Contacts of the helix formed by residues 827 - 837 (chain N) in PDB entry 6AH0
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 827 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824N PRO 4.2 9.3 + - - -
825N GLN 3.2 3.9 - - - -
826N ARG* 1.3 70.8 - - - +
828N THR* 1.3 63.1 + - - +
829N LYS 3.3 2.6 - - - +
830N SER* 3.3 12.5 + - - -
831N VAL 3.7 4.2 + - - -
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Residues in contact with THR 828 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826N ARG 2.9 11.8 + - - -
827N ARG* 1.3 67.8 - - - +
829N LYS* 1.3 58.1 + - - +
830N SER 3.0 1.8 - - - -
831N VAL* 2.3 30.3 + - - +
832N ASP* 2.7 10.6 + - - -
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Residues in contact with LYS 829 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826N ARG* 4.6 2.6 - - - +
827N ARG 3.3 4.0 - - - +
828N THR* 1.3 74.3 - - - +
830N SER* 1.3 56.3 + - - +
832N ASP* 4.2 2.9 - - - +
833N ALA* 2.9 27.2 + - - -
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Residues in contact with SER 830 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827N ARG 3.3 9.7 + - - -
828N THR 3.0 1.4 - - - -
829N LYS* 1.3 76.0 - - - +
831N VAL* 1.3 61.0 + - - +
833N ALA* 4.1 1.3 - - - +
834N LEU* 3.2 18.2 + - - -
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Residues in contact with VAL 831 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827N ARG 3.7 4.0 + - - -
828N THR* 2.3 23.9 + - - +
830N SER* 1.3 69.4 - - - +
832N ASP* 1.3 49.2 - - - +
834N LEU* 3.2 2.5 + - - +
835N LYS* 2.7 32.9 + - - -
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Residues in contact with ASP 832 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828N THR 2.7 14.8 + - - -
829N LYS* 3.3 4.0 + - - +
831N VAL* 1.3 69.1 - - - +
833N ALA* 1.3 56.1 + - - +
835N LYS* 2.8 4.6 + - - +
836N LYS* 2.5 36.6 + - - -
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Residues in contact with ALA 833 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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814N TRP* 6.0 5.6 - - - +
829N LYS 2.9 15.7 + - - -
830N SER* 4.2 1.6 - - - +
832N ASP* 1.3 75.8 - - - +
834N LEU* 1.3 58.3 + - - +
836N LYS* 5.2 0.7 - - - +
837N CYS* 3.6 16.5 + - - +
838N GLU 4.2 3.6 + - - +
843N VAL* 6.1 1.9 - - - -
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Residues in contact with LEU 834 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830N SER 3.2 15.6 + - - -
831N VAL* 3.4 4.7 - - - +
832N ASP 3.1 0.6 - - - -
833N ALA* 1.3 74.0 - - - +
835N LYS* 1.3 59.0 + - - +
838N GLU* 3.0 27.0 - - - -
839N HIS 4.1 1.3 + - - -
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Residues in contact with LYS 835 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831N VAL 2.7 18.5 + - - -
832N ASP* 3.4 2.2 - - - +
834N LEU* 1.3 77.0 - - - +
836N LYS* 1.3 64.2 + - - +
837N CYS 3.4 0.6 - - - -
838N GLU* 3.3 8.1 + - - +
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Residues in contact with LYS 836 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809N ASN* 4.6 14.5 - - - +
832N ASP 2.5 20.1 + - - -
833N ALA* 4.8 0.7 - - - +
835N LYS* 1.3 74.7 - - - +
837N CYS* 1.3 57.6 + - - +
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Residues in contact with CYS 837 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809N ASN* 4.3 16.7 + - - +
810N SER 5.9 0.4 - - - -
811N GLY* 6.1 2.5 - - - -
833N ALA 3.6 10.7 + - - -
836N LYS* 1.3 72.2 - - - +
838N GLU* 1.3 68.7 + - - +
839N HIS* 4.5 1.2 - - - -
840N ASP* 4.8 2.1 + - - -
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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
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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