Contacts of the helix formed by residues 866 - 888 (chain C) 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 ASP 866 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862C LEU 3.7 8.0 + - - +
863C TYR* 3.1 16.1 + - - +
864C PHE 3.9 1.6 - - - +
865C SER* 1.3 81.4 - - - +
867C PHE* 1.3 64.4 + - - +
868C TRP* 4.6 2.0 - - + +
869C ASN* 3.7 15.0 - - + +
870C LYS* 3.1 23.4 + - - +
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Residues in contact with PHE 867 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865C SER 3.7 1.8 + - - -
866C ASP* 1.3 70.8 - - - +
868C TRP* 1.3 111.6 + + + +
870C LYS* 3.1 9.2 + - + +
871C LEU* 2.9 56.1 + - + +
928C LYS* 3.3 41.7 - - + +
931C MET* 6.4 2.5 - - + -
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Residues in contact with TRP 868 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866C ASP* 3.6 1.9 - - + +
867C PHE* 1.3 108.7 - + + +
869C ASN* 1.3 61.2 + - - +
871C LEU* 3.3 9.8 + - + +
872C ASP* 2.9 28.4 + - - +
908C LEU 4.3 10.5 - - - -
909C ARG* 4.2 29.4 + - - +
911C MET* 3.9 11.9 - - + -
912C HIS* 3.4 65.2 - + + +
915C THR* 4.8 11.7 - - + +
924C ILE* 4.9 11.4 - - + -
928C LYS* 3.8 14.0 - - - +
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Residues in contact with ASN 869 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843C GLU* 5.1 11.9 - - - +
863C TYR* 3.3 30.3 - - + +
864C PHE* 5.3 1.3 - - - -
866C ASP* 3.7 12.4 + - + +
867C PHE 3.2 0.6 - - - -
868C TRP* 1.3 78.8 - - - +
870C LYS* 1.3 57.4 + - - +
872C ASP* 3.3 7.0 + - - +
873C VAL* 3.0 36.6 + - + +
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Residues in contact with LYS 870 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864C PHE* 4.6 10.5 + - - +
866C ASP 3.1 19.7 + - - +
867C PHE* 3.1 8.4 + - - +
869C ASN* 1.3 77.0 - - - +
871C LEU* 1.3 60.7 + - + +
873C VAL* 3.3 13.0 - - + +
874C GLY* 2.9 24.9 + - - -
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Residues in contact with LEU 871 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867C PHE* 2.9 52.4 + - + +
868C TRP* 3.7 13.7 - - + +
869C ASN 3.3 0.2 - - - -
870C LYS* 1.3 79.9 - - + +
872C ASP* 1.3 57.5 + - - +
874C GLY* 3.3 2.5 + - - -
875C ALA* 3.0 28.2 + - - +
905C LEU* 3.8 39.3 - - + +
908C LEU* 5.9 4.7 - - + -
909C ARG* 5.9 4.9 - - - -
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Residues in contact with ASP 872 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839C LEU* 6.1 4.5 - - + -
843C GLU* 5.7 10.5 - - + +
868C TRP 2.9 18.3 + - - +
869C ASN* 3.5 9.0 - - - +
870C LYS 3.3 0.2 - - - -
871C LEU* 1.3 76.5 - - - +
873C VAL* 1.3 59.7 + - + +
875C ALA* 3.2 8.1 + - - +
876C ILE* 2.9 38.7 + - + +
906C PHE* 5.6 1.9 - - - -
909C ARG* 5.0 14.8 - - - +
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Residues in contact with VAL 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843C GLU* 6.1 4.5 - - + -
869C ASN* 3.0 18.7 + - + +
870C LYS* 3.3 19.3 - - - +
872C ASP* 1.3 74.2 - - + +
874C GLY* 1.3 60.7 + - - +
876C ILE* 3.4 15.9 + - + +
877C LEU* 2.9 28.9 + - - +
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Residues in contact with GLY 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870C LYS 2.9 15.3 + - - -
871C LEU* 3.3 4.5 + - - -
873C VAL* 1.3 77.8 - - - +
875C ALA* 1.3 55.4 + - - +
877C LEU* 3.3 6.4 + - - +
878C LEU* 2.9 29.6 + - - +
905C LEU* 3.9 10.3 - - - +
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Residues in contact with ALA 875 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871C LEU 3.0 14.0 + - - +
872C ASP* 3.2 9.6 + - - +
874C GLY* 1.3 73.7 - - - +
876C ILE* 1.3 61.6 + - - +
878C LEU* 4.5 0.7 - - - +
879C PHE* 2.9 28.2 + - - +
902C ASP* 3.2 13.5 - - - +
905C LEU* 3.6 19.8 - - + +
906C PHE* 3.6 36.6 - - + -
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Residues in contact with ILE 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836C LEU* 5.4 9.0 - - + -
839C LEU* 5.7 4.7 - - + -
840C VAL* 3.7 33.4 - - + -
843C GLU* 5.7 8.3 - - + -
872C ASP* 2.9 28.0 + - + +
873C VAL* 3.7 20.6 - - + +
874C GLY 3.3 0.2 - - - -
875C ALA* 1.3 76.9 - - + +
877C LEU* 1.3 57.9 + - - +
879C PHE* 3.3 6.9 + - - +
880C VAL* 3.0 32.2 + - + +
906C PHE* 5.3 3.4 - - + -
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Residues in contact with LEU 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873C VAL 2.9 18.1 + - - +
874C GLY* 3.7 6.5 - - - +
876C ILE* 1.3 77.3 - - - +
878C LEU* 1.3 57.3 + - - +
