Contacts of the helix formed by residues 819 - 835 (chain C) in PDB entry 6DBT
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 819 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817C HIS 2.3 22.4 + - - +
818C CYS* 1.3 95.3 - - - +
820C ILE* 1.3 53.2 + - + +
821C GLY 3.3 2.2 - - - -
822C ASN* 2.9 8.8 + - - +
823C ALA* 2.5 38.1 + - - +
876C ALA* 5.1 8.7 - - + +
877C ARG* 5.7 1.6 - - - +
880C MET* 3.6 14.0 - - - +
908C TYR* 3.4 15.9 + - - +
912C LYS* 3.0 26.3 - - - -
915C TRP* 3.2 18.4 - - - -
916C ARG* 5.2 2.6 + - - -
957C TYR* 4.2 0.4 - - - -
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Residues in contact with ILE 820 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817C HIS* 4.2 32.4 - - + +
818C CYS 4.5 0.2 - - - +
819C ASP* 1.3 76.7 - - + +
821C GLY* 1.3 63.1 + - - +
823C ALA* 3.6 7.1 - - - +
824C THR* 3.0 28.4 + - + +
871C MET* 3.2 37.7 - - + +
872C ASN* 4.7 8.5 - - - -
873C GLY* 5.4 1.6 - - - +
876C ALA* 5.4 2.5 - - + -
957C TYR* 4.7 1.5 - - + -
48H A 5.0 29.8 - - - +
49H G 5.8 1.8 - - - +
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Residues in contact with GLY 821 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C ASP 3.3 0.4 - - - -
820C ILE* 1.3 79.0 - - - +
822C ASN* 1.3 59.6 + - - +
824C THR* 3.2 10.6 - - - +
825C GLU* 2.9 30.9 + - - +
955C THR* 4.2 23.0 - - - +
957C TYR* 4.2 13.8 - - - -
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Residues in contact with ASN 822 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818C CYS 2.5 32.1 + - - -
819C ASP* 2.9 14.3 + - - +
821C GLY* 1.3 75.8 - - - +
823C ALA* 1.3 57.2 + - - +
825C GLU* 3.2 7.7 + - - +
826C PHE* 2.9 42.1 + - + -
880C MET* 5.8 0.7 - - - -
908C TYR* 4.4 19.0 + - + +
915C TRP* 4.4 9.7 - - - -
955C THR* 5.9 0.2 - - - +
957C TYR* 4.0 17.0 - - - +
958C LEU* 4.5 17.1 + - + +
961C THR* 4.7 9.0 - - - +
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Residues in contact with ALA 823 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C ASP 2.5 19.6 + - - +
820C ILE* 3.3 5.6 + - - +
822C ASN* 1.3 72.9 - - - +
824C THR* 1.3 58.0 + - - +
826C PHE* 3.2 13.2 + - - +
827C TYR* 2.9 24.4 + - - +
871C MET* 3.8 16.1 - - + +
875C TYR* 5.8 1.6 - - + -
876C ALA* 3.7 33.0 - - + +
879C LEU* 4.9 7.7 - - + +
880C MET* 5.5 6.0 - - + -
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Residues in contact with THR 824 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820C ILE* 3.0 18.2 + - + +
821C GLY* 3.2 20.9 - - - +
823C ALA* 1.3 76.0 - - - +
825C GLU* 1.3 60.1 + - - +
827C TYR* 3.2 12.5 - - - +
828C LYS* 2.9 33.4 + - - +
871C MET* 3.6 28.1 - - - +
955C THR* 5.9 1.6 - - + +
49H G 4.1 11.4 + - - +
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Residues in contact with GLU 825 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821C GLY 2.9 19.8 + - - +
822C ASN* 3.4 9.9 - - - +
823C ALA 3.1 0.2 - - - -
824C THR* 1.3 77.9 - - - +
826C PHE* 1.3 65.2 + - + +
828C LYS* 3.2 19.6 + - - +
829C ILE* 2.9 35.4 + - + +
949C ARG* 4.4 3.6 - - - -
950C TYR* 2.3 46.1 + - + +
953C LYS* 5.9 0.2 - - - -
955C THR* 3.6 25.2 + - - -
958C LEU* 5.2 11.2 - - + -
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Residues in contact with PHE 826 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822C ASN* 2.9 28.5 + - + -
823C ALA* 3.7 6.5 - - - +
825C GLU* 1.3 76.4 - - + +
827C TYR* 1.3 65.4 + - - +
829C ILE* 3.2 25.1 + - + +
830C PHE* 2.9 43.4 + + + -
879C LEU* 5.5 7.9 - - + -
880C MET* 4.5 11.2 - - + -
904C LEU* 4.7 13.7 - - + -
905C MET* 4.4 21.1 - - + -
908C TYR* 3.8 55.4 - + + -
938C PHE* 4.8 11.9 - + - -
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Residues in contact with TYR 827 (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 ALA 2.9 12.9 + - - +
824C THR* 3.2 19.5 - - - +
826C PHE* 1.3 76.1 - - - +
828C LYS* 1.3 59.0 + - + +
830C PHE* 3.3 7.7 + - - +
831C GLN* 2.9 34.3 + - - +
852C ARG* 3.3 53.6 + - + +
855C LEU* 4.6 14.1 - - + +
856C ASP* 4.0 14.9 + - - +
868C VAL* 4.5 16.1 + - + -
871C MET* 4.9 11.9 - - + -
