Contacts of the helix formed by residues 844 - 862 (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 SER 844 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840C LYS* 4.5 2.4 + - - -
842C ASN 4.6 2.3 + - - -
843C PRO* 1.3 77.1 - - - +
845C ARG* 1.3 70.3 + - - +
846C GLU 3.4 2.2 - - - -
847C GLU* 2.7 36.0 + - - +
848C ARG* 3.7 21.9 + - - -
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Residues in contact with ARG 845 (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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844C SER* 1.3 78.8 - - - +
846C GLU* 1.3 72.0 + - + +
848C ARG* 3.6 30.7 + - - +
849C ARG* 3.3 29.4 + - - +
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Residues in contact with GLU 846 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844C SER* 4.6 1.0 - - - -
845C ARG* 1.3 84.9 - - + +
847C GLU* 1.3 55.9 + - - +
848C ARG 3.2 2.0 - - - -
849C ARG* 3.0 36.0 + - - +
850C ARG* 2.5 51.9 + - + +
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Residues in contact with GLU 847 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840C LYS* 2.0 37.6 + - - -
843C PRO* 3.5 0.3 - - - +
844C SER* 2.7 40.4 + - - +
845C ARG 3.7 0.4 - - - -
846C GLU* 1.3 76.9 - - - +
848C ARG* 1.3 57.7 + - - +
850C ARG* 3.3 28.3 + - - +
851C TRP* 2.9 52.9 + - + -
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Residues in contact with ARG 848 (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* 2.7 34.9 + - + +
832C ASP* 5.3 4.0 - - - +
843C PRO* 3.5 38.6 + - + +
844C SER 3.7 13.3 + - - +
845C ARG* 3.6 39.8 + - - +
847C GLU* 1.3 78.7 - - - +
849C ARG* 1.3 57.9 + - + +
851C TRP* 3.3 11.6 + - + +
852C ARG 2.9 18.7 + - - -
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Residues in contact with ARG 849 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831C GLN* 4.5 1.3 - - - +
845C ARG* 3.3 24.9 - - - +
846C GLU* 3.0 38.6 + - - +
848C ARG* 1.3 79.7 - - + +
850C ARG* 1.3 58.9 + - - +
852C ARG* 3.4 15.6 + - - +
853C SER* 2.9 27.9 + - - -
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Residues in contact with ARG 850 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846C GLU* 2.5 27.7 + - + +
847C GLU* 3.3 45.4 + - - +
849C ARG* 1.3 71.2 - - - +
851C TRP* 1.3 69.0 + - + +
853C SER* 3.2 9.1 + - - -
854C THR* 2.9 30.1 + - - +
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Residues in contact with TRP 851 (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* 3.2 32.5 - - + +
832C ASP* 5.0 4.3 - - - -
834C ILE* 3.2 29.9 - - + +
835C GLY* 3.5 32.5 - - - -
836C GLU 5.6 0.9 - - - -
837C VAL* 6.2 2.2 - - + -
840C LYS* 4.5 15.7 - - + -
843C PRO* 3.5 39.0 - - + -
847C GLU* 2.9 37.2 + - + +
848C ARG* 3.6 12.8 - - + +
850C ARG* 1.3 89.8 - - - +
852C ARG* 1.3 59.9 + - - +
854C THR* 3.1 10.7 - - + +
855C LEU* 2.9 25.2 + - - +
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Residues in contact with ARG 852 (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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827C TYR* 3.3 43.8 + - + +
831C GLN* 3.2 33.9 + - - +
848C ARG 2.9 10.6 + - - +
849C ARG* 3.7 15.9 - - - +
850C ARG 3.3 0.2 - - - -
851C TRP* 1.3 76.2 - - - +
853C SER* 1.3 56.6 + - - +
855C LEU* 3.5 9.4 + - + +
856C ASP* 2.9 30.3 + - + +
868C VAL 6.1 0.2 - - - -
50H A 5.2 8.5 + - - -
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Residues in contact with SER 853 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849C ARG 2.9 17.5 + - - -
850C ARG* 3.5 10.3 - - - -
851C TRP 3.2 0.4 - - - -
852C ARG* 1.3 77.4 - - - +
854C THR* 1.3 58.5 + - - +
856C ASP* 3.2 7.0 + - - +
857C LYS* 3.0 44.9 + - - +
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Residues in contact with THR 854 (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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834C ILE* 3.6 15.5 - - + -
850C ARG 2.9 14.8 + - - +
