Contacts of the helix formed by residues 841 - 846 (chain B) in PDB entry 2HRC
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 HIS 841 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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626B ILE* 5.1 0.7 - - - -
631B PRO* 4.3 8.5 - - - -
632B ILE* 3.6 14.8 - - + -
834B PRO* 5.9 0.4 - - + -
837B PHE* 3.3 49.3 - + + -
839B SER 3.3 8.4 + - - -
840B ASP* 1.3 77.4 - - - +
842B ILE* 1.3 70.8 + - + +
843B GLU* 3.3 50.7 + - + -
844B THR* 3.0 15.5 + - + -
845B LEU* 3.0 27.0 + - - +
924B CL 3.6 15.0 - - + -
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Residues in contact with ILE 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B GLN* 3.8 35.0 - - + +
623B TYR* 3.7 34.5 - - + +
626B ILE* 3.8 21.8 - - + +
841B HIS* 1.3 79.1 - - + +
843B GLU* 1.3 74.3 + - + +
846B TYR* 3.1 41.2 + - + +
847B GLU* 3.1 10.3 + - - +
924B CL 3.3 10.7 - - + +
1605B CHD 5.7 9.0 - - + +
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Residues in contact with GLU 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762B ALA* 5.3 0.7 - - - -
763B HIS* 3.1 47.0 + - + +
802B GLN* 3.2 26.8 + - - +
803B SER* 3.8 15.9 - - - +
837B PHE* 5.3 4.2 - - - +
841B HIS* 3.1 35.1 + - + +
842B ILE* 1.3 87.4 - - + +
844B THR* 1.3 59.5 + - + +
847B GLU* 3.3 7.4 - - - +
848B LEU* 3.2 22.7 + - - +
1602B IMD 4.6 5.0 - - - -
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Residues in contact with THR 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834B PRO* 3.6 36.1 - - + -
839B SER 4.8 1.3 - - - +
840B ASP* 2.8 24.8 + - - -
841B HIS* 3.0 29.8 + - + -
843B GLU* 1.3 80.5 - - + +
845B LEU* 1.3 65.5 + - - +
846B TYR 3.3 1.6 - - - -
848B LEU* 3.7 6.5 - - + +
849B ASP* 3.1 37.7 + - - +
867B ARG* 3.8 9.9 - - - +
870B SER* 4.1 9.6 - - - +
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Residues in contact with LEU 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626B ILE* 3.4 38.4 - - + +
631B PRO* 3.9 33.0 - - + -
840B ASP* 3.8 26.2 - - + +
841B HIS 3.0 11.9 + - - +
844B THR* 1.3 84.9 + - - +
846B TYR* 1.3 58.3 + - - +
849B ASP* 3.4 20.6 - - - +
850B ILE* 3.6 8.5 - - - +
867B ARG* 3.9 11.7 - - - +
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Residues in contact with TYR 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B GLU* 6.1 0.7 - - - +
622B GLN* 3.5 55.8 + - + +
625B ARG* 4.0 29.4 + - + +
626B ILE* 3.7 4.5 - - + -
842B ILE* 3.1 31.1 + - + +
845B LEU* 1.3 78.5 - - - +
847B GLU* 1.3 68.6 + - + +
848B LEU 3.4 0.2 - - - -
850B ILE* 2.8 44.5 + - + +
851B GLU* 2.8 42.0 + - + +
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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