Contacts of the helix formed by residues 730 - 737 (chain C) in PDB entry 6DBV
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 730 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619C CYS 4.8 3.3 - - - +
620C ASP* 3.5 14.8 - - - +
684C GLU* 5.1 5.1 - - - +
729C TYR* 1.3 74.4 - - - +
731C GLU* 1.3 69.1 + - + +
732C LYS* 2.8 9.3 + - + +
733C MET* 3.0 16.3 + - - +
734C VAL* 2.8 17.8 + - - -
814C ASP* 6.0 2.5 - - - +
817C HIS* 5.5 11.4 - - + +
980C SER* 5.1 5.1 + - - +
1103C CA 3.2 23.2 - - - -
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Residues in contact with GLU 731 (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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729C TYR 4.2 0.2 + - - -
730C ASP* 1.3 70.9 - - - +
732C LYS* 1.3 63.1 + - - +
734C VAL* 3.3 11.1 - - - +
735C ARG* 3.0 35.6 + - + +
814C ASP* 5.1 5.7 - - + +
817C HIS* 3.9 10.0 + - + -
956C ASN* 5.0 4.6 + - - -
957C TYR* 2.5 43.3 + - - -
960C LYS* 4.2 23.1 + - - +
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Residues in contact with LYS 732 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C GLU* 4.5 24.3 + - - +
730C ASP* 2.8 12.7 + - - +
731C GLU* 1.3 77.7 - - - +
733C MET* 1.3 63.1 + - - +
735C ARG* 3.3 6.4 + - - +
736C GLU* 3.0 27.1 + - + +
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Residues in contact with MET 733 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619C CYS* 3.5 38.1 - - - +
620C ASP* 5.7 2.7 - - - -
640C VAL* 5.2 2.2 - - + -
684C GLU* 3.8 33.0 - - + +
690C LEU* 3.7 26.5 - - + -
729C TYR* 4.9 11.0 - - + -
730C ASP* 3.0 16.3 + - - +
732C LYS* 1.3 79.7 - - - +
734C VAL* 1.3 56.3 + - - +
736C GLU* 3.7 12.3 - - + -
737C MET* 2.8 60.8 + - + +
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Residues in contact with VAL 734 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727C THR 5.2 1.3 - - - +
729C TYR* 3.4 33.1 - - + +
730C ASP 2.8 27.1 + - - +
731C GLU* 3.3 14.1 - - - +
733C MET* 1.3 77.1 - - - +
735C ARG* 1.3 65.2 + - + +
737C MET* 3.3 3.2 + - - +
738C GLU* 3.2 21.1 + - + +
750C THR* 3.7 32.3 - - + +
809C THR* 5.5 6.0 - - + +
811C PRO* 4.2 16.4 - - + -
812C THR 6.2 0.2 - - - +
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Residues in contact with ARG 735 (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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731C GLU* 3.0 24.2 + - - +
732C LYS* 3.6 7.2 - - - +
734C VAL* 1.3 75.9 - - + +
736C GLU* 1.3 57.8 + - + +
738C GLU* 2.6 27.2 + - - +
739C GLY* 3.0 12.8 + - - -
740C LEU* 3.6 43.5 + - - +
741C GLU 3.6 19.2 + - - +
742C ALA* 4.2 7.8 - - + +
743C SER* 2.8 41.0 + - - +
747C TYR 4.6 5.8 + - - -
748C ILE* 3.1 33.1 + - - +
750C THR* 4.4 15.6 + - - -
956C ASN* 4.6 4.4 + - - -
960C LYS* 5.7 1.6 - - - +
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Residues in contact with GLU 736 (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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684C GLU 5.6 3.5 - - - +
685C SER 5.2 6.7 - - - +
687C HIS* 2.8 61.8 + - + +
732C LYS* 3.0 21.7 + - + +
733C MET* 2.8 24.6 + - + +
735C ARG* 1.3 71.9 - - + +
737C MET* 1.3 58.6 + - + +
739C GLY* 4.7 2.9 + - - +
740C LEU 5.7 0.7 - - - -
742C ALA* 6.1 0.9 - - - +
806C PHE* 4.5 0.7 - - - -
36D TRP* 5.2 5.2 - - - -
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Residues in contact with MET 737 (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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619C CYS* 5.1 2.7 - - - -
642C PHE* 6.3 0.2 - - + -
687C HIS* 5.4 2.7 - - + -
690C LEU* 4.4 15.7 - - + -
694C LEU* 4.3 11.7 - - + -
729C TYR* 4.8 12.1 - - + -
733C MET* 2.8 45.9 + - + +
734C VAL* 3.6 4.3 - - - +
736C GLU* 1.3 80.2 - - + +
738C GLU* 1.3 60.9 + - - +
739C GLY 3.8 0.4 - - - -
772C HIS* 5.7 0.2 + - - -
805C PRO* 4.2 7.7 - - - +
806C PHE* 3.4 33.7 - - + -
807C MET* 3.3 63.0 + - + +
809C THR* 4.4 7.8 - - + +
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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