875C TYR* 3.1 39.5 - + - -
879C LEU* 4.5 7.0 - - + +
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Residues in contact with LYS 828 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
824C THR* 2.9 20.9 + - - +
825C GLU* 3.2 22.2 + - - +
827C TYR* 1.3 75.9 - - + +
829C ILE* 1.3 66.7 + - - +
831C GLN* 3.2 8.8 + - + +
832C ASP 2.9 19.2 + - - -
949C ARG* 3.1 43.7 + - - +
953C LYS* 4.1 18.3 - - - +
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Residues in contact with ILE 829 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825C GLU* 2.9 18.4 + - + +
826C PHE* 3.4 37.0 - - + +
828C LYS* 1.3 77.1 - - - +
830C PHE* 1.3 71.6 + - + +
832C ASP* 3.3 1.4 + - - +
833C GLU* 2.9 37.8 + - + +
901C LEU* 5.3 2.9 - - + -
904C LEU* 3.8 19.7 - - + -
942C LEU* 5.9 2.7 - - + -
946C PHE* 3.5 37.0 - - + -
948C TYR* 4.6 2.7 - - - +
949C ARG* 4.2 7.2 - - - +
950C TYR* 4.3 17.5 - - + +
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Residues in contact with PHE 830 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826C PHE* 2.9 33.0 + + + +
827C TYR* 3.8 3.6 - - - +
829C ILE* 1.3 89.1 - - + +
831C GLN* 1.3 61.6 + - - +
833C GLU* 3.6 6.2 - - + +
834C ILE* 3.0 33.8 + - - +
855C LEU* 3.5 26.0 - - + -
859C LEU* 5.3 5.4 - - + -
879C LEU* 5.4 17.7 - - + -
884C ALA* 4.5 9.2 - - + -
885C VAL* 3.8 23.6 - - + -
888C VAL* 3.5 45.4 - - + +
901C LEU* 4.4 16.8 - - + -
904C LEU* 6.1 2.2 - - + -
905C MET* 5.4 2.7 - - + -
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Residues in contact with GLN 831 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827C TYR* 2.9 24.4 + - - +
828C LYS* 3.2 10.7 + - + +
830C PHE* 1.3 76.9 - - - +
832C ASP* 1.3 64.6 + - - +
833C GLU 3.8 0.2 + - - -
834C ILE* 5.1 0.9 - - - -
835C GLY 3.9 4.0 + - - -
848C ARG* 2.7 53.0 + - + +
849C ARG* 4.1 0.6 - - - +
851C TRP* 3.2 27.7 - - + +
852C ARG* 3.2 50.3 + - - +
855C LEU* 4.3 7.0 - - + +
949C ARG* 5.4 0.9 - - - +
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Residues in contact with ASP 832 (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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828C LYS 2.9 8.7 + - - +
829C ILE 3.6 2.2 - - - +
831C GLN* 1.3 82.1 - - - +
833C GLU* 1.3 60.2 + - - +
835C GLY 2.7 23.0 - - - +
836C GLU* 4.7 0.3 - - - -
837C VAL* 3.3 23.7 + - + +
843C PRO* 5.1 8.2 - - - +
848C ARG* 5.3 4.2 - - - +
851C TRP* 5.0 7.2 - - - -
948C TYR* 2.9 34.9 + - + +
949C ARG* 2.7 39.3 + - - +
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Residues in contact with GLU 833 (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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829C ILE* 2.9 31.3 + - - +
830C PHE* 3.1 10.2 + - + +
832C ASP* 1.3 85.0 - - - +
834C ILE* 1.3 66.9 + - - +
835C GLY 3.4 2.0 - - - +
836C GLU* 4.2 7.1 - - - +
837C VAL* 5.3 2.0 - - - +
838C TYR* 4.9 1.7 - - - -
888C VAL* 5.4 4.0 - - + -
892C VAL* 3.2 42.1 - - + +
893C PRO* 4.0 3.1 - - - +
897C ARG* 3.0 42.3 + - + +
901C LEU* 4.0 24.5 - - + -
946C PHE* 4.1 11.6 - - - -
948C TYR* 5.3 2.8 + - - -
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Residues in contact with ILE 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830C PHE 3.0 16.7 + - - +
831C GLN* 4.3 0.7 - - - +
832C ASP 3.6 0.2 - - - -
833C GLU* 1.3 78.7 - - - +
835C GLY* 1.3 60.5 + - - +
836C GLU* 3.5 2.9 + - - +
851C TRP* 3.2 55.0 - - + +
854C THR* 3.6 12.1 - - + -
855C LEU* 3.4 31.9 - - + +
888C VAL* 5.1 4.7 - - + -
891C LEU* 3.8 26.2 - - + +
892C VAL* 5.2 2.9 - - + +
893C PRO* 4.2 13.7 - - - +
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Residues in contact with GLY 835 (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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831C GLN 3.9 1.2 + - - -
832C ASP* 2.7 28.5 - - - +
833C GLU 4.2 0.4 - - - -
834C ILE* 1.3 79.9 - - - +
836C GLU* 1.3 59.1 + - - -
837C VAL* 2.9 8.0 + - - +
851C TRP* 3.5 46.2 - - - -
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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