Contacts of the helix formed by residues 886 - 898 (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 SER 886 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389B GLN* 4.3 10.3 + - - +
449B THR* 3.2 40.5 + - - -
450B SER* 4.7 0.3 + - - -
884B ILE* 4.2 3.9 - - - +
885B GLY* 1.3 76.9 - - - +
887B GLU* 1.3 57.4 + - - +
888B ALA* 3.7 7.6 + - - +
889B GLU* 3.0 25.0 + - - +
890B LYS* 2.9 30.5 + - - +
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Residues in contact with GLU 887 (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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386B LYS* 3.6 20.5 + - - +
389B GLN* 4.9 3.4 + - - -
440B GLU* 3.3 35.2 - - + +
441B GLU* 4.1 25.4 - - + +
444B LEU* 5.4 3.8 - - + +
881B TYR* 5.6 0.3 + - - -
885B GLY* 3.5 4.4 + - - +
886B SER* 1.3 72.7 - - - +
888B ALA* 1.3 56.7 + - - +
890B LYS* 2.8 43.4 + - - +
891B ASN* 2.9 32.4 + - - -
922B GLN* 5.8 2.3 + - - -
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Residues in contact with ALA 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLU* 4.8 12.1 - - - +
444B LEU 5.4 5.2 - - - +
450B SER* 3.5 21.1 - - - +
454B ASP* 3.3 30.4 - - + +
886B SER* 3.8 4.5 - - - +
887B GLU* 1.3 79.3 - - - +
889B GLU* 1.3 61.8 + - - +
891B ASN* 3.2 19.4 + - - +
892B LYS* 3.3 18.7 + - - +
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Residues in contact with GLU 889 (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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449B THR* 3.3 34.3 + - - +
846B TRP* 4.3 17.9 - - - -
860B MET* 3.9 26.7 - - - +
864B PHE* 4.3 9.4 - - + -
880B LYS* 5.6 0.7 - - - +
884B ILE* 3.5 25.3 - - + +
886B SER* 3.0 22.6 + - - +
888B ALA* 1.3 72.6 - - - +
890B LYS* 1.3 60.7 + - - +
892B LYS* 3.0 11.7 + - - +
893B ILE* 2.9 29.3 + - + +
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Residues in contact with LYS 890 (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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881B TYR* 3.4 68.1 + - + +
884B ILE* 3.6 33.4 + - + +
886B SER 2.9 18.8 + - - +
887B GLU* 2.8 44.2 + - - +
889B GLU* 1.3 78.0 - - - +
891B ASN* 1.3 57.6 + - - +
893B ILE* 3.2 3.9 + - - -
894B LEU* 2.8 24.8 + - - +
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Residues in contact with ASN 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLU* 2.7 45.7 + - - +
881B TYR* 5.6 1.0 + - - -
887B GLU 2.9 13.0 + - - +
888B ALA* 3.6 9.6 + - - +
889B GLU 3.2 0.4 - - - -
890B LYS* 1.3 76.2 - - - +
892B LYS* 1.3 62.7 + - + +
894B LEU* 3.4 5.5 + - - +
895B GLU* 3.1 23.9 + - - +
923B LYS* 2.8 32.4 + - - +
926B PHE* 4.0 9.9 - - + -
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Residues in contact with LYS 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B THR 3.6 13.1 + - - -
451B SER* 3.5 33.6 - - - +
454B ASP* 2.6 30.9 + - - +
857B THR 3.9 3.4 - - - -
860B MET* 3.7 29.4 - - + +
861B THR* 3.3 30.3 + - - +
864B PHE* 4.2 15.6 - - + +
888B ALA 3.3 10.8 + - - +
889B GLU* 3.0 9.7 + - - +
891B ASN* 1.3 79.7 - - + +
893B ILE* 1.3 60.3 + - - +
895B GLU* 3.6 6.6 + - - +