880C VAL* 3.3 12.4 - - + +
881C ALA* 3.0 29.5 + - - +
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Residues in contact with LEU 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C GLY 2.9 17.4 + - - +
875C ALA* 3.9 3.8 - - - +
877C LEU* 1.3 76.3 - - - +
879C PHE* 1.3 57.4 + - - +
881C ALA* 3.7 7.2 - - + +
882C GLY* 2.9 23.4 + - - -
898C ILE* 3.7 31.4 - - + +
899C LEU* 5.5 0.3 - - - +
901C LEU* 4.0 14.1 - - + +
902C ASP* 3.6 37.1 - - + +
905C LEU* 5.0 9.6 - - + -
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Residues in contact with PHE 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813C PHE* 4.3 23.6 - + - -
832C ILE* 5.1 8.7 - - + -
833C TYR* 4.8 18.6 - - + -
836C LEU* 3.6 35.7 - - + -
875C ALA 2.9 15.4 + - - +
876C ILE* 3.7 5.6 - - - +
878C LEU* 1.3 78.3 - - - +
880C VAL* 1.3 61.6 + - + +
882C GLY* 3.3 1.4 + - - -
883C LEU* 2.9 55.9 + - + +
899C LEU* 5.1 15.4 - - + +
902C ASP* 3.2 24.8 + - - +
906C PHE* 5.0 0.9 - + - -
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Residues in contact with VAL 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876C ILE* 3.0 22.0 + - + +
877C LEU* 3.3 20.9 - - + +
879C PHE* 1.3 81.0 - - + +
881C ALA* 1.3 61.3 + - - +
883C LEU* 4.2 9.0 - - + +
884C THR* 3.4 23.3 + - - +
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Residues in contact with ALA 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877C LEU 3.0 17.7 + - - +
878C LEU* 3.7 11.0 - - + +
879C PHE 3.2 0.2 - - - -
880C VAL* 1.3 79.6 - - + +
882C GLY* 1.3 58.3 + - - +
884C THR* 3.3 10.7 - - - +
885C CYS* 3.0 27.1 + - - +
898C ILE* 4.7 5.2 - - + -
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Residues in contact with GLY 882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878C LEU 2.9 12.2 + - - -
879C PHE 3.3 0.4 + - - -
881C ALA* 1.3 76.7 - - - +
883C LEU* 1.3 57.7 + - - +
885C CYS* 3.7 7.0 - - - +
886C ARG* 2.9 28.4 + - - +
895C GLY* 4.3 2.2 - - - -
898C ILE* 3.7 23.1 - - - +
899C LEU* 3.7 22.0 - - - +
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Residues in contact with LEU 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833C TYR* 5.3 9.6 - - + -
879C PHE* 2.9 44.9 + - + +
880C VAL* 4.2 10.8 - - + +
881C ALA 3.3 0.2 - - - -
882C GLY* 1.3 79.1 - - - +
884C THR* 1.3 62.3 + - - +
886C ARG* 3.1 6.3 + - - +
887C LEU* 3.0 50.4 + - + +
899C LEU* 4.3 2.4 - - - +
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Residues in contact with THR 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880C VAL 3.4 14.6 + - - +
881C ALA* 3.3 17.9 + - - +
883C LEU* 1.3 80.2 - - - +
885C CYS* 1.3 63.2 + - - +
887C LEU* 3.9 7.8 + - - +
888C ILE* 3.8 23.2 + - - +
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Residues in contact with CYS 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881C ALA 3.0 18.7 + - - +
882C GLY* 3.7 9.0 - - - +
883C LEU 3.2 0.2 - - - -
884C THR* 1.3 79.3 - - + +
886C ARG* 1.3 61.3 + - - +
888C ILE* 3.3 3.4 + - - +
891C THR* 2.3 47.3 + - - +
894C PRO* 3.7 15.5 - - - -
895C GLY* 3.3 28.0 - - - -
898C ILE* 5.6 4.3 - - + -
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Residues in contact with ARG 886 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820C ASP 5.8 0.4 + - - -
821C PHE* 3.7 33.2 - - + -
822C GLN* 2.5 32.6 + - - +
823C PRO* 3.7 20.2 + - + +
824C VAL 3.0 15.0 + - - -
825C PRO* 3.5 27.1 - - - +
826C SER* 4.0 5.1 - - - +
829C GLU* 4.7 13.8 - - - +
882C GLY 2.9 17.5 + - - +
883C LEU* 3.1 6.9 + - - +
885C CYS* 1.3 76.7 - - - +
887C LEU* 1.3 85.4 + - - +
888C ILE 3.3 9.4 - - - +
889C PRO* 4.3 2.8 - - - +
891C THR 4.6 4.5 - - - -
892C LEU* 5.4 5.5 - - + +
895C GLY* 4.6 4.9 - - - -
899C LEU* 5.5 4.7 - - + -
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Residues in contact with LEU 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823C PRO 5.9 2.2 - - - +
825C PRO* 6.2 4.5 - - + -
883C LEU* 3.0 43.5 + - + +
884C THR* 3.9 8.5 + - - +
885C CYS 3.4 0.4 - - - -
886C ARG* 1.3 102.2 - - - +
888C ILE* 1.3 64.3 + - + +
889C PRO* 3.4 9.4 - - - +
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Residues in contact with ILE 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884C THR* 3.8 15.6 + - - +
885C CYS* 3.3 5.6 + - - +
886C ARG 3.2 4.9 - - - +
887C LEU* 1.3 80.0 - - + +
889C PRO* 1.3 72.6 - - + +
890C ALA* 3.9 13.7 - - + +
891C THR* 3.0 39.5 + - + +
892C LEU 4.3 0.2 + - - -
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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