B LEU* 3.8 32.8 - - + -
786B VAL* 3.9 17.3 - - + -
815B LEU* 3.9 19.1 - - + -
818B VAL* 3.9 16.8 - - + -
833B PHE* 3.0 33.0 + - + +
834B VAL 3.7 6.7 - - - +
836B ASP* 1.3 75.9 - - - +
838B ARG* 1.3 61.0 + - - +
840B ILE* 3.1 17.5 + - - +
841B PHE* 3.2 24.3 - - + -
864B PHE* 3.7 43.7 - - + -
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Residues in contact with ARG 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763B GLU* 3.0 41.8 + - - -
767B LEU* 4.6 5.1 - - - +
834B VAL* 2.9 40.9 + - - +
835B GLN* 4.1 5.8 - - - +
837B MET* 1.3 72.1 - - - +
839B LEU* 1.3 64.6 + - - +
841B PHE* 3.2 10.2 + - - +
842B HIS* 3.0 23.1 + - - +
861B GLN* 3.9 13.4 + - - +
864B PHE* 4.1 8.2 - - + -
865B GLU* 2.8 41.6 + - - +
868B PHE* 3.9 8.3 - - - -
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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
----------------------------------------------------------
811B LYS* 3.5 52.9 - - + +
813B MET* 3.9 13.0 - - + -
835B GLN 3.0 17.2 + - - +
836B ASP* 3.5 11.9 - - - +
837B MET 3.3 0.2 - - - -
838B ARG* 1.3 76.7 - - - +
840B ILE* 1.3 64.4 + - - +
842B HIS* 4.1 14.1 - - + -
843B ASN* 3.0 49.3 + - - +
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Residues in contact with ILE 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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795B PHE* 3.7 34.4 - - + +
813B MET* 3.5 38.1 - - + +
814B TRP 3.6 26.0 - - - +
815B LEU* 3.7 21.5 - - + -
818B VAL* 4.2 7.0 - - + -
836B ASP 3.3 8.0 + - - +
837B MET* 3.1 15.1 + - + +
839B LEU* 1.3 78.0 - - - +
841B PHE* 1.3 70.5 + - + +
843B ASN* 3.5 4.6 + - - +
844B HIS* 3.2 24.9 + - - +
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Residues in contact with PHE 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B VAL* 4.8 7.4 - - + -
795B PHE* 4.2 17.7 - + + -
815B LEU* 5.2 3.4 - - + -
837B MET* 3.2 36.6 - - + -
838B ARG* 3.2 3.4 + - - +
839B LEU 3.2 0.2 - - - -
840B ILE* 1.3 90.4 - - + +
842B HIS* 1.3 66.6 + - - +
844B HIS* 3.4 6.5 + - - +
845B LYS* 3.1 24.5 + - - +
857B GLY* 3.6 20.2 - - - +
860B VAL* 3.4 36.6 - - + -
861B GLN* 3.3 50.3 - - + +
864B PHE* 4.3 16.8 - + + -
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Residues in contact with HIS 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838B ARG 3.0 17.0 + - - +
839B LEU* 3.6 15.5 - - + +
840B ILE 3.3 0.2 - - - -
841B PHE* 1.3 76.9 - - - +
843B ASN* 1.3 78.2 + - - +
845B LYS* 3.3 20.1 + - - +
846B GLU* 3.1 51.4 + - + +
861B GLN* 4.9 1.2 + - - -
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Residues in contact with ASN 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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801B TYR* 3.9 18.8 + - + +
809B PRO* 4.0 20.1 - - + +
811B LYS 2.9 29.6 + - - +
812B PRO* 3.9 9.1 - - - +
813B MET* 4.0 6.0 + - - +
839B LEU* 3.0 30.2 + - - +
840B ILE* 3.8 4.2 - - - +
842B HIS* 1.3 92.3 - - - +
844B HIS* 1.3 63.6 + - - +
846B GLU* 3.2 6.1 + - - +
847B PHE* 3.1 24.8 + - - +
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Residues in contact with HIS 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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794B PHE* 5.7 1.1 - - + -
795B PHE* 3.4 29.7 - + + -
801B TYR* 4.7 4.4 + - - -
840B ILE 3.2 12.5 + - - +
841B PHE* 3.5 9.4 - - - +
843B ASN* 1.3 78.1 - - - +
845B LYS* 1.3 64.7 + - + +
847B PHE* 3.3 2.4 + - - -
848B TYR* 3.1 58.3 + + - +
853B PHE* 2.9 43.5 + + - -
854B THR* 3.7 11.2 - - - -
856B LEU* 4.6 0.4 - - + -
857B GLY* 3.5 25.1 + - - -
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Residues in contact with LYS 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 PHE 3.1 12.9 + - - +
842B HIS* 3.7 25.2 + - - +
844B HIS* 1.3 80.9 - - + +
846B GLU* 1.3 85.3 + - - +
849B ARG* 2.9 28.8 + - - +
854B THR* 3.8 22.2 - - - +
857B GLY* 6.5 0.2 - - - -
858B ILE* 5.9 8.7 - - + -
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Residues in contact with GLU 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 HIS* 3.1 45.8 + - + +
843B ASN* 3.2 6.4 + - - +
845B LYS* 1.3 96.9 + - - +
847B PHE* 1.3 57.5 + - - +
849B ARG* 2.8 57.7 + - - +
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Residues in contact with PHE 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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800B TYR 4.7 2.2 - - - -
801B TYR* 3.4 57.9 - + + -
802B ASN* 3.7 25.8 - - - -
843B ASN 3.1 15.8 + - - +
844B HIS* 3.9 2.7 - - - +
846B GLU* 1.3 81.2 - - - +
848B TYR* 1.3 101.2 + + + +
849B ARG* 3.4 6.0 - - - +
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Residues in contact with TYR 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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800B TYR 5.2 4.2 + - - -
801B TYR* 5.5 4.7 - + - -
844B HIS* 3.1 49.7 + + - +
847B PHE* 1.3 105.2 - + + +
849B ARG* 1.3 71.1 + - - +
850B GLU 3.0 1.0 + - - -
851B ASP* 2.9 30.1 + - + +
853B PHE* 3.6 38.0 - + + -
854B THR* 4.1 20.9 - - - +
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Residues in contact with ARG 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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845B LYS* 2.9 18.0 + - - +
846B GLU* 2.8 67.1 + - - +
847B PHE 3.8 6.1 - - - +
848B TYR* 1.3 77.8 - - - +
850B GLU* 1.3 78.6 + - - +
851B ASP 3.7 5.7 - - - +
854B THR* 3.7 15.1 + - - +
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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
------------------------------------------------------------
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