896B ALA* 3.3 18.9 + - - +
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Residues in contact with ILE 893 (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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846B TRP* 5.1 2.2 - - + -
864B PHE* 3.6 24.7 - - + -
877B LEU* 3.5 39.0 - - + +
880B LYS* 4.1 20.6 - - + -
881B TYR* 4.1 11.9 - - + +
884B ILE* 4.0 26.5 - - + -
889B GLU* 2.9 21.2 + - - +
890B LYS* 3.2 8.0 + - - +
892B LYS* 1.3 74.8 - - - +
894B LEU* 1.3 61.6 + - - +
896B ALA* 2.9 19.8 + - - +
897B LEU* 2.9 22.2 + - + +
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Residues in contact with LEU 894 (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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881B TYR* 3.9 15.5 - - + +
890B LYS 2.8 20.5 + - - +
891B ASN* 3.9 5.4 - - - +
893B ILE* 1.3 75.0 - - - +
895B GLU* 1.3 61.9 + - - +
897B LEU* 3.2 7.7 + - + +
898B ALA* 3.0 23.7 + - + +
909B LEU* 4.3 12.8 - - + -
919B PHE* 3.9 23.3 - - + -
923B LYS* 3.7 46.2 - - + -
926B PHE* 4.1 10.1 - - + -
927B ILE* 3.8 28.3 - - + -
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Residues in contact with GLU 895 (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* 3.9 1.9 - - - +
861B THR* 3.6 15.9 - - + +
865B LYS* 3.0 34.2 + - - -
891B ASN 3.1 12.5 + - - +
892B LYS* 3.8 7.4 - - - +
894B LEU* 1.3 76.6 - - - +
896B ALA* 1.3 59.9 + - - +
898B ALA* 3.7 4.8 + - - -
899B SER* 2.9 28.7 + - - +
926B PHE* 3.3 36.3 - - + -
930B THR* 4.0 9.8 - - + +
933B ARG* 5.4 6.8 + - - -
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Residues in contact with ALA 896 (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* 3.5 47.1 - - + +
865B LYS* 3.5 14.4 - - + +
868B ALA* 3.3 18.2 - - + +
877B LEU* 4.3 3.6 - - + -
892B LYS 3.3 5.5 + - - +
893B ILE 2.9 10.1 + - - +
895B GLU* 1.3 77.2 - - - +
897B LEU* 1.3 66.4 + - - +
899B SER* 3.1 15.4 + - - -
900B SER 3.7 1.0 + - - -
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Residues in contact with LEU 897 (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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874B TRP* 3.1 66.2 + - + +
877B LEU* 3.7 16.2 - - + -
878B LEU* 4.0 27.6 - - + +
881B TYR* 4.7 3.1 - - + -
893B ILE* 2.9 31.6 + - + +
894B LEU* 3.2 11.6 + - - +
896B ALA* 1.3 76.7 - - - +
898B ALA* 1.3 57.4 + - - +
899B SER 3.2 4.3 + - - -
900B SER* 3.2 12.3 + - - -
905B LYS* 5.6 0.2 - - - +
906B LEU* 4.1 0.9 - - - +
909B LEU* 3.7 18.6 - - + +
919B PHE* 4.6 15.3 - - + -
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Residues in contact with ALA 898 (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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894B LEU* 3.0 18.6 + - + +
895B GLU* 4.2 0.7 - - - +
896B ALA 3.3 0.2 - - - -
897B LEU* 1.3 74.4 - - - +
899B SER* 1.3 56.5 + - - +
900B SER 3.3 2.0 - - - -
906B LEU* 3.2 18.3 - - - +
909B LEU* 3.6 18.3 - - + +
926B PHE* 6.2 0.7 - - + -
927B ILE* 4.5 10.8 - - + +
930B THR* 3.6 33.9 - - + +
931B VAL* 4.0 16.7 - - + +
934B HIS* 5.2 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