Contacts of the helix formed by residues 861 - 874 (chain H) in PDB entry 6BAA
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 861 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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860H LEU* 1.3 76.1 - - - +
862H VAL* 1.3 55.8 + - - +
863H HIS* 3.3 7.9 - - + +
864H LEU* 3.6 11.0 - - + +
865H SER* 2.4 35.8 + - - -
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Residues in contact with VAL 862 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861H ASP* 1.3 75.1 - - - +
863H HIS* 1.3 57.5 + - - +
865H SER* 2.4 28.7 + - - +
866H ASP* 2.9 13.7 + - - +
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Residues in contact with HIS 863 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861H ASP* 3.3 4.8 - - + +
862H VAL* 1.3 77.4 - - - +
864H LEU* 1.3 58.1 + - - +
866H ASP* 3.2 10.1 + - - +
867H HIS* 2.9 25.3 + - - +
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Residues in contact with LEU 864 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860H LEU* 3.6 21.9 - - + +
861H ASP* 3.1 20.1 + - + +
863H HIS* 1.3 76.9 - - - +
865H SER* 1.3 59.8 + - - +
867H HIS* 3.2 12.6 - - + +
868H LEU* 2.8 28.2 + - - +
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Residues in contact with SER 865 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857H PHE* 4.5 19.9 - - - +
860H LEU* 4.5 2.4 - - - +
861H ASP 2.4 27.9 + - - -
862H VAL* 2.4 31.0 + - - +
864H LEU* 1.3 67.5 - - - +
866H ASP* 1.3 57.9 + - - +
868H LEU* 3.3 7.1 + - - +
869H MET* 2.8 29.3 + - - +
893H TYR* 4.1 17.5 + - - -
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Residues in contact with ASP 866 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862H VAL 2.9 8.4 + - - +
863H HIS* 3.2 12.8 + - - +
865H SER* 1.3 78.3 + - - +
867H HIS* 1.3 59.8 + - - +
869H MET* 3.3 8.4 - - - +
870H GLN* 2.9 30.5 + - - +
893H TYR* 4.0 8.1 - - - +
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Residues in contact with HIS 867 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804H GLU 3.3 19.1 - - - -
805H ALA* 2.4 29.9 + - - -
806H CYS* 4.1 2.9 - - - -
807H SER* 3.1 33.7 + - - -
863H HIS 2.9 13.1 + - - +
864H LEU* 3.2 15.7 - - + +
866H ASP* 1.3 77.9 - - - +
868H LEU* 1.3 58.9 + - - +
870H GLN* 3.3 4.5 + - - +
871H ALA* 2.8 32.0 + - + +
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Residues in contact with LEU 868 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805H ALA 5.8 0.2 - - - -
856H PRO* 5.7 7.0 - - + +
857H PHE* 4.8 15.0 - - + +
860H LEU* 6.1 1.6 - - + -
864H LEU 2.8 18.4 + - - +
865H SER* 3.7 7.9 - - - +
867H HIS* 1.3 72.4 - - - +
869H MET* 1.3 60.4 + - - +
871H ALA* 4.8 2.9 - - - -
872H GLY* 2.8 27.4 + - - +
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Residues in contact with MET 869 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865H SER 2.8 14.3 + - - +
866H ASP* 3.3 9.6 - - - +
868H LEU* 1.3 75.0 - - - +
870H GLN* 1.3 57.8 + - - +
872H GLY* 3.3 1.3 + - - -
873H ILE* 2.9 30.9 + - - +
893H TYR* 3.5 41.3 - - + +
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Residues in contact with GLN 870 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866H ASP 2.9 20.7 + - - +
867H HIS* 3.9 5.6 - - - +
869H MET* 1.3 73.9 - - - +
871H ALA* 1.3 62.6 + - - +
873H ILE* 3.4 8.0 + - - +
874H LEU* 3.2 21.5 + - - +
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Residues in contact with ALA 871 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805H ALA* 3.5 41.8 - - + +
867H HIS* 2.8 20.3 + - + +
868H LEU* 4.5 3.1 - - - +
870H GLN* 1.3 75.2 - - - +
872H GLY* 1.3 61.7 + - - +
874H LEU* 3.3 8.3 - - - +
875H GLU* 3.0 25.7 + - - +
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Residues in contact with GLY 872 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868H LEU 2.8 20.3 + - - -
869H MET 3.8 0.4 - - - -
871H ALA* 1.3 75.4 - - - +
873H ILE* 1.3 57.6 + - - +
874H LEU 3.0 1.6 - - - -
875H GLU* 2.9 9.2 + - - +
876H LEU* 2.9 36.6 + - - +
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Residues in contact with ILE 873 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869H MET 2.9 17.1 + - - +
870H GLN* 3.7 8.3 - - - +
871H ALA 3.3 0.2 - - - -
872H GLY* 1.3 75.1 - - - +
874H LEU* 1.3 56.0 + - - +
875H GLU 3.4 0.4 - - - -
876H LEU* 3.5 31.9 - - + +
877H LEU* 3.8 8.3 - - - +
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Residues in contact with LEU 874 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870H GLN 3.2 15.0 + - - +
871H ALA* 3.3 9.4 + - - +
872H GLY 3.0 0.4 - - - -
873H ILE* 1.3 76.9 - - - +
875H GLU* 1.3 56.3 + - - +
877H LEU* 4.3 7.0 - - - -
878H ARG* 3.3 20.3 + - - +
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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