851C TRP* 3.1 26.0 - - + +
853C SER* 1.3 72.2 - - - +
855C LEU* 1.3 60.0 + - - +
857C LYS* 3.6 4.6 + - - +
858C GLN* 2.9 28.2 + - - +
891C LEU* 3.5 17.5 - - + +
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Residues in contact with LEU 855 (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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827C TYR* 4.6 21.3 - - + +
830C PHE* 3.5 36.8 - - + +
831C GLN* 4.3 6.5 - - + +
834C ILE* 3.4 13.0 - - + -
851C TRP 2.9 17.5 + - - +
852C ARG* 3.7 8.3 - - - +
854C THR* 1.3 78.8 - - - +
856C ASP* 1.3 56.4 + - - +
858C GLN* 3.2 11.1 + - + +
859C LEU* 3.0 49.0 + - + +
888C VAL* 3.6 27.8 - - + -
891C LEU* 5.2 0.4 - - + -
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Residues in contact with ASP 856 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827C TYR* 4.0 15.3 + - - +
852C ARG* 2.9 19.7 + - + +
853C SER* 3.2 8.3 + - - +
855C LEU* 1.3 78.8 - - - +
857C LYS* 1.3 60.1 + - + +
859C LEU* 3.4 4.8 + - - +
860C ARG* 2.8 27.4 + - - +
865C LEU 3.9 6.9 - - - +
866C LYS 4.7 0.7 - - - -
867C PRO* 3.0 54.3 - - - +
868C VAL 4.2 0.3 + - - -
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Residues in contact with LYS 857 (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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853C SER* 3.0 29.1 + - - +
854C THR* 4.2 5.2 - - - +
856C ASP* 1.3 74.3 - - + +
858C GLN* 1.3 59.8 + - - +
860C ARG* 3.4 20.4 - - + +
861C LYS* 2.9 27.0 + - - +
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Residues in contact with GLN 858 (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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854C THR 2.9 19.4 + - - +
855C LEU* 3.2 12.6 - - + +
856C ASP 3.2 0.2 - - - -
857C LYS* 1.3 76.8 - - - +
859C LEU* 1.3 66.2 + - + +
861C LYS* 2.8 23.3 + - - +
862C LYS* 2.3 47.4 + - - +
887C ALA 2.2 35.8 + - - +
888C VAL* 4.0 0.4 - - - +
890C GLU* 2.8 24.6 + - - +
891C LEU* 3.3 37.5 - - + +
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Residues in contact with LEU 859 (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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830C PHE* 5.3 5.8 - - + -
855C LEU* 3.0 37.9 + - + +
856C ASP* 4.1 4.0 - - - +
858C GLN* 1.3 75.9 - - + +
860C ARG* 1.3 49.7 + - - +
862C LYS* 4.9 0.2 - - - -
863C MET* 3.1 16.2 + - + +
864C LYS* 2.5 32.1 + - - -
865C LEU* 3.4 14.0 + - + +
875C TYR* 4.8 7.2 - - + +
879C LEU* 3.5 31.2 - - + -
884C ALA* 3.7 22.4 - - + +
887C ALA* 3.7 30.7 - - + -
888C VAL 5.0 0.9 - - - +
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Residues in contact with ARG 860 (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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856C ASP* 2.8 18.6 + - - +
857C LYS* 3.4 22.2 - - + +
859C LEU* 1.3 78.1 - - - +
861C LYS* 1.3 58.0 + - - +
864C LYS* 3.1 57.6 - - + +
865C LEU 4.0 5.8 + - - +
866C LYS* 3.2 51.2 - - - +
867C PRO* 4.1 10.4 - - - +
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Residues in contact with LYS 861 (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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857C LYS 2.9 11.2 + - - +
858C GLN* 2.8 16.7 + - - +
860C ARG* 1.3 79.9 - - - +
862C LYS* 1.3 108.0 + - + +
864C LYS* 4.6 5.5 - - - +
890C GLU* 3.0 24.6 + - - -
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Residues in contact with LYS 862 (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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858C GLN* 2.3 50.3 + - - -
859C LEU* 4.8 0.4 - - - +
861C LYS* 1.3 123.2 - - + +
863C MET* 1.3 72.5 + - + +
864C LYS* 3.4 3.9 + - - +
887C ALA* 3.5 27.8 - - + -
890C GLU* 3.2 17.3 - - + +
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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
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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