Contacts of the helix formed by residues 842 - 850 (chain B) in PDB entry 6M04
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 VAL 842 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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817B LEU* 4.4 7.9 - - + +
818B GLY* 3.7 27.4 - - - +
823B LEU* 6.2 4.9 - - + -
834B LEU* 3.8 52.5 - - + +
837B THR 4.1 1.8 - - - +
838B LEU* 3.3 27.8 - - + +
841B GLU* 1.3 74.1 - - - +
843B LYS* 1.3 63.1 + - + +
844B GLU 3.3 0.9 - - - -
845B ALA* 3.5 6.2 - - + +
846B LEU* 2.9 38.5 + - + +
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Residues in contact with LYS 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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834B LEU 4.8 1.8 - - - +
835B PHE* 3.6 57.1 + - + +
838B LEU 3.8 3.1 + - - +
839B PRO* 3.3 36.9 - - + +
842B VAL* 1.3 82.1 - - + +
844B GLU* 1.3 58.5 + - - +
846B LEU* 3.4 8.6 + - + +
847B ASN* 2.9 31.6 + - - +
778C ARG* 4.9 7.9 - - - +
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Residues in contact with GLU 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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839B PRO 4.2 6.0 + - - +
840B LEU* 3.3 40.3 - - + +
841B GLU 4.2 2.0 - - - +
842B VAL 3.3 1.8 - - - +
843B LYS* 1.3 76.6 - - - +
845B ALA* 1.3 57.7 + - - +
847B ASN* 3.9 15.5 + - - +
848B GLN* 2.9 53.5 + - - +
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Residues in contact with ALA 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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818B GLY* 5.0 2.5 - - - +
820B CYS 4.4 6.3 - - - +
821B ARG* 3.8 34.0 - - + +
823B LEU* 5.5 3.8 - - + +
841B GLU 3.4 19.5 + - - +
842B VAL* 3.3 10.0 + - + +
843B LYS 3.2 0.6 - - - -
844B GLU* 1.3 79.1 - - - +
846B LEU* 1.3 59.2 + - + +
848B GLN* 3.8 3.3 - - - +
849B ASP* 2.9 36.1 + - - +
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Residues in contact with LEU 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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823B LEU* 3.4 31.9 - - + +
824B LYS* 3.4 31.4 - - + +
825B LYS* 6.2 0.2 - - - +
830B VAL* 4.7 22.7 - - + -
834B LEU* 5.8 3.4 - - + -
835B PHE* 4.8 11.2 - - + -
842B VAL* 2.9 23.7 + - + +
843B LYS* 4.0 8.7 - - + +
845B ALA* 1.3 77.1 - - + +
847B ASN* 1.3 57.6 + - - +
849B ASP* 4.0 4.4 - - - +
850B ILE* 3.1 31.0 + - + +
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Residues in contact with ASN 847 (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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843B LYS 2.9 18.5 + - - +
844B GLU* 3.9 18.1 + - - +
845B ALA 3.2 0.2 - - - -
846B LEU* 1.3 75.1 - - - +
848B GLN* 1.3 61.7 + - + +
849B ASP 3.3 0.9 - - - -
850B ILE 3.0 28.4 - - - +
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Residues in contact with GLN 848 (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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821B ARG* 4.0 30.2 + - - +
844B GLU* 2.9 39.9 + - - +
845B ALA* 4.1 2.9 - - - +
847B ASN* 1.3 74.1 - - + +
849B ASP* 1.3 66.2 + - - +
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Residues in contact with ASP 849 (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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821B ARG* 2.9 29.2 - - - +
822B MET* 3.3 18.3 - - - +
823B LEU 3.2 23.0 - - - +
824B LYS* 3.4 24.1 + - + +
845B ALA 2.9 18.0 + - - +
846B LEU* 4.1 4.2 - - - +
848B GLN* 1.3 81.0 - - - +
850B ILE* 1.3 60.2 + - - +
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Residues in contact with ILE 850 (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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824B LYS* 3.4 19.5 - - - +
846B LEU* 3.1 18.5 + - + +
847B ASN* 3.0 28.4 - - - +
849B ASP* 1.3 80.3 - - - +
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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