Contacts of the helix formed by residues 859 - 868 (chain B) in PDB entry 5MJ6
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 859 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808B TRP* 3.9 44.0 - - + -
809B THR 4.4 2.9 - - - +
820B ARG* 4.3 9.4 - - - -
824B LEU* 4.0 15.9 - - + -
842B LEU* 4.8 2.9 - - + -
855B LEU* 4.4 3.6 - - + -
856B PRO* 2.9 33.7 + - + +
858B ASP* 1.3 82.9 - - - +
860B MET* 1.3 60.1 + - - +
861B THR 3.3 2.0 - - - -
862B THR* 3.3 9.7 + - - -
863B VAL* 2.9 43.7 + - + +
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Residues in contact with MET 860 (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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448B ASN 5.6 0.9 - - - +
449B THR* 3.1 29.6 - - - +
855B LEU* 3.9 28.7 - - + +
856B PRO 3.5 6.6 + - - +
857B THR* 3.7 25.9 + - + +
858B ASP 3.6 1.4 - - - -
859B VAL* 1.3 79.3 - - - +
861B THR* 1.3 53.9 + - - +
863B VAL* 3.3 4.7 + - - +
864B PHE* 2.8 56.9 + - + -
889B GLU* 3.9 30.1 - - + +
892B LYS* 3.7 27.4 - - + +
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Residues in contact with THR 861 (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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825B GLU* 3.2 24.7 - - - +
857B THR 5.2 0.4 + - - -
858B ASP 5.5 0.4 - - - -
859B VAL 3.3 0.4 - - - -
860B MET* 1.3 78.9 - - - +
862B THR* 1.3 58.0 + - - +
864B PHE* 3.3 4.3 + - - +
865B LYS* 2.9 37.5 + - + +
892B LYS* 3.3 39.3 - - - +
895B GLU* 3.6 24.1 - - + +
896B ALA* 4.7 0.5 - - - +
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Residues in contact with THR 862 (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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808B TRP* 4.1 17.9 - - + -
821B SER* 4.7 1.9 + - - -
824B LEU* 4.3 6.9 - - + +
825B GLU* 3.0 40.0 + - - +
828B CYS* 3.5 35.9 - - + -
839B ALA* 4.4 1.8 - - + -
858B ASP 5.7 0.2 + - - -
859B VAL* 3.3 13.0 + - - +
861B THR* 1.3 78.4 - - - +
863B VAL* 1.3 63.9 + - - +
865B LYS* 3.4 3.0 + - - +
866B VAL* 3.1 23.7 + - - +
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Residues in contact with VAL 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808B TRP* 4.3 13.2 - - + -
839B ALA* 3.7 9.4 - - + +
842B LEU* 4.1 16.6 - - + -
843B PHE* 3.6 40.7 - - + +
855B LEU* 4.0 20.4 - - + -
859B VAL* 2.9 39.2 + - + +
860B MET* 3.7 5.6 - - - +
862B THR* 1.3 75.2 - - - +
864B PHE* 1.3 57.8 + - + +
866B VAL* 3.3 4.9 + - - +
867B GLY 3.0 22.0 + - - -
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Residues in contact with PHE 864 (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 PHE* 4.3 5.8 - + - -
846B TRP* 3.7 36.6 - + - -
855B LEU* 3.6 22.9 - - + -
860B MET* 2.8 54.7 + - + +
861B THR 3.8 2.0 - - - +
863B VAL* 1.3 73.2 - - + +
865B LYS* 1.3 60.9 + - - +
867B GLY* 3.1 2.1 + - - +
868B ALA* 2.8 31.9 + - - +
877B LEU* 3.5 19.9 - - + +
889B GLU* 4.3 8.3 - - + -
892B LYS* 4.2 6.7 - - + +
893B ILE* 3.6 36.3 - - + -
896B ALA* 3.5 15.9 - - + -
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Residues in contact with LYS 865 (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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825B GLU* 2.9 42.3 + - - +
829B THR* 4.7 6.9 + - - +
861B THR* 2.9 20.0 + - + +
862B THR* 3.6 5.6 - - - +
864B PHE* 1.3 77.2 - - - +
866B VAL* 1.3 63.2 + - + +
868B ALA* 3.7 5.4 + - - +
869B LYS* 3.3 32.0 + - - +
895B GLU* 3.0 36.1 + - - -
896B ALA* 3.5 20.8 - - - +
899B SER* 3.6 21.1 - - - +
934B HIS* 5.7 4.9 - - - -
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Residues in contact with VAL 866 (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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828B CYS* 4.4 19.5 - - + +
836B SER* 3.7 21.1 - - - +
839B ALA* 3.7 17.5 - - + -
840B MET* 3.5 50.3 - - + +
862B THR 3.1 15.2 + - - +
863B VAL 3.6 7.0 - - - +
864B PHE 3.1 0.4 - - - -
865B LYS* 1.3 75.6 - - + +
867B GLY* 1.3 67.0 + - - +
868B ALA 3.3 0.5 + - - -
869B LYS* 3.3 18.7 + - - +
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Residues in contact with GLY 867 (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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840B MET* 4.4 3.6 - - - -
843B PHE* 3.5 40.1 - - - -
863B VAL 3.0 10.9 + - - -
864B PHE 3.1 3.5 + - - -
866B VAL* 1.3 78.8 - - - +
868B ALA* 1.3 56.6 + - - +
869B LYS 3.1 5.2 + - - -
870B THR* 3.2 24.4 + - - +
873B GLY* 3.6 6.3 - - - -
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Residues in contact with ALA 868 (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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864B PHE 2.8 19.2 + - - +
865B LYS 4.2 4.0 - - - +
866B VAL 3.2 0.8 - - - -
867B GLY* 1.3 72.7 - - - +
869B LYS* 1.3 63.0 + - - +
870B THR 3.2 5.0 + - - +
874B TRP* 3.4 34.2 - - + +
877B LEU* 3.7 16.1 - - + +
896B ALA 3.3 28.7 - - - +
897B LEU* 4.5 0.2 - - - -
899B SER 5.7 0.4 - - - -
900B SER* 4.3 9.7 + - - +
905B LYS* 5.7 0.3 + - - -